%0 Journal Article %J NPJ Genom Med %D 2024 %T Bi-allelic variants in CELSR3 are implicated in central nervous system and urinary tract anomalies. %A Stegmann, Jil D %A Kalanithy, Jeshurun C %A Dworschak, Gabriel C %A Ishorst, Nina %A Mingardo, Enrico %A Lopes, Filipa M %A Ho, Yee Mang %A Grote, Phillip %A Lindenberg, Tobias T %A Yilmaz, Öznur %A Channab, Khadija %A Seltzsam, Steve %A Shril, Shirlee %A Hildebrandt, Friedhelm %A Boschann, Felix %A Heinen, André %A Jolly, Angad %A Myers, Katherine %A McBride, Kim %A Bekheirnia, Mir Reza %A Bekheirnia, Nasim %A Scala, Marcello %A Morleo, Manuela %A Nigro, Vincenzo %A Torella, Annalaura %A Pinelli, Michele %A Capra, Valeria %A Accogli, Andrea %A Maitz, Silvia %A Spano, Alice %A Olson, Rory J %A Klee, Eric W %A Lanpher, Brendan C %A Jang, Se Song %A Chae, Jong-Hee %A Steinbauer, Philipp %A Rieder, Dietmar %A Janecke, Andreas R %A Vodopiutz, Julia %A Vogel, Ida %A Blechingberg, Jenny %A Cohen, Jennifer L %A Riley, Kacie %A Klee, Victoria %A Walsh, Laurence E %A Begemann, Matthias %A Elbracht, Miriam %A Eggermann, Thomas %A Stoppe, Arzu %A Stuurman, Kyra %A van Slegtenhorst, Marjon %A Barakat, Tahsin Stefan %A Mulhern, Maureen S %A Sands, Tristan T %A Cytrynbaum, Cheryl %A Weksberg, Rosanna %A Isidori, Federica %A Pippucci, Tommaso %A Severi, Giulia %A Montanari, Francesca %A Kruer, Michael C %A Bakhtiari, Somayeh %A Darvish, Hossein %A Reutter, Heiko %A Hagelueken, Gregor %A Geyer, Matthias %A Woolf, Adrian S %A Posey, Jennifer E %A Lupski, James R %A Odermatt, Benjamin %A Hilger, Alina C %X

CELSR3 codes for a planar cell polarity protein. We describe twelve affected individuals from eleven independent families with bi-allelic variants in CELSR3. Affected individuals presented with an overlapping phenotypic spectrum comprising central nervous system (CNS) anomalies (7/12), combined CNS anomalies and congenital anomalies of the kidneys and urinary tract (CAKUT) (3/12) and CAKUT only (2/12). Computational simulation of the 3D protein structure suggests the position of the identified variants to be implicated in penetrance and phenotype expression. CELSR3 immunolocalization in human embryonic urinary tract and transient suppression and rescue experiments of Celsr3 in fluorescent zebrafish reporter lines further support an embryonic role of CELSR3 in CNS and urinary tract formation.

%B NPJ Genom Med %V 9 %P 18 %8 2024 Mar 01 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/38429302?dopt=Abstract %R 10.1038/s41525-024-00398-9 %0 Journal Article %J medRxiv %D 2024 %T Biallelic variation in the choline and ethanolamine transporter FLVCR1 underlies a pleiotropic disease spectrum from adult neurodegeneration to severe developmental disorders %A Calame, Daniel G %A Wong, Jovi Huixin %A Panda, Puravi %A Nguyen, Dat Tuan %A Leong, Nancy C P %A Sangermano, Riccardo %A Patankar, Sohil G %A Abdel-Hamid, Mohamed %A Alabdi, Lama %A Safwat, Sylvia %A Flannery, Kyle P %A Dardas, Zain %A Fatih, Jawid M %A Murali, Chaya %A Kannan, Varun %A Lotze, Timothy E %A Herman, Isabella %A Ammouri, Farah %A Rezich, Brianna %A Efthymiou, Stephanie %A Alavi, Shahryar %A Murphy, David %A Firoozfar, Zahra %A Nasab, Mahya Ebrahimi %A Bahreini, Amir %A Ghasemi, Majid %A Haridy, Nourelhoda A %A Goldouzi, Hamid Reza %A Eghbal, Fatemeh %A Karimiani, Ehsan Ghayoor %A Srinivasan, Varunvenkat M %A Gowda, Vykuntaraju K %A Du, Haowei %A Jhangiani, Shalini N %A Coban-Akdemir, Zeynep %A Marafi, Dana %A Rodan, Lance %A Isikay, Sedat %A Rosenfeld, Jill A %A Ramanathan, Subhadra %A Staton, Michael %A Clark, Robin D %A Wenman, Catharina %A Loughlin, Sam %A Saad, Ramy %A Ashraf, Tazeen %A Male, Alison %A Tadros, Shereen %A Boostani, Reza %A Abdel-Salam, Ghada M H %A Zaki, Maha %A Abdalla, Ebtesam %A Manzini, M Chiara %A Pehlivan, Davut %A Posey, Jennifer E %A Richard A Gibbs %A Houlden, Henry %A Alkuraya, Fowzan S %A Bujakowska, Kinga %A Maroofian, Reza %A Lupski, James R %A Nguyen, Long Nam %X

FLVCR1 encodes Feline leukemia virus subgroup C receptor 1 (FLVCR1), a solute carrier (SLC) transporter within the Major Facilitator Superfamily. FLVCR1 is a widely expressed transmembrane protein with plasma membrane and mitochondrial isoforms implicated in heme, choline, and ethanolamine transport. While Flvcr1 knockout mice die in utero with skeletal malformations and defective erythropoiesis reminiscent of Diamond-Blackfan anemia, rare biallelic pathogenic FLVCR1 variants are linked to childhood or adult-onset neurodegeneration of the retina, spinal cord, and peripheral nervous system. We ascertained from research and clinical exome sequencing 27 individuals from 20 unrelated families with biallelic ultra-rare missense and predicted loss-of-function (pLoF) FLVCR1 variant alleles. We characterize an expansive FLVCR1 phenotypic spectrum ranging from adult-onset retinitis pigmentosa to severe developmental disorders with microcephaly, reduced brain volume, epilepsy, spasticity, and premature death. The most severely affected individuals, including three individuals with homozygous pLoF variants, share traits with Flvcr1 knockout mice and Diamond-Blackfan anemia including macrocytic anemia and congenital skeletal malformations. Pathogenic FLVCR1 missense variants primarily lie within transmembrane domains and reduce choline and ethanolamine transport activity compared with wild-type FLVCR1 with minimal impact on FLVCR1 stability or subcellular localization. Several variants disrupt splicing in a mini-gene assay which may contribute to genotype-phenotype correlations. Taken together, these data support an allele-specific gene dosage model in which phenotypic severity reflects residual FLVCR1 activity. This study expands our understanding of Mendelian disorders of choline and ethanolamine transport and demonstrates the importance of choline and ethanolamine in neurodevelopment and neuronal homeostasis.

%B medRxiv %8 2024 Feb 13 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/38405817?dopt=Abstract %R 10.1101/2024.02.09.24302464 %0 Journal Article %J Clin Genet %D 2024 %T Expanding the phenotype of PPP1R21-related neurodevelopmental disorder. %A Almannai, Mohammed %A Marafi, Dana %A Zaki, Maha S %A Maroofian, Reza %A Efthymiou, Stephanie %A Saadi, Nebal Waill %A Filimban, Bilal %A Dafsari, Hormos Salimi %A Rahman, Fatima %A Maqbool, Shazia %A Faqeih, Eissa %A Al Mutairi, Fuad %A Alsharhan, Hind %A Abdelaty, Omar %A Bin-Hasan, Saadoun %A Duan, Ruizhi %A Noureldeen, Mahmoud M %A Alqattan, Alaa %A Houlden, Henry %A Hunter, Jill V %A Posey, Jennifer E %A Lupski, James R %A El-Hattab, Ayman W %X

PPP1R21 encodes for a conserved protein that is involved in endosomal maturation. Biallelic pathogenic variants in PPP1R21 have been associated with a syndromic neurodevelopmental disorder from studying 13 affected individuals. In this report, we present 11 additional individuals from nine unrelated families and their clinical, radiological, and molecular findings. We identified eight different variants in PPP1R21, of which six were novel variants. Global developmental delay and hypotonia are neurological features that were observed in all individuals. There is also a similar pattern of dysmorphic features with coarse faces as a gestalt observed in several individuals. Common findings in 75% of individuals with available brain imaging include delays in myelination, wavy outline of the bodies of the lateral ventricles, and slight prominence of the bodies of the lateral ventricles. PPP1R21-related neurodevelopmental disorder is associated with a consistent phenotype and should be considered in highly consanguineous individuals presenting with developmental delay/intellectual disability along with coarse facial features.

%B Clin Genet %8 2024 Feb 14 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/38356149?dopt=Abstract %R 10.1111/cge.14492 %0 Journal Article %J Am J Med Genet A %D 2024 %T Phenotypic heterogeneity associated with KIF21A: Two new cases and review of the literature. %A Bhola, Priya T %A Mishra, Radha %A Posey, Jennifer E %A Hamilton, Leslie E %A Graham, Gail E %A Punetha, Jaya %A Lupski, James R %A Boycott, Kym M %A D'Amours, Damien %A Kernohan, Kristin D %K Humans %K Kinesins %K Mutation %K Nervous System Diseases %K Phenotype %X

Our understanding of genetic and phenotypic heterogeneity associated with the clinical spectrum of rare diseases continues to expand. Thorough phenotypic descriptions and model organism functional studies are valuable tools in dissecting the biology of the disease process. Kinesin genes are well known to be associated with specific disease phenotypes and a subset of kinesin genes, including KIF21A, have been associated with more than one disease. Here we report two patients with KIF21A variants identified by exome sequencing; one with biallelic variants, supporting a novel KIF21A related syndrome with recessive inheritance and the second report of this condition, and another with a heterozygous de novo variant allele representing a phenotypic expansion of the condition described to date. We provide detailed phenotypic information on both families, including a novel neuropathology finding of neuroaxonal dystrophy associated with biallelic variants in KIF21A. Additionally, we studied the dominant variant in Saccharomyces cerevisiae to assess variant pathogenicity and found that this variant appears to impair protein function. KIF21A associated disease has mounting evidence for phenotypic heterogeneity; further patients and study of an allelic series are required to define the phenotypic spectrum and further explore the molecular etiology for each of these conditions.

%B Am J Med Genet A %V 194 %P e63455 %8 2024 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/37921537?dopt=Abstract %R 10.1002/ajmg.a.63455 %0 Journal Article %J Am J Hum Genet %D 2024 %T Variants in ZFX are associated with an X-linked neurodevelopmental disorder with recurrent facial gestalt. %A Shepherdson, James L %A Hutchison, Katie %A Don, Dilan Wellalage %A McGillivray, George %A Choi, Tae-Ik %A Allan, Carolyn A %A Amor, David J %A Banka, Siddharth %A Basel, Donald G %A Buch, Laura D %A Carere, Deanna Alexis %A Carroll, Renée %A Clayton-Smith, Jill %A Crawford, Ali %A Dunø, Morten %A Faivre, Laurence %A Gilfillan, Christopher P %A Gold, Nina B %A Gripp, Karen W %A Hobson, Emma %A Holtz, Alexander M %A Innes, A Micheil %A Isidor, Bertrand %A Jackson, Adam %A Katsonis, Panagiotis %A Amel Riazat Kesh, Leila %A Küry, Sébastien %A Lecoquierre, François %A Lockhart, Paul %A Maraval, Julien %A Matsumoto, Naomichi %A McCarrier, Julie %A McCarthy, Josephine %A Miyake, Noriko %A Moey, Lip Hen %A Németh, Andrea H %A Østergaard, Elsebet %A Patel, Rushina %A Pope, Kate %A Posey, Jennifer E %A Schnur, Rhonda E %A Shaw, Marie %A Stolerman, Elliot %A Taylor, Julie P %A Wadman, Erin %A Wakeling, Emma %A White, Susan M %A Wong, Lawrence C %A Lupski, James R %A Lichtarge, Olivier %A Corbett, Mark A %A Gecz, Jozef %A Nicolet, Charles M %A Farnham, Peggy J %A Kim, Cheol-Hee %A Shinawi, Marwan %K Animals %K Female %K Humans %K Hyperparathyroidism %K Intellectual Disability %K Male %K Mutation, Missense %K Neurodevelopmental Disorders %K Phenotype %K Transcription Factors %K Zebrafish %X

Pathogenic variants in multiple genes on the X chromosome have been implicated in syndromic and non-syndromic intellectual disability disorders. ZFX on Xp22.11 encodes a transcription factor that has been linked to diverse processes including oncogenesis and development, but germline variants have not been characterized in association with disease. Here, we present clinical and molecular characterization of 18 individuals with germline ZFX variants. Exome or genome sequencing revealed 11 variants in 18 subjects (14 males and 4 females) from 16 unrelated families. Four missense variants were identified in 11 subjects, with seven truncation variants in the remaining individuals. Clinical findings included developmental delay/intellectual disability, behavioral abnormalities, hypotonia, and congenital anomalies. Overlapping and recurrent facial features were identified in all subjects, including thickening and medial broadening of eyebrows, variations in the shape of the face, external eye abnormalities, smooth and/or long philtrum, and ear abnormalities. Hyperparathyroidism was found in four families with missense variants, and enrichment of different tumor types was observed. In molecular studies, DNA-binding domain variants elicited differential expression of a small set of target genes relative to wild-type ZFX in cultured cells, suggesting a gain or loss of transcriptional activity. Additionally, a zebrafish model of ZFX loss displayed an altered behavioral phenotype, providing additional evidence for the functional significance of ZFX. Our clinical and experimental data support that variants in ZFX are associated with an X-linked intellectual disability syndrome characterized by a recurrent facial gestalt, neurocognitive and behavioral abnormalities, and an increased risk for congenital anomalies and hyperparathyroidism.

%B Am J Hum Genet %V 111 %P 487-508 %8 2024 Mar 07 %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/38325380?dopt=Abstract %R 10.1016/j.ajhg.2024.01.007 %0 Journal Article %J medRxiv %D 2024 %T Variant-specific pathophysiological mechanisms of AFF3 differently influence transcriptome profiles. %A Bassani, Sissy %A Chrast, Jacqueline %A Ambrosini, Giovanna %A Voisin, Norine %A Schütz, Frédéric %A Brusco, Alfredo %A Sirchia, Fabio %A Turban, Lydia %A Schubert, Susanna %A Jamra, Rami Abou %A Schlump, Jan-Ulrich %A DeMille, Desiree %A Bayrak-Toydemir, Pinar %A Nelson, Gary Rex %A Wong, Kristen Nicole %A Duncan, Laura %A Mosera, Mackenzie %A Gilissen, Christian %A Vissers, Lisenka E L M %A Pfundt, Rolph %A Kersseboom, Rogier %A Yttervik, Hilde %A Hansen, Geir Åsmund Myge %A Falkenberg Smeland, Marie %A Butler, Kameryn M %A Lyons, Michael J %A Carvalho, Claudia M B %A Zhang, Chaofan %A Lupski, James R %A Potocki, Lorraine %A Flores-Gallegos, Leticia %A Morales-Toquero, Rodrigo %A Petit, Florence %A Yalcin, Binnaz %A Tuttle, Annabelle %A Elloumi, Houda Zghal %A Mccormick, Lane %A Kukolich, Mary %A Klaas, Oliver %A Horvath, Judit %A Scala, Marcello %A Iacomino, Michele %A Operto, Francesca %A Zara, Federico %A Writzl, Karin %A Maver, Ales %A Haanpää, Maria K %A Pohjola, Pia %A Arikka, Harri %A Iseli, Christian %A Guex, Nicolas %A Reymond, Alexandre %X

BACKGROUND: We previously described the KINSSHIP syndrome, an autosomal dominant disorder associated with intellectual disability (ID), mesomelic dysplasia and horseshoe kidney,caused by variants in the degron of AFF3. Mouse knock-ins and overexpression in zebrafish provided evidence for a dominant-negative (DN) mode-of-action, wherein an increased level of AFF3 resulted in pathological effects.

METHODS: Evolutionary constraints suggest that other mode-of-inheritance could be at play. We challenged this hypothesis by screening ID cohorts for individuals with predicted-to-be deleterious variants in . We used both animal and cellular models to assess the deleteriousness of the identified variants.

RESULTS: We identified an individual with a KINSSHIP-like phenotype carrying a partial duplication of further strengthening the hypothesis that an increased level of AFF3 is pathological. We also detected seventeen individuals displaying a milder syndrome with either heterozygous LoF or biallelic missense variants in . Consistent with semi-dominance, we discovered three patients with homozygous LoF and one compound heterozygote for a LoF and a missense variant, who presented more severe phenotypes than their heterozygous parents. Matching zebrafish knockdowns exhibit neurological defects that could be rescued by expressing human mRNA, confirming their association with the ablation of . Conversely, some of the human mRNAs carrying missense variants identified in affected individuals did not complement. Overexpression of mutated mRNAs in zebrafish embryos produced a significant increase of abnormal larvae compared to wild-type overexpression further demonstrating deleteriousness. To further assess the effect of variation, we profiled the transcriptome of fibroblasts from affected individuals and engineered isogenic cells harboring +/+, DN/DN, LoF/+, LoF/LoF or DN/LoF genotypes. The expression of more than a third of the AFF3 bound loci is modified in either the DN/DN or the LoF/LoF lines. While the same pathways are affected, only about one-third of the differentially expressed genes are common to these homozygote datasets, indicating that LoF and DN variants largely modulate transcriptomes differently, e.g. the DNA repair pathway displayed opposite modulation.

CONCLUSIONS: Our results and the high pleiotropy shown by variation at this locus suggest that minute changes in function are deleterious.

%B medRxiv %8 2024 Jan 17 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/38293053?dopt=Abstract %R 10.1101/2024.01.14.24301100 %0 Journal Article %J J Immunol %D 2024 %T β-Actin G342D as a Cause of NK Cell Deficiency Impairing Lytic Synapse Termination. %A Reed, Abigail E %A Peraza, Jackeline %A van den Haak, Frederique %A Hernandez, Evelyn R %A Richard A Gibbs %A Chinn, Ivan K %A Lupski, James R %A Marchi, Enrica %A Reshef, Ran %A Alobeid, Bachir %A Mace, Emily M %A Orange, Jordan S %K Actins %K Blood Platelets %K Cell Line %K Humans %K Immunologic Deficiency Syndromes %K Killer Cells, Natural %X

NK cell deficiency (NKD) occurs when an individual's major clinical immunodeficiency derives from abnormal NK cells and is associated with several genetic etiologies. Three categories of β-actin-related diseases with over 60 ACTB (β-actin) variants have previously been identified, none with a distinct NK cell phenotype. An individual with mild developmental delay, macrothrombocytopenia, and susceptibility to infections, molluscum contagiosum virus, and EBV-associated lymphoma had functional NKD for over a decade. A de novo ACTB variant encoding G342D β-actin was identified and was consistent with the individual's developmental and platelet phenotype. This novel variant also was found to have direct impact in NK cells because its expression in the human NK cell line YTS (YTS-NKD) caused increased cell spreading in lytic immune synapses created on activating surfaces. YTS-NKD cells were able to degranulate and perform cytotoxicity, but they demonstrated defective serial killing because of prolonged conjugation to the killed target cell and thus were effectively unable to terminate lytic synapses. G342D β-actin results in a novel, to our knowledge, mechanism of functional NKD via increased synaptic spreading and defective lytic synapse termination with resulting impaired serial killing, leading to overall reductions in NK cell cytotoxicity.

%B J Immunol %V 212 %P 962-973 %8 2024 Mar 15 %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/38315012?dopt=Abstract %R 10.4049/jimmunol.2300671 %0 Journal Article %J Brain %D 2023 %T Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. %A Kaiyrzhanov, Rauan %A Rad, Aboulfazl %A Lin, Sheng-Jia %A Bertoli-Avella, Aida %A Kallemeijn, Wouter W %A Godwin, Annie %A Zaki, Maha S %A Huang, Kevin %A Lau, Tracy %A Petree, Cassidy %A Efthymiou, Stephanie %A Ghayoor Karimiani, Ehsan %A Hempel, Maja %A Normand, Elizabeth A %A Rudnik-Schöneborn, Sabine %A Schatz, Ulrich A %A Baggelaar, Marc P %A Ilyas, Muhammad %A Sultan, Tipu %A Alvi, Javeria Raza %A Ganieva, Manizha %A Fowler, Ben %A Aanicai, Ruxandra %A Akay Tayfun, Gulsen %A Al Saman, Abdulaziz %A Alswaid, Abdulrahman %A Amiri, Nafise %A Asilova, Nilufar %A Shotelersuk, Vorasuk %A Yeetong, Patra %A Azam, Matloob %A Babaei, Meisam %A Bahrami Monajemi, Gholamreza %A Mohammadi, Pouria %A Samie, Saeed %A Banu, Selina Husna %A Basto, Jorge Pinto %A Kortüm, Fanny %A Bauer, Mislen %A Bauer, Peter %A Beetz, Christian %A Garshasbi, Masoud %A Hameed Issa, Awatif %A Eyaid, Wafaa %A Ahmed, Hind %A Hashemi, Narges %A Hassanpour, Kazem %A Herman, Isabella %A Ibrohimov, Sherozjon %A Abdul-Majeed, Ban A %A Imdad, Maria %A Isrofilov, Maksudjon %A Kaiyal, Qassem %A Khan, Suliman %A Kirmse, Brian %A Koster, Janet %A Lourenço, Charles Marques %A Mitani, Tadahiro %A Moldovan, Oana %A Murphy, David %A Najafi, Maryam %A Pehlivan, Davut %A Rocha, Maria Eugenia %A Salpietro, Vincenzo %A Schmidts, Miriam %A Shalata, Adel %A Mahroum, Mohammad %A Talbeya, Jawabreh Kassem %A Taylor, Robert W %A Vazquez, Dayana %A Vetro, Annalisa %A Waterham, Hans R %A Zaman, Mashaya %A Schrader, Tina A %A Chung, Wendy K %A Guerrini, Renzo %A Lupski, James R %A Gleeson, Joseph %A Suri, Mohnish %A Jamshidi, Yalda %A Bhatia, Kailash P %A Vona, Barbara %A Schrader, Michael %A Severino, Mariasavina %A Guille, Matthew %A Tate, Edward W %A Varshney, Gaurav K %A Houlden, Henry %A Maroofian, Reza %X

The acyl-CoA-binding domain-containing protein 6 (ACBD6) is ubiquitously expressed, plays a role in the acylation of lipids and proteins, and regulates the N-myristoylation of proteins via N-myristoyltransferase enzymes (NMTs). However, its precise function in cells is still unclear, as is the consequence of ACBD6 defects on human pathophysiology. Utilizing exome sequencing and extensive international data sharing efforts, we identified 45 affected individuals from 28 unrelated families (consanguinity 93%) with bi-allelic pathogenic, predominantly loss-of-function (18/20) variants in ACBD6. We generated zebrafish and Xenopus tropicalis acbd6 knockouts by CRISPR/Cas9 and characterized the role of ACBD6 on protein N-myristoylation with YnMyr chemical proteomics in the model organisms and human cells, with the latter also being subjected further to ACBD6 peroxisomal localization studies. The affected individuals (23 males and 22 females), with ages ranging from 1 to 50 years old, typically present with a complex and progressive disease involving moderate-to-severe global developmental delay/intellectual disability (100%) with significant expressive language impairment (98%), movement disorders (97%), facial dysmorphism (95%), and mild cerebellar ataxia (85%) associated with gait impairment (94%), limb spasticity/hypertonia (76%), oculomotor (71%) and behavioural abnormalities (65%), overweight (59%), microcephaly (39%) and epilepsy (33%). The most conspicuous and common movement disorder was dystonia (94%), frequently leading to early-onset progressive postural deformities (97%), limb dystonia (55%), and cervical dystonia (31%). A jerky tremor in the upper limbs (63%), a mild head tremor (59%), parkinsonism/hypokinesia developing with advancing age (32%), and simple motor and vocal tics were among other frequent movement disorders. Midline brain malformations including corpus callosum abnormalities (70%), hypoplasia/agenesis of the anterior commissure (66%), short midbrain and small inferior cerebellar vermis (38% each), as well as hypertrophy of the clava (24%) were common neuroimaging findings. acbd6-deficient zebrafish and Xenopus models effectively recapitulated many clinical phenotypes reported in patients including movement disorders, progressive neuromotor impairment, seizures, microcephaly, craniofacial dysmorphism, and midbrain defects accompanied by developmental delay with increased mortality over time. Unlike ACBD5, ACBD6 did not show a peroxisomal localisation and ACBD6-deficiency was not associated with altered peroxisomal parameters in patient fibroblasts. Significant differences in YnMyr-labelling were observed for 68 co- and 18 post-translationally N-myristoylated proteins in patient-derived fibroblasts. N-Myristoylation was similarly affected in acbd6-deficient zebrafish and Xenopus tropicalis models, including Fus, Marcks, and Chchd-related proteins implicated in neurological diseases. The present study provides evidence that bi-allelic pathogenic variants in ACBD6 lead to a distinct neurodevelopmental syndrome accompanied by complex and progressive cognitive and movement disorders.

%B Brain %8 2023 Nov 10 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/37951597?dopt=Abstract %R 10.1093/brain/awad380 %0 Journal Article %J Am J Med Genet A %D 2023 %T A biallelic frameshift indel in PPP1R35 as a cause of primary microcephaly. %A Dawood, Moez %A Akay, Gulsen %A Mitani, Tadahiro %A Marafi, Dana %A Fatih, Jawid M %A Gezdirici, Alper %A Najmabadi, Hossein %A Kahrizi, Kimia %A Punetha, Jaya %A Grochowski, Christopher M %A Du, Haowei %A Jolly, Angad %A Li, He %A Coban-Akdemir, Zeynep %A Fritz J Sedlazeck %A Hunter, Jill V %A Jhangiani, Shalini N %A Donna M Muzny %A Pehlivan, Davut %A Posey, Jennifer E %A Carvalho, Claudia M B %A Richard A Gibbs %A James R Lupski %K Codon, Terminator %K Frameshift Mutation %K Humans %K Infant, Newborn %K Iran %K Microcephaly %K Microtubule-Associated Proteins %K Pedigree %X

Protein phosphatase 1 regulatory subunit 35 (PPP1R35) encodes a centrosomal protein required for recruiting microtubule-binding elongation machinery. Several proteins in this centriole biogenesis pathway correspond to established primary microcephaly (MCPH) genes, and multiple model organism studies hypothesize PPP1R35 as a candidate MCPH gene. Here, using exome sequencing (ES) and family-based rare variant analyses, we report a homozygous, frameshifting indel deleting the canonical stop codon in the last exon of PPP1R35 [Chr7: c.753_*3delGGAAGCGTAGACCinsCG (p.Trp251Cysfs*22)]; the variant allele maps in a 3.7 Mb block of absence of heterozygosity (AOH) in a proband with severe MCPH (-4.3 SD at birth, -6.1 SD by 42 months), pachygyria, and global developmental delay from a consanguineous Turkish kindred. Droplet digital PCR (ddPCR) confirmed mutant mRNA expression in fibroblasts. In silico prediction of the translation of mutant PPP1R35 is expected to be elongated by 18 amino acids before encountering a downstream stop codon. This complex indel allele is absent in public databases (ClinVar, gnomAD, ARIC, 1000 genomes) and our in-house database of 14,000+ exomes including 1800+ Turkish exomes supporting predicted pathogenicity. Comprehensive literature searches for PPP1R35 variants yielded two probands affected with severe microcephaly (-15 SD and -12 SD) with the same homozygous indel from a single, consanguineous, Iranian family from a cohort of 404 predominantly Iranian families. The lack of heterozygous cases in two large cohorts representative of the genetic background of these two families decreased our suspicion of a founder allele and supports the contention of a recurrent mutation. We propose two potential secondary structure mutagenesis models for the origin of this variant allele mediated by hairpin formation between complementary GC rich segments flanking the stop codon via secondary structure mutagenesis.

%B Am J Med Genet A %V 191 %P 794-804 %8 2023 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/36598158?dopt=Abstract %R 10.1002/ajmg.a.63080 %0 Journal Article %J Brain %D 2023 %T Biallelic MED27 variants lead to variable ponto-cerebello-lental degeneration with movement disorders. %A Maroofian, Reza %A Kaiyrzhanov, Rauan %A Cali, Elisa %A Zamani, Mina %A Zaki, Maha S %A Ferla, Matteo %A Tortora, Domenico %A Sadeghian, Saeid %A Saadi, Saadia Maryam %A Abdullah, Uzma %A Karimiani, Ehsan Ghayoor %A Efthymiou, Stephanie %A Yesil, Gozde %A Alavi, Shahryar %A Al Shamsi, Aisha M %A Tajsharghi, Homa %A Abdel-Hamid, Mohamed S %A Saadi, Nebal Waill %A Al Mutairi, Fuad %A Alabdi, Lama %A Beetz, Christian %A Ali, Zafar %A Toosi, Mehran Beiraghi %A Rudnik-Schöneborn, Sabine %A Babaei, Meisam %A Isohanni, Pirjo %A Muhammad, Jameel %A Khan, Sheraz %A Al Shalan, Maha %A Hickey, Scott E %A Marom, Daphna %A Elhanan, Emil %A Kurian, Manju A %A Marafi, Dana %A Saberi, Alihossein %A Hamid, Mohammad %A Spaull, Robert %A Meng, Linyan %A Lalani, Seema %A Maqbool, Shazia %A Rahman, Fatima %A Seeger, Jürgen %A Palculict, Timothy Blake %A Lau, Tracy %A Murphy, David %A Mencacci, Niccolo Emanuele %A Steindl, Katharina %A Begemann, Anaïs %A Rauch, Anita %A Akbas, Sinan %A Aslanger, Ayça Dilruba %A Salpietro, Vincenzo %A Yousaf, Hammad %A Ben-Shachar, Shay %A Ejeskär, Katarina %A Al Aqeel, Aida I %A High, Frances A %A Armstrong-Javors, Amy E %A Zahraei, Seyed Mohammadsaleh %A Seifi, Tahereh %A Zeighami, Jawaher %A Shariati, Gholamreza %A Sedaghat, Alireza %A Asl, Samaneh Noroozi %A Shahrooei, Mohmmad %A Zifarelli, Giovanni %A Burglen, Lydie %A Ravelli, Claudia %A Zschocke, Johannes %A Schatz, Ulrich A %A Ghavideldarestani, Maryam %A Kamel, Walaa A %A Van Esch, Hilde %A Hackenberg, Annette %A Taylor, Jenny C %A Al-Gazali, Lihadh %A Bauer, Peter %A Gleeson, Joseph J %A Alkuraya, Fowzan Sami %A Lupski, James R %A Galehdari, Hamid %A Azizimalamiri, Reza %A Chung, Wendy K %A Baig, Shahid Mahmood %A Houlden, Henry %A Severino, Mariasavina %K Adolescent %K Adult %K Atrophy %K Cataract %K Cerebellum %K Child %K Child, Preschool %K Epilepsy %K Epilepsy, Generalized %K Female %K Humans %K Infant %K Mediator Complex %K Middle Aged %K Movement Disorders %K Neurodevelopmental Disorders %K Phenotype %K Young Adult %X

MED27 is a subunit of the Mediator multiprotein complex, which is involved in transcriptional regulation. Biallelic MED27 variants have recently been suggested to be responsible for an autosomal recessive neurodevelopmental disorder with spasticity, cataracts and cerebellar hypoplasia. We further delineate the clinical phenotype of MED27-related disease by characterizing the clinical and radiological features of 57 affected individuals from 30 unrelated families with biallelic MED27 variants. Using exome sequencing and extensive international genetic data sharing, 39 unpublished affected individuals from 18 independent families with biallelic missense variants in MED27 have been identified (29 females, mean age at last follow-up 17 ± 12.4 years, range 0.1-45). Follow-up and hitherto unreported clinical features were obtained from the published 12 families. Brain MRI scans from 34 cases were reviewed. MED27-related disease manifests as a broad phenotypic continuum ranging from developmental and epileptic-dyskinetic encephalopathy to variable neurodevelopmental disorder with movement abnormalities. It is characterized by mild to profound global developmental delay/intellectual disability (100%), bilateral cataracts (89%), infantile hypotonia (74%), microcephaly (62%), gait ataxia (63%), dystonia (61%), variably combined with epilepsy (50%), limb spasticity (51%), facial dysmorphism (38%) and death before reaching adulthood (16%). Brain MRI revealed cerebellar atrophy (100%), white matter volume loss (76.4%), pontine hypoplasia (47.2%) and basal ganglia atrophy with signal alterations (44.4%). Previously unreported 39 affected individuals had seven homozygous pathogenic missense MED27 variants, five of which were recurrent. An emerging genotype-phenotype correlation was observed. This study provides a comprehensive clinical-radiological description of MED27-related disease, establishes genotype-phenotype and clinical-radiological correlations and suggests a differential diagnosis with syndromes of cerebello-lental neurodegeneration and other subtypes of 'neuro-MEDopathies'.

%B Brain %V 146 %P 5031-5043 %8 2023 Dec 01 %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/37517035?dopt=Abstract %R 10.1093/brain/awad257 %0 Journal Article %J J Inherit Metab Dis %D 2023 %T Biallelic missense variants in COG3 cause a congenital disorder of glycosylation with impairment of retrograde vesicular trafficking. %A Duan, Ruizhi %A Marafi, Dana %A Xia, Zhi-Jie %A Ng, Bobby G %A Maroofian, Reza %A Sumya, Farhana Taher %A Saad, Ahmed K %A Du, Haowei %A Fatih, Jawid M %A Hunter, Jill V %A Elbendary, Hasnaa M %A Baig, Shahid M %A Abdullah, Uzma %A Ali, Zafar %A Efthymiou, Stephanie %A Murphy, David %A Mitani, Tadahiro %A Withers, Marjorie A %A Jhangiani, Shalini N %A Coban-Akdemir, Zeynep %A Calame, Daniel G %A Pehlivan, Davut %A Richard A Gibbs %A Posey, Jennifer E %A Houlden, Henry %A Lupashin, Vladimir V %A Zaki, Maha S %A Freeze, Hudson H %A Lupski, James R %K Adaptor Proteins, Vesicular Transport %K Congenital Disorders of Glycosylation %K Fibroblasts %K Glycosylation %K Humans %K Phenotype %X

Biallelic variants in genes for seven out of eight subunits of the conserved oligomeric Golgi complex (COG) are known to cause recessive congenital disorders of glycosylation (CDG) with variable clinical manifestations. COG3 encodes a constituent subunit of the COG complex that has not been associated with disease traits in humans. Herein, we report two COG3 homozygous missense variants in four individuals from two unrelated consanguineous families that co-segregated with COG3-CDG presentations. Clinical phenotypes of affected individuals include global developmental delay, severe intellectual disability, microcephaly, epilepsy, facial dysmorphism, and variable neurological findings. Biochemical analysis of serum transferrin from one family showed the loss of a single sialic acid. Western blotting on patient-derived fibroblasts revealed reduced COG3 and COG4. Further experiments showed delayed retrograde vesicular recycling in patient cells. This report adds to the knowledge of the COG-CDG network by providing collective evidence for a COG3-CDG rare disease trait and implicating a likely pathology of the disorder as the perturbation of Golgi trafficking.

%B J Inherit Metab Dis %V 46 %P 1195-1205 %8 2023 Nov %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/37711075?dopt=Abstract %R 10.1002/jimd.12679 %0 Journal Article %J Am J Hum Genet %D 2023 %T Bi-allelic SNAPC4 variants dysregulate global alternative splicing and lead to neuroregression and progressive spastic paraparesis. %A Frost, F Graeme %A Morimoto, Marie %A Sharma, Prashant %A Ruaud, Lyse %A Belnap, Newell %A Calame, Daniel G %A Uchiyama, Yuri %A Matsumoto, Naomichi %A Oud, Machteld M %A Ferreira, Elise A %A Narayanan, Vinodh %A Rangasamy, Sampath %A Huentelman, Matt %A Emrick, Lisa T %A Sato-Shirai, Ikuko %A Kumada, Satoko %A Wolf, Nicole I %A Steinbach, Peter J %A Huang, Yan %A Pusey, Barbara N %A Passemard, Sandrine %A Levy, Jonathan %A Drunat, Séverine %A Vincent, Marie %A Guet, Agnès %A Agolini, Emanuele %A Novelli, Antonio %A Digilio, Maria Cristina %A Rosenfeld, Jill A %A Murphy, Jennifer L %A James R Lupski %A Vezina, Gilbert %A Macnamara, Ellen F %A Adams, David R %A Acosta, Maria T %A Tifft, Cynthia J %A Gahl, William A %A Malicdan, May Christine V %K Adolescent %K Alleles %K Alternative Splicing %K Child %K Child, Preschool %K DNA-Binding Proteins %K Female %K HeLa Cells %K Humans %K Infant %K Male %K Paraparesis, Spastic %K Pedigree %K Protein Isoforms %K Protein Structure, Secondary %K RNA, Small Nuclear %K RNA-Seq %K Transcription Factors %X

The vast majority of human genes encode multiple isoforms through alternative splicing, and the temporal and spatial regulation of those isoforms is critical for organismal development and function. The spliceosome, which regulates and executes splicing reactions, is primarily composed of small nuclear ribonucleoproteins (snRNPs) that consist of small nuclear RNAs (snRNAs) and protein subunits. snRNA gene transcription is initiated by the snRNA-activating protein complex (SNAPc). Here, we report ten individuals, from eight families, with bi-allelic, deleterious SNAPC4 variants. SNAPC4 encoded one of the five SNAPc subunits that is critical for DNA binding. Most affected individuals presented with delayed motor development and developmental regression after the first year of life, followed by progressive spasticity that led to gait alterations, paraparesis, and oromotor dysfunction. Most individuals had cerebral, cerebellar, or basal ganglia volume loss by brain MRI. In the available cells from affected individuals, SNAPC4 abundance was decreased compared to unaffected controls, suggesting that the bi-allelic variants affect SNAPC4 accumulation. The depletion of SNAPC4 levels in HeLa cell lines via genomic editing led to decreased snRNA expression and global dysregulation of alternative splicing. Analysis of available fibroblasts from affected individuals showed decreased snRNA expression and global dysregulation of alternative splicing compared to unaffected cells. Altogether, these data suggest that these bi-allelic SNAPC4 variants result in loss of function and underlie the neuroregression and progressive spasticity in these affected individuals.

%B Am J Hum Genet %V 110 %P 663-680 %8 2023 Apr 06 %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/36965478?dopt=Abstract %R 10.1016/j.ajhg.2023.03.001 %0 Journal Article %J Am J Hum Genet %D 2023 %T Bi-allelic TTI1 variants cause an autosomal-recessive neurodevelopmental disorder with microcephaly. %A Serey-Gaut, Margaux %A Cortes, Marisol %A Makrythanasis, Periklis %A Suri, Mohnish %A Taylor, Alexander M R %A Sullivan, Jennifer A %A Asleh, Ayat N %A Mitra, Jaba %A Dar, Mohamad A %A McNamara, Amy %A Shashi, Vandana %A Dugan, Sarah %A Song, Xiaofei %A Rosenfeld, Jill A %A Cabrol, Christelle %A Iwaszkiewicz, Justyna %A Zoete, Vincent %A Pehlivan, Davut %A Akdemir, Zeynep Coban %A Roeder, Elizabeth R %A Littlejohn, Rebecca Okashah %A Dibra, Harpreet K %A Byrd, Philip J %A Stewart, Grant S %A Geckinli, Bilgen B %A Posey, Jennifer %A Westman, Rachel %A Jungbluth, Chelsy %A Eason, Jacqueline %A Sachdev, Rani %A Evans, Carey-Anne %A Lemire, Gabrielle %A VanNoy, Grace E %A O'Donnell-Luria, Anne %A Mau-Them, Frédéric Tran %A Juven, Aurélien %A Piard, Juliette %A Nixon, Cheng Yee %A Zhu, Ying %A Ha, Taekjip %A Buckley, Michael F %A Thauvin, Christel %A Essien Umanah, George K %A Van Maldergem, Lionel %A James R Lupski %A Roscioli, Tony %A Dawson, Valina L %A Dawson, Ted M %A Antonarakis, Stylianos E %K HEK293 Cells %K Humans %K Intracellular Signaling Peptides and Proteins %K Microcephaly %K Movement Disorders %K Neurodevelopmental Disorders %K TOR Serine-Threonine Kinases %X

Telomere maintenance 2 (TELO2), Tel2 interacting protein 2 (TTI2), and Tel2 interacting protein 1 (TTI1) are the three components of the conserved Triple T (TTT) complex that modulates activity of phosphatidylinositol 3-kinase-related protein kinases (PIKKs), including mTOR, ATM, and ATR, by regulating the assembly of mTOR complex 1 (mTORC1). The TTT complex is essential for the expression, maturation, and stability of ATM and ATR in response to DNA damage. TELO2- and TTI2-related bi-allelic autosomal-recessive (AR) encephalopathies have been described in individuals with moderate to severe intellectual disability (ID), short stature, postnatal microcephaly, and a movement disorder (in the case of variants within TELO2). We present clinical, genomic, and functional data from 11 individuals in 9 unrelated families with bi-allelic variants in TTI1. All present with ID, and most with microcephaly, short stature, and a movement disorder. Functional studies performed in HEK293T cell lines and fibroblasts and lymphoblastoid cells derived from 4 unrelated individuals showed impairment of the TTT complex and of mTOR pathway activity which is improved by treatment with Rapamycin. Our data delineate a TTI1-related neurodevelopmental disorder and expand the group of disorders related to the TTT complex.

%B Am J Hum Genet %V 110 %P 499-515 %8 2023 Mar 02 %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/36724785?dopt=Abstract %R 10.1016/j.ajhg.2023.01.006 %0 Journal Article %J Genet Med %D 2023 %T Biallelic variants in HECT E3 paralogs, HECTD4 and UBE3C, encoding ubiquitin ligases cause neurodevelopmental disorders that overlap with Angelman syndrome. %A Faqeih, Eissa A %A Alghamdi, Malak Ali %A Almahroos, Marwa A %A Alharby, Essa %A Almuntashri, Makki %A Alshangiti, Amnah M %A Clément, Prouteau %A Calame, Daniel G %A Qebibo, Leila %A Burglen, Lydie %A Doco-Fenzy, Martine %A Mastrangelo, Mario %A Torella, Annalaura %A Manti, Filippo %A Nigro, Vincenzo %A Alban, Ziegler %A Alharbi, Ghadeer Saleh %A Hashmi, Jamil Amjad %A Alraddadi, Rawya %A Alamri, Razan %A Mitani, Tadahiro %A Magalie, Barth %A Coban-Akdemir, Zeynep %A Geckinli, Bilgen Bilge %A Pehlivan, Davut %A Romito, Antonio %A Karageorgou, Vasiliki %A Martini, Javier %A Colin, Estelle %A Bonneau, Dominique %A Bertoli-Avella, Aida %A James R Lupski %A Pastore, Annalisa %A Peake, Roy W A %A Dallol, Ashraf %A Alfadhel, Majid %A Almontashiri, Naif A M %K Angelman Syndrome %K Humans %K Neurodevelopmental Disorders %K Phenotype %K Ubiquitin %K Ubiquitin-Protein Ligases %X

PURPOSE: Pathogenic variants in genes encoding ubiquitin E3 ligases are known to cause neurodevelopmental syndromes. Additional neurodevelopmental disorders associated with the other genes encoding E3 ligases are yet to be identified.

METHODS: Chromosomal analysis and exome sequencing were used to identify the genetic causes in 10 patients from 7 unrelated families with syndromic neurodevelopmental, seizure, and movement disorders and neurobehavioral phenotypes.

RESULTS: In total, 4 patients were found to have 3 different homozygous loss-of-function (LoF) variants, and 3 patients had 4 compound heterozygous missense variants in the candidate E3 ligase gene, HECTD4, that were rare, absent from controls as homozygous, and predicted to be deleterious in silico. In 3 patients from 2 families with Angelman-like syndrome, paralog-directed candidate gene approach detected 2 LoF variants in the other candidate E3 ligase gene, UBE3C, a paralog of the Angelman syndrome E3 ligase gene, UBE3A. The RNA studies in 4 patients with LoF variants in HECTD4 and UBE3C provided evidence for the LoF effect.

CONCLUSION: HECTD4 and UBE3C are novel biallelic rare disease genes, expand the association of the other HECT E3 ligase group with neurodevelopmental syndromes, and could explain some of the missing heritability in patients with a suggestive clinical diagnosis of Angelman syndrome.

%B Genet Med %V 25 %P 100323 %8 2023 Feb %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/36401616?dopt=Abstract %R 10.1016/j.gim.2022.10.006 %0 Journal Article %J Genet Med %D 2023 %T Biallelic variants in SLC4A10 encoding a sodium-dependent bicarbonate transporter lead to a neurodevelopmental disorder. %A Maroofian, Reza %A Zamani, Mina %A Kaiyrzhanov, Rauan %A Liebmann, Lutz %A Karimiani, Ehsan Ghayoor %A Vona, Barbara %A Huebner, Antje K %A Calame, Daniel G %A Misra, Vinod K %A Sadeghian, Saeid %A Azizimalamiri, Reza %A Mohammadi, Mohammad Hasan %A Zeighami, Jawaher %A Heydaran, Sogand %A Toosi, Mehran Beiraghi %A Akhondian, Javad %A Babaei, Meisam %A Hashemi, Narges %A Schnur, Rhonda E %A Suri, Mohnish %A Setzke, Jonas %A Wagner, Matias %A Brunet, Theresa %A Grochowski, Christopher M %A Emrick, Lisa %A Chung, Wendy K %A Hellmich, Ute A %A Schmidts, Miriam %A Lupski, James R %A Galehdari, Hamid %A Severino, Mariasavina %A Houlden, Henry %A Hübner, Christian A %X

PURPOSE: SLC4A10 encodes a plasma membrane-bound transporter, which mediates Na-dependent HCO import, thus mediating net acid extrusion. Slc4a10 knockout mice show collapsed brain ventricles, an increased seizure threshold, mild behavioral abnormalities, impaired vision, and deafness.

METHODS: Utilizing exome/genome sequencing in families with undiagnosed neurodevelopmental disorders and international data sharing, 11 patients from 6 independent families with biallelic variants in SLC4A10 were identified. Clinico-radiological and dysmorphology assessments were conducted. A minigene assay, localization studies, intracellular pH recordings, and protein modeling were performed to study the possible functional consequences of the variant alleles.

RESULTS: The families harbor 8 segregating ultra-rare biallelic SLC4A10 variants (7 missense and 1 splicing). Phenotypically, patients present with global developmental delay/intellectual disability and central hypotonia, accompanied by variable speech delay, microcephaly, cerebellar ataxia, facial dysmorphism, and infrequently, epilepsy. Neuroimaging features range from some non-specific to distinct neuroradiological findings, including slit ventricles and a peculiar form of bilateral curvilinear nodular heterotopia. In silico analyses showed 6 of 7 missense variants affect evolutionarily conserved residues. Functional analyses supported the pathogenicity of 4 of 7 missense variants.

CONCLUSION: We provide evidence that pathogenic biallelic SLC4A10 variants can lead to neurodevelopmental disorders characterized by variable abnormalities of the central nervous system, including altered brain ventricles, thus resembling several features observed in knockout mice.

%B Genet Med %V 26 %P 101034 %8 2023 Dec 03 %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/38054405?dopt=Abstract %R 10.1016/j.gim.2023.101034 %0 Journal Article %J Am J Hum Genet %D 2023 %T Bi-allelic variants in the ESAM tight-junction gene cause a neurodevelopmental disorder associated with fetal intracranial hemorrhage. %A Lecca, Mauro %A Pehlivan, Davut %A Suñer, Damià Heine %A Weiss, Karin %A Coste, Thibault %A Zweier, Markus %A Oktay, Yavuz %A Danial-Farran, Nada %A Rosti, Vittorio %A Bonasoni, Maria Paola %A Malara, Alessandro %A Contrò, Gianluca %A Zuntini, Roberta %A Pollazzon, Marzia %A Pascarella, Rosario %A Neri, Alberto %A Fusco, Carlo %A Marafi, Dana %A Mitani, Tadahiro %A Posey, Jennifer Ellen %A Bayramoglu, Sadik Etka %A Gezdirici, Alper %A Hernandez-Rodriguez, Jessica %A Cladera, Emilia Amengual %A Miravet, Elena %A Roldan-Busto, Jorge %A Ruiz, María Angeles %A Bauzá, Cristofol Vives %A Ben-Sira, Liat %A Sigaudy, Sabine %A Begemann, Anaïs %A Unger, Sheila %A Gungor, Serdal %A Hiz, Semra %A Sonmezler, Ece %A Zehavi, Yoav %A Jerdev, Michael %A Balduini, Alessandra %A Zuffardi, Orsetta %A Horvath, Rita %A Lochmüller, Hanns %A Rauch, Anita %A Garavelli, Livia %A Tournier-Lasserve, Elisabeth %A Spiegel, Ronen %A James R Lupski %A Errichiello, Edoardo %K Alleles %K Animals %K Brain Diseases %K Cell Adhesion Molecules %K Endothelial Cells %K Humans %K Intracranial Hemorrhages %K Mice %K Nervous System Malformations %K Neurodevelopmental Disorders %K Tight Junctions %X

The blood-brain barrier (BBB) is an essential gatekeeper for the central nervous system and incidence of neurodevelopmental disorders (NDDs) is higher in infants with a history of intracerebral hemorrhage (ICH). We discovered a rare disease trait in thirteen individuals, including four fetuses, from eight unrelated families associated with homozygous loss-of-function variant alleles of ESAM which encodes an endothelial cell adhesion molecule. The c.115del (p.Arg39Glyfs33) variant, identified in six individuals from four independent families of Southeastern Anatolia, severely impaired the in vitro tubulogenic process of endothelial colony-forming cells, recapitulating previous evidence in null mice, and caused lack of ESAM expression in the capillary endothelial cells of damaged brain. Affected individuals with bi-allelic ESAM variants showed profound global developmental delay/unspecified intellectual disability, epilepsy, absent or severely delayed speech, varying degrees of spasticity, ventriculomegaly, and ICH/cerebral calcifications, the latter being also observed in the fetuses. Phenotypic traits observed in individuals with bi-allelic ESAM variants overlap very closely with other known conditions characterized by endothelial dysfunction due to mutation of genes encoding tight junction molecules. Our findings emphasize the role of brain endothelial dysfunction in NDDs and contribute to the expansion of an emerging group of diseases that we propose to rename as "tightjunctionopathies."

%B Am J Hum Genet %V 110 %P 681-690 %8 2023 Apr 06 %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/36996813?dopt=Abstract %R 10.1016/j.ajhg.2023.03.005 %0 Journal Article %J Genet Med %D 2023 %T Brain monoamine vesicular transport disease caused by homozygous SLC18A2 variants: A study in 42 affected individuals. %A Saida, Ken %A Maroofian, Reza %A Sengoku, Toru %A Mitani, Tadahiro %A Pagnamenta, Alistair T %A Marafi, Dana %A Zaki, Maha S %A O'Brien, Thomas J %A Karimiani, Ehsan Ghayoor %A Kaiyrzhanov, Rauan %A Takizawa, Marina %A Ohori, Sachiko %A Leong, Huey Yin %A Akay, Gulsen %A Galehdari, Hamid %A Zamani, Mina %A Romy, Ratna %A Carroll, Christopher J %A Toosi, Mehran Beiraghi %A Ashrafzadeh, Farah %A Imannezhad, Shima %A Malek, Hadis %A Ahangari, Najmeh %A Tomoum, Hoda %A Gowda, Vykuntaraju K %A Srinivasan, Varunvenkat M %A Murphy, David %A Dominik, Natalia %A Elbendary, Hasnaa M %A Rafat, Karima %A Yilmaz, Sanem %A Kanmaz, Seda %A Serin, Mine %A Krishnakumar, Deepa %A Gardham, Alice %A Maw, Anna %A Rao, Tekki Sreenivasa %A Alsubhi, Sarah %A Srour, Myriam %A Buhas, Daniela %A Jewett, Tamison %A Goldberg, Rachel E %A Shamseldin, Hanan %A Frengen, Eirik %A Misceo, Doriana %A Strømme, Petter %A Magliocco Ceroni, José Ricardo %A Kim, Chong Ae %A Yesil, Gozde %A Sengenc, Esma %A Guler, Serhat %A Hull, Mariam %A Parnes, Mered %A Aktas, Dilek %A Anlar, Banu %A Bayram, Yavuz %A Pehlivan, Davut %A Posey, Jennifer E %A Alavi, Shahryar %A Madani Manshadi, Seyed Ali %A Alzaidan, Hamad %A Al-Owain, Mohammad %A Alabdi, Lama %A Abdulwahab, Ferdous %A Sekiguchi, Futoshi %A Hamanaka, Kohei %A Fujita, Atsushi %A Uchiyama, Yuri %A Mizuguchi, Takeshi %A Miyatake, Satoko %A Miyake, Noriko %A Elshafie, Reem M %A Salayev, Kamran %A Guliyeva, Ulviyya %A Alkuraya, Fowzan S %A Gleeson, Joseph G %A Monaghan, Kristin G %A Langley, Katherine G %A Yang, Hui %A Motavaf, Mahsa %A Safari, Saeid %A Alipour, Mozhgan %A Ogata, Kazuhiro %A Brown, André E X %A James R Lupski %A Houlden, Henry %A Matsumoto, Naomichi %K Amines %K Animals %K Brain %K Brain Diseases %K Caenorhabditis elegans %K Dystonia %K Humans %K Movement Disorders %K Rats %K Vesicular Monoamine Transport Proteins %X

PURPOSE: Brain monoamine vesicular transport disease is an infantile-onset movement disorder that mimics cerebral palsy. In 2013, the homozygous SLC18A2 variant, p.Pro387Leu, was first reported as a cause of this rare disorder, and dopamine agonists were efficient for treating affected individuals from a single large family. To date, only 6 variants have been reported. In this study, we evaluated genotype-phenotype correlations in individuals with biallelic SLC18A2 variants.

METHODS: A total of 42 affected individuals with homozygous SLC18A2 variant alleles were identified. We evaluated genotype-phenotype correlations and the missense variants in the affected individuals based on the structural modeling of rat VMAT2 encoded by Slc18a2, with cytoplasm- and lumen-facing conformations. A Caenorhabditis elegans model was created for functional studies.

RESULTS: A total of 19 homozygous SLC18A2 variants, including 3 recurrent variants, were identified using exome sequencing. The affected individuals typically showed global developmental delay, hypotonia, dystonia, oculogyric crisis, and autonomic nervous system involvement (temperature dysregulation/sweating, hypersalivation, and gastrointestinal dysmotility). Among the 58 affected individuals described to date, 16 (28%) died before the age of 13 years. Of the 17 patients with p.Pro237His, 9 died, whereas all 14 patients with p.Pro387Leu survived. Although a dopamine agonist mildly improved the disease symptoms in 18 of 21 patients (86%), some affected individuals with p.Ile43Phe and p.Pro387Leu showed milder phenotypes and presented prolonged survival even without treatment. The C. elegans model showed behavioral abnormalities.

CONCLUSION: These data expand the phenotypic and genotypic spectra of SLC18A2-related disorders.

%B Genet Med %V 25 %P 90-102 %8 2023 Jan %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/36318270?dopt=Abstract %R 10.1016/j.gim.2022.09.010 %0 Journal Article %J Eur J Hum Genet %D 2023 %T Broadening the phenotypic and molecular spectrum of FINCA syndrome: Biallelic NHLRC2 variants in 15 novel individuals. %A Sczakiel, Henrike L %A Zhao, Max %A Wollert-Wulf, Brigitte %A Danyel, Magdalena %A Ehmke, Nadja %A Stoltenburg, Corinna %A Damseh, Nadirah %A Al-Ashhab, Motee %A Balci, Tugce B %A Osmond, Matthew %A Andrade, Andrea %A Schallner, Jens %A Porrmann, Joseph %A McDonald, Kimberly %A Liao, Mingjuan %A Oppermann, Henry %A Platzer, Konrad %A Dierksen, Nadine %A Mojarrad, Majid %A Eslahi, Atieh %A Bakaeean, Behnaz %A Calame, Daniel G %A Lupski, James R %A Firoozfar, Zahra %A Seyedhassani, Seyed Mohammad %A Mohammadi, Seyed Ahmad %A Anwaar, Najwa %A Rahman, Fatima %A Seelow, Dominik %A Janz, Martin %A Horn, Denise %A Maroofian, Reza %A Boschann, Felix %K Disease Progression %K Fibrosis %K HEK293 Cells %K Humans %K Intellectual Disability %K Movement Disorders %K Phenotype %K Seizures %K Syndrome %X

FINCA syndrome [MIM: 618278] is an autosomal recessive multisystem disorder characterized by fibrosis, neurodegeneration and cerebral angiomatosis. To date, 13 patients from nine families with biallelic NHLRC2 variants have been published. In all of them, the recurrent missense variant p.(Asp148Tyr) was detected on at least one allele. Common manifestations included lung or muscle fibrosis, respiratory distress, developmental delay, neuromuscular symptoms and seizures often followed by early death due to rapid disease progression.Here, we present 15 individuals from 12 families with an overlapping phenotype associated with nine novel NHLRC2 variants identified by exome analysis. All patients described here presented with moderate to severe global developmental delay and variable disease progression. Seizures, truncal hypotonia and movement disorders were frequently observed. Notably, we also present the first eight cases in which the recurrent p.(Asp148Tyr) variant was not detected in either homozygous or compound heterozygous state.We cloned and expressed all novel and most previously published non-truncating variants in HEK293-cells. From the results of these functional studies, we propose a potential genotype-phenotype correlation, with a greater reduction in protein expression being associated with a more severe phenotype.Taken together, our findings broaden the known phenotypic and molecular spectrum and emphasize that NHLRC2-related disease should be considered in patients presenting with intellectual disability, movement disorders, neuroregression and epilepsy with or without pulmonary involvement.

%B Eur J Hum Genet %V 31 %P 905-917 %8 2023 Aug %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/37188825?dopt=Abstract %R 10.1038/s41431-023-01382-0 %0 Journal Article %J Brain %D 2023 %T Cation leak through the ATP1A3 pump causes spasticity and intellectual disability. %A Calame, Daniel G %A Moreno Vadillo, Cristina %A Berger, Seth %A Lotze, Timothy %A Shinawi, Marwan %A Poupak, Javaher %A Heller, Corina %A Cohen, Julie %A Person, Richard %A Telegrafi, Aida %A Phitsanuwong, Chalongchai %A Fiala, Kaylene %A Thiffault, Isabelle %A Del Viso, Florencia %A Zhou, Dihong %A Fleming, Emily A %A Pastinen, Tomi %A Fatemi, Ali %A Thomas, Sruthi %A Pascual, Samuel I %A Torres, Rosa J %A Prior, Carmen %A Gómez-González, Clara %A Biskup, Saskia %A Lupski, James R %A Maric, Dragan %A Holmgren, Miguel %A Regier, Debra %A Yano, Sho T %K Cations %K Cerebellar Ataxia %K Humans %K Intellectual Disability %K Muscle Spasticity %K Mutation %K Phenotype %K Sodium-Potassium-Exchanging ATPase %K Syndrome %X

ATP1A3 encodes the α3 subunit of the sodium-potassium ATPase, one of two isoforms responsible for powering electrochemical gradients in neurons. Heterozygous pathogenic ATP1A3 variants produce several distinct neurological syndromes, yet the molecular basis for phenotypic variability is unclear. We report a novel recurrent variant, ATP1A3(NM_152296.5):c.2324C>T; p.(Pro775Leu), in nine individuals associated with the primary clinical features of progressive or non-progressive spasticity and developmental delay/intellectual disability. No patients fulfil diagnostic criteria for ATP1A3-associated syndromes, including alternating hemiplegia of childhood, rapid-onset dystonia-parkinsonism or cerebellar ataxia-areflexia-pes cavus-optic atrophy-sensorineural hearing loss (CAPOS), and none were suspected of having an ATP1A3-related disorder. Uniquely among known ATP1A3 variants, P775L causes leakage of sodium ions and protons into the cell, associated with impaired sodium binding/occlusion kinetics favouring states with fewer bound ions. These phenotypic and electrophysiologic studies demonstrate that ATP1A3:c.2324C>T; p.(Pro775Leu) results in mild ATP1A3-related phenotypes resembling complex hereditary spastic paraplegia or idiopathic spastic cerebral palsy. Cation leak provides a molecular explanation for this genotype-phenotype correlation, adding another mechanism to further explain phenotypic variability and highlighting the importance of biophysical properties beyond ion transport rate in ion transport diseases.

%B Brain %V 146 %P 3162-3171 %8 2023 Aug 01 %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/37043503?dopt=Abstract %R 10.1093/brain/awad124 %0 Journal Article %J Genet Med %D 2023 %T Clinical and functional heterogeneity associated with the disruption of retinoic acid receptor beta. %A Caron, Véronique %A Chassaing, Nicolas %A Ragge, Nicola %A Boschann, Felix %A Ngu, Angelina My-Hoa %A Meloche, Elisabeth %A Chorfi, Sarah %A Lakhani, Saquib A %A Ji, Weizhen %A Steiner, Laurie %A Marcadier, Julien %A Jansen, Philip R %A van de Pol, Laura A %A van Hagen, Johanna M %A Russi, Alvaro Serrano %A Le Guyader, Gwenaël %A Nordenskjöld, Magnus %A Nordgren, Ann %A Anderlid, Britt-Marie %A Plaisancié, Julie %A Stoltenburg, Corinna %A Horn, Denise %A Drenckhahn, Anne %A Hamdan, Fadi F %A Lefebvre, Mathilde %A Attié-Bitach, Tania %A Forey, Peggy %A Smirnov, Vasily %A Ernould, Françoise %A Jacquemont, Marie-Line %A Grotto, Sarah %A Alcantud, Alberto %A Coret, Alicia %A Ferrer-Avargues, Rosario %A Srivastava, Siddharth %A Vincent-Delorme, Catherine %A Romoser, Shelby %A Safina, Nicole %A Saade, Dimah %A Lupski, James R %A Calame, Daniel G %A Geneviève, David %A Chatron, Nicolas %A Schluth-Bolard, Caroline %A Myers, Kenneth A %A Dobyns, William B %A Calvas, Patrick %A Salmon, Caroline %A Holt, Richard %A Elmslie, Frances %A Allaire, Marc %A Prigozhin, Daniil M %A Tremblay, André %A Michaud, Jacques L %K Humans %K Microphthalmos %K Receptors, Retinoic Acid %K Retinoids %X

PURPOSE: Dominant variants in the retinoic acid receptor beta (RARB) gene underlie a syndromic form of microphthalmia, known as MCOPS12, which is associated with other birth anomalies and global developmental delay with spasticity and/or dystonia. Here, we report 25 affected individuals with 17 novel pathogenic or likely pathogenic variants in RARB. This study aims to characterize the functional impact of these variants and describe the clinical spectrum of MCOPS12.

METHODS: We used in vitro transcriptional assays and in silico structural analysis to assess the functional relevance of RARB variants in affecting the normal response to retinoids.

RESULTS: We found that all RARB variants tested in our assays exhibited either a gain-of-function or a loss-of-function activity. Loss-of-function variants disrupted RARB function through a dominant-negative effect, possibly by disrupting ligand binding and/or coactivators' recruitment. By reviewing clinical data from 52 affected individuals, we found that disruption of RARB is associated with a more variable phenotype than initially suspected, with the absence in some individuals of cardinal features of MCOPS12, such as developmental eye anomaly or motor impairment.

CONCLUSION: Our study indicates that pathogenic variants in RARB are functionally heterogeneous and associated with extensive clinical heterogeneity.

%B Genet Med %V 25 %P 100856 %8 2023 Aug %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/37092537?dopt=Abstract %R 10.1016/j.gim.2023.100856 %0 Journal Article %J Brain %D 2023 %T The clinical and genetic spectrum of autosomal-recessive TOR1A-related disorders. %A Saffari, Afshin %A Lau, Tracy %A Tajsharghi, Homa %A Karimiani, Ehsan Ghayoor %A Kariminejad, Ariana %A Efthymiou, Stephanie %A Zifarelli, Giovanni %A Sultan, Tipu %A Toosi, Mehran Beiraghi %A Sedighzadeh, Sahar %A Siu, Victoria Mok %A Ortigoza-Escobar, Juan Darío %A AlShamsi, Aisha M %A Ibrahim, Shahnaz %A Al-Sannaa, Nouriya Abbas %A Al-Hertani, Walla %A Sandra, Whalen %A Tarnopolsky, Mark %A Alavi, Shahryar %A Li, Chumei %A Day-Salvatore, Debra-Lynn %A Martínez-González, Maria Jesús %A Levandoski, Kristin M %A Bedoukian, Emma %A Madan-Khetarpal, Suneeta %A Idleburg, Michaela J %A Menezes, Minal Juliet %A Siddharth, Aishwarya %A Platzer, Konrad %A Oppermann, Henry %A Smitka, Martin %A Collins, Felicity %A Lek, Monkol %A Shahrooei, Mohmmad %A Ghavideldarestani, Maryam %A Herman, Isabella %A Rendu, John %A Faure, Julien %A Baker, Janice %A Bhambhani, Vikas %A Calderwood, Laurel %A Akhondian, Javad %A Imannezhad, Shima %A Mirzadeh, Hanieh Sadat %A Hashemi, Narges %A Doosti, Mohammad %A Safi, Mojtaba %A Ahangari, Najmeh %A Torbati, Paria Najarzadeh %A Abedini, Soheila %A Salpietro, Vincenzo %A Gulec, Elif Yilmaz %A Eshaghian, Safieh %A Ghazavi, Mohammadreza %A Pascher, Michael T %A Vogel, Marina %A Abicht, Angela %A Moutton, Sebastien %A Bruel, Ange-Line %A Rieubland, Claudine %A Gallati, Sabina %A Strom, Tim M %A Lochmüller, Hanns %A Mohammadi, Mohammad Hasan %A Alvi, Javeria Raza %A Zackai, Elaine H %A Keena, Beth A %A Skraban, Cara M %A Berger, Seth I %A Andrew, Erin H %A Rahimian, Elham %A Morrow, Michelle M %A Wentzensen, Ingrid M %A Millan, Francisca %A Henderson, Lindsay B %A Dafsari, Hormos Salimi %A Jungbluth, Heinz %A Gomez-Ospina, Natalia %A McRae, Anne %A Peter, Merlene %A Veltra, Danai %A Marinakis, Nikolaos M %A Sofocleous, Christalena %A Ashrafzadeh, Farah %A Pehlivan, Davut %A Lemke, Johannes R %A Melki, Judith %A Benezit, Audrey %A Bauer, Peter %A Weis, Denisa %A James R Lupski %A Senderek, Jan %A Christodoulou, John %A Chung, Wendy K %A Goodchild, Rose %A Offiah, Amaka C %A Moreno-De-Luca, Andres %A Suri, Mohnish %A Ebrahimi-Fakhari, Darius %A Houlden, Henry %A Maroofian, Reza %K Cross-Sectional Studies %K Dystonia %K Dystonic Disorders %K Humans %K Male %K Molecular Chaperones %K Mutation %K Nervous System Malformations %K Phenotype %X

In the field of rare diseases, progress in molecular diagnostics led to the recognition that variants linked to autosomal-dominant neurodegenerative diseases of later onset can, in the context of biallelic inheritance, cause devastating neurodevelopmental disorders and infantile or childhood-onset neurodegeneration. TOR1A-associated arthrogryposis multiplex congenita 5 (AMC5) is a rare neurodevelopmental disorder arising from biallelic variants in TOR1A, a gene that in the heterozygous state is associated with torsion dystonia-1 (DYT1 or DYT-TOR1A), an early-onset dystonia with reduced penetrance. While 15 individuals with AMC5-TOR1A have been reported (less than 10 in detail), a systematic investigation of the full disease-associated spectrum has not been conducted. Here, we assess the clinical, radiological and molecular characteristics of 57 individuals from 40 families with biallelic variants in TOR1A. Median age at last follow-up was 3 years (0-24 years). Most individuals presented with severe congenital flexion contractures (95%) and variable developmental delay (79%). Motor symptoms were reported in 79% and included lower limb spasticity and pyramidal signs, as well as gait disturbances. Facial dysmorphism was an integral part of the phenotype, with key features being a broad/full nasal tip, narrowing of the forehead and full cheeks. Analysis of disease-associated manifestations delineated a phenotypic spectrum ranging from normal cognition and mild gait disturbance to congenital arthrogryposis, global developmental delay, intellectual disability, absent speech and inability to walk. In a subset, the presentation was consistent with foetal akinesia deformation sequence with severe intrauterine abnormalities. Survival was 71%, with higher mortality in males. Death occurred at a median age of 1.2 months (1 week-9 years), due to respiratory failure, cardiac arrest or sepsis. Analysis of brain MRI studies identified non-specific neuroimaging features, including a hypoplastic corpus callosum (72%), foci of signal abnormality in the subcortical and periventricular white matter (55%), diffuse white matter volume loss (45%), mega cisterna magna (36%) and arachnoid cysts (27%). The molecular spectrum included 22 distinct variants, defining a mutational hotspot in the C-terminal domain of the Torsin-1A protein. Genotype-phenotype analysis revealed an association of missense variants in the 3-helix bundle domain to an attenuated phenotype, while missense variants near the Walker A/B motif as well as biallelic truncating variants were linked to early death. In summary, this systematic cross-sectional analysis of a large cohort of individuals with biallelic TOR1A variants across a wide age-range delineates the clinical and genetic spectrum of TOR1A-related autosomal-recessive disease and highlights potential predictors for disease severity and survival.

%B Brain %V 146 %P 3273-3288 %8 2023 Aug 01 %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/36757831?dopt=Abstract %R 10.1093/brain/awad039 %0 Journal Article %J Cell Discov %D 2023 %T Excess folic acid intake increases DNA de novo point mutations. %A Cao, Xuanye %A Xu, Jianfeng %A Lin, Ying L %A Cabrera, Robert M %A Chen, Qiuying %A Zhang, Chaofan %A Steele, John W %A Han, Xiao %A Gross, Steven S %A Wlodarczyk, Bogdan J %A James R Lupski %A Li, Wei %A Wang, Hongyan %A Finnell, Richard H %A Lei, Yunping %B Cell Discov %V 9 %P 22 %8 2023 Feb 28 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/36849450?dopt=Abstract %R 10.1038/s41421-022-00512-0 %0 Journal Article %J Nat Commun %D 2023 %T FOXI3 pathogenic variants cause one form of craniofacial microsomia. %A Mao, Ke %A Borel, Christelle %A Ansar, Muhammad %A Jolly, Angad %A Makrythanasis, Periklis %A Froehlich, Christine %A Iwaszkiewicz, Justyna %A Wang, Bingqing %A Xu, Xiaopeng %A Li, Qiang %A Blanc, Xavier %A Zhu, Hao %A Chen, Qi %A Jin, Fujun %A Ankamreddy, Harinarayana %A Singh, Sunita %A Zhang, Hongyuan %A Wang, Xiaogang %A Chen, Peiwei %A Ranza, Emmanuelle %A Paracha, Sohail Aziz %A Shah, Syed Fahim %A Guida, Valentina %A Piceci-Sparascio, Francesca %A Melis, Daniela %A Dallapiccola, Bruno %A Digilio, Maria Cristina %A Novelli, Antonio %A Magliozzi, Monia %A Fadda, Maria Teresa %A Streff, Haley %A Machol, Keren %A Lewis, Richard A %A Zoete, Vincent %A Squeo, Gabriella Maria %A Prontera, Paolo %A Mancano, Giorgia %A Gori, Giulia %A Mariani, Milena %A Selicorni, Angelo %A Psoni, Stavroula %A Fryssira, Helen %A Douzgou, Sofia %A Marlin, Sandrine %A Biskup, Saskia %A De Luca, Alessandro %A Merla, Giuseppe %A Zhao, Shouqin %A Cox, Timothy C %A Groves, Andrew K %A Lupski, James R %A Zhang, Qingguo %A Zhang, Yong-Biao %A Antonarakis, Stylianos E %K Animals %K Facial Asymmetry %K Forkhead Transcription Factors %K Goldenhar Syndrome %K Mice %K Pedigree %X

Craniofacial microsomia (CFM; also known as Goldenhar syndrome), is a craniofacial developmental disorder of variable expressivity and severity with a recognizable set of abnormalities. These birth defects are associated with structures derived from the first and second pharyngeal arches, can occur unilaterally and include ear dysplasia, microtia, preauricular tags and pits, facial asymmetry and other malformations. The inheritance pattern is controversial, and the molecular etiology of this syndrome is largely unknown. A total of 670 patients belonging to unrelated pedigrees with European and Chinese ancestry with CFM, are investigated. We identify 18 likely pathogenic variants in 21 probands (3.1%) in FOXI3. Biochemical experiments on transcriptional activity and subcellular localization of the likely pathogenic FOXI3 variants, and knock-in mouse studies strongly support the involvement of FOXI3 in CFM. Our findings indicate autosomal dominant inheritance with reduced penetrance, and/or autosomal recessive inheritance. The phenotypic expression of the FOXI3 variants is variable. The penetrance of the likely pathogenic variants in the seemingly dominant form is reduced, since a considerable number of such variants in affected individuals were inherited from non-affected parents. Here we provide suggestive evidence that common variation in the FOXI3 allele in trans with the pathogenic variant could modify the phenotypic severity and accounts for the incomplete penetrance.

%B Nat Commun %V 14 %P 2026 %8 2023 Apr 11 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/37041148?dopt=Abstract %R 10.1038/s41467-023-37703-6 %0 Journal Article %J N Engl J Med %D 2023 %T Genomics in Clinical Practice. %A Posey, Jennifer E %A James R Lupski %K Clinical Competence %K Genomic Medicine %K Genomics %K Humans %K Patient Care %B N Engl J Med %V 388 %P 1619-1620 %8 2023 Apr 27 %G eng %N 17 %1 https://www.ncbi.nlm.nih.gov/pubmed/37043638?dopt=Abstract %R 10.1056/NEJMe2302643 %0 Journal Article %J Hum Mol Genet %D 2023 %T Hemizygous variants in protein phosphatase 1 regulatory subunit 3F (PPP1R3F) are associated with a neurodevelopmental disorder characterized by developmental delay, intellectual disability and autistic features. %A Liu, Zhigang %A Xin, Baozhong %A Smith, Iris N %A Sency, Valerie %A Szekely, Julia %A Alkelai, Anna %A Shuldiner, Alan %A Efthymiou, Stephanie %A Rajabi, Farrah %A Coury, Stephanie %A Brownstein, Catherine A %A Rudnik-Schöneborn, Sabine %A Bruel, Ange-Line %A Thevenon, Julien %A Zeidler, Shimriet %A Jayakar, Parul %A Schmidt, Axel %A Cremer, Kirsten %A Engels, Hartmut %A Peters, Sophia O %A Zaki, Maha S %A Duan, Ruizhi %A Zhu, Changlian %A Xu, Yiran %A Gao, Chao %A Sepulveda-Morales, Tania %A Maroofian, Reza %A Alkhawaja, Issam A %A Khawaja, Mariam %A Alhalasah, Hunaida %A Houlden, Henry %A Madden, Jill A %A Turchetti, Valentina %A Marafi, Dana %A Agrawal, Pankaj B %A Schatz, Ulrich %A Rotenberg, Ari %A Rotenberg, Joshua %A Mancini, Grazia M S %A Bakhtiari, Somayeh %A Kruer, Michael %A Thiffault, Isabelle %A Hirsch, Steffen %A Hempel, Maja %A Stühn, Lara G %A Haack, Tobias B %A Posey, Jennifer E %A Lupski, James R %A Lee, Hyunpil %A Sarn, Nicholas B %A Eng, Charis %A Gonzaga-Jauregui, Claudia %A Zhang, Bin %A Wang, Heng %K Autism Spectrum Disorder %K Autistic Disorder %K Glucose %K Glycogen %K Humans %K Intellectual Disability %K Male %K Neurodevelopmental Disorders %K Protein Phosphatase 1 %X

Protein phosphatase 1 regulatory subunit 3F (PPP1R3F) is a member of the glycogen targeting subunits (GTSs), which belong to the large group of regulatory subunits of protein phosphatase 1 (PP1), a major eukaryotic serine/threonine protein phosphatase that regulates diverse cellular processes. Here, we describe the identification of hemizygous variants in PPP1R3F associated with a novel X-linked recessive neurodevelopmental disorder in 13 unrelated individuals. This disorder is characterized by developmental delay, mild intellectual disability, neurobehavioral issues such as autism spectrum disorder, seizures and other neurological findings including tone, gait and cerebellar abnormalities. PPP1R3F variants segregated with disease in affected hemizygous males that inherited the variants from their heterozygous carrier mothers. We show that PPP1R3F is predominantly expressed in brain astrocytes and localizes to the endoplasmic reticulum in cells. Glycogen content in PPP1R3F knockout astrocytoma cells appears to be more sensitive to fluxes in extracellular glucose levels than in wild-type cells, suggesting that PPP1R3F functions in maintaining steady brain glycogen levels under changing glucose conditions. We performed functional studies on nine of the identified variants and observed defects in PP1 binding, protein stability, subcellular localization and regulation of glycogen metabolism in most of them. Collectively, the genetic and molecular data indicate that deleterious variants in PPP1R3F are associated with a new X-linked disorder of glycogen metabolism, highlighting the critical role of GTSs in neurological development. This research expands our understanding of neurodevelopmental disorders and the role of PP1 in brain development and proper function.

%B Hum Mol Genet %V 32 %P 2981-2995 %8 2023 Oct 04 %G eng %N 20 %1 https://www.ncbi.nlm.nih.gov/pubmed/37531237?dopt=Abstract %R 10.1093/hmg/ddad124 %0 Journal Article %J Nucleic Acids Res %D 2023 %T HMZDupFinder: a robust computational approach for detecting intragenic homozygous duplications from exome sequencing data. %A Du, Haowei %A Dardas, Zain %A Jolly, Angad %A Grochowski, Christopher M %A Jhangiani, Shalini N %A Li, He %A Donna M Muzny %A Fatih, Jawid M %A Yesil, Gozde %A Elcioglu, Nursel H %A Gezdirici, Alper %A Marafi, Dana %A Pehlivan, Davut %A Calame, Daniel G %A Carvalho, Claudia M B %A Posey, Jennifer E %A Gambin, Tomasz %A Coban-Akdemir, Zeynep %A Lupski, James R %X

Homozygous duplications contribute to genetic disease by altering gene dosage or disrupting gene regulation and can be more deleterious to organismal biology than heterozygous duplications. Intragenic exonic duplications can result in loss-of-function (LoF) or gain-of-function (GoF) alleles that when homozygosed, i.e. brought to homozygous state at a locus by identity by descent or state, could potentially result in autosomal recessive (AR) rare disease traits. However, the detection and functional interpretation of homozygous duplications from exome sequencing data remains a challenge. We developed a framework algorithm, HMZDupFinder, that is designed to detect exonic homozygous duplications from exome sequencing (ES) data. The HMZDupFinder algorithm can efficiently process large datasets and accurately identifies small intragenic duplications, including those associated with rare disease traits. HMZDupFinder called 965 homozygous duplications with three or less exons from 8,707 ES with a recall rate of 70.9% and a precision of 16.1%. We experimentally confirmed 8/10 rare homozygous duplications. Pathogenicity assessment of these copy number variant alleles allowed clinical genomics contextualization for three homozygous duplications alleles, including two affecting known OMIM disease genes EDAR (MIM# 224900), TNNT1(MIM# 605355), and one variant in a novel candidate disease gene: PAAF1.

%B Nucleic Acids Res %8 2023 Dec 28 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/38153174?dopt=Abstract %R 10.1093/nar/gkad1223 %0 Journal Article %J Am J Hum Genet %D 2023 %T Monoallelic variation in DHX9, the gene encoding the DExH-box helicase DHX9, underlies neurodevelopment disorders and Charcot-Marie-Tooth disease. %A Calame, Daniel G %A Guo, Tianyu %A Wang, Chen %A Garrett, Lillian %A Jolly, Angad %A Dawood, Moez %A Kurolap, Alina %A Henig, Noa Zunz %A Fatih, Jawid M %A Herman, Isabella %A Du, Haowei %A Mitani, Tadahiro %A Becker, Lore %A Rathkolb, Birgit %A Gerlini, Raffaele %A Seisenberger, Claudia %A Marschall, Susan %A Hunter, Jill V %A Gerard, Amanda %A Heidlebaugh, Alexis %A Challman, Thomas %A Spillmann, Rebecca C %A Jhangiani, Shalini N %A Coban-Akdemir, Zeynep %A Lalani, Seema %A Liu, Lingxiao %A Revah-Politi, Anya %A Iglesias, Alejandro %A Guzman, Edwin %A Baugh, Evan %A Boddaert, Nathalie %A Rondeau, Sophie %A Ormieres, Clothide %A Barcia, Giulia %A Tan, Queenie K G %A Thiffault, Isabelle %A Pastinen, Tomi %A Sheikh, Kazim %A Biliciler, Suur %A Mei, Davide %A Melani, Federico %A Shashi, Vandana %A Yaron, Yuval %A Steele, Mary %A Wakeling, Emma %A Østergaard, Elsebet %A Nazaryan-Petersen, Lusine %A Millan, Francisca %A Santiago-Sim, Teresa %A Thevenon, Julien %A Bruel, Ange-Line %A Thauvin-Robinet, Christel %A Popp, Denny %A Platzer, Konrad %A Gawlinski, Pawel %A Wiszniewski, Wojciech %A Marafi, Dana %A Pehlivan, Davut %A Posey, Jennifer E %A Richard A Gibbs %A Gailus-Durner, Valerie %A Guerrini, Renzo %A Fuchs, Helmut %A Hrabě de Angelis, Martin %A Hölter, Sabine M %A Cheung, Hoi-Hung %A Gu, Shen %A Lupski, James R %K Animals %K Cell Line %K Charcot-Marie-Tooth Disease %K DEAD-box RNA Helicases %K Dichlorodiphenyl Dichloroethylene %K DNA Helicases %K Humans %K Mammals %K Mice %K Neoplasm Proteins %K Neurodevelopmental Disorders %X

DExD/H-box RNA helicases (DDX/DHX) are encoded by a large paralogous gene family; in a subset of these human helicase genes, pathogenic variation causes neurodevelopmental disorder (NDD) traits and cancer. DHX9 encodes a BRCA1-interacting nuclear helicase regulating transcription, R-loops, and homologous recombination and exhibits the highest mutational constraint of all DDX/DHX paralogs but remains unassociated with disease traits in OMIM. Using exome sequencing and family-based rare-variant analyses, we identified 20 individuals with de novo, ultra-rare, heterozygous missense or loss-of-function (LoF) DHX9 variant alleles. Phenotypes ranged from NDDs to the distal symmetric polyneuropathy axonal Charcot-Marie-Tooth disease (CMT2). Quantitative Human Phenotype Ontology (HPO) analysis demonstrated genotype-phenotype correlations with LoF variants causing mild NDD phenotypes and nuclear localization signal (NLS) missense variants causing severe NDD. We investigated DHX9 variant-associated cellular phenotypes in human cell lines. Whereas wild-type DHX9 was restricted to the nucleus, NLS missense variants abnormally accumulated in the cytoplasm. Fibroblasts from an individual with an NLS variant also showed abnormal cytoplasmic DHX9 accumulation. CMT2-associated missense variants caused aberrant nucleolar DHX9 accumulation, a phenomenon previously associated with cellular stress. Two NDD-associated variants, p.Gly411Glu and p.Arg761Gln, altered DHX9 ATPase activity. The severe NDD-associated variant p.Arg141Gln did not affect DHX9 localization but instead increased R-loop levels and double-stranded DNA breaks. Dhx9 mice exhibited hypoactivity in novel environments, tremor, and sensorineural hearing loss. All together, these results establish DHX9 as a critical regulator of mammalian neurodevelopment and neuronal homeostasis.

%B Am J Hum Genet %V 110 %P 1394-1413 %8 2023 Aug 03 %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/37467750?dopt=Abstract %R 10.1016/j.ajhg.2023.06.013 %0 Journal Article %J Clin Genet %D 2023 %T Novel LSS variants in alopecia and intellectual disability syndrome: New case report and clinical spectrum of LSS-related rare disease traits. %A Elbendary, Hasnaa M %A Marafi, Dana %A Saad, Ahmed K %A Elhossini, Rasha %A Duan, Ruizhi %A Rafat, Karima %A Jhangiani, Shalini N %A Richard A Gibbs %A Pehlivan, Davut %A Calame, Daniel G %A Posey, Jennifer E %A James R Lupski %A Zaki, Maha S %K Alopecia %K Humans %K Intellectual Disability %K Male %K Mutation %K Phenotype %K Rare Diseases %K Syndrome %X

Pathogenic biallelic variants in LSS are associated with three Mendelian rare disease traits including congenital cataract type 44, autosomal recessive hypotrichosis type 14, and alopecia-intellectual disability syndrome type 4 (APMR4). We performed trio research exome sequencing on a family with a four-year-old male with global developmental delay, epilepsy and striking alopecia, and identified novel compound heterozygous LSS splice site (c.14+2T>C) and missense (c.1357 G>A; p.V453L) variant alleles. Rare features associated with APMR4 such as cryptorchidism, micropenis, mild cortical brain atrophy and thin corpus callosum were detected. Previously unreported APMR4 findings including cerebellar involvement in the form of unsteady ataxic gait, small vermis with prominent folia, were noted. A review of all reported variants to date in 29 families with LSS-related phenotypes showed an emerging genotype-phenotype correlation. Our report potentially expands LSS-related phenotypic spectrum and highlights the importance of performing brain imaging in LSS-related conditions.

%B Clin Genet %V 104 %P 344-349 %8 2023 Sep %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/37157980?dopt=Abstract %R 10.1111/cge.14348 %0 Journal Article %J Am J Hum Genet %D 2023 %T PLS3 missense variants affecting the actin-binding domains cause X-linked congenital diaphragmatic hernia and body-wall defects. %A Petit, Florence %A Longoni, Mauro %A Wells, Julie %A Maser, Richard S %A Bogenschutz, Eric L %A Dysart, Matthew J %A Contreras, Hannah T M %A Frénois, Frederic %A Pober, Barbara R %A Clark, Robin D %A Giampietro, Philip F %A Ropers, Hilger H %A Hu, Hao %A Loscertales, Maria %A Wagner, Richard %A Ai, Xingbin %A Brand, Harrison %A Jourdain, Anne-Sophie %A Delrue, Marie-Ange %A Gilbert-Dussardier, Brigitte %A Devisme, Louise %A Keren, Boris %A McCulley, David J %A Qiao, Lu %A Hernan, Rebecca %A Wynn, Julia %A Scott, Tiana M %A Calame, Daniel G %A Coban-Akdemir, Zeynep %A Hernandez, Patricia %A Hernandez-Garcia, Andres %A Yonath, Hagith %A Lupski, James R %A Shen, Yufeng %A Chung, Wendy K %A Scott, Daryl A %A Bult, Carol J %A Donahoe, Patricia K %A High, Frances A %K Actins %K Adult %K Animals %K Hernias, Diaphragmatic, Congenital %K Humans %K Male %K Mice %K Mutation, Missense %K Osteoporosis %X

Congenital diaphragmatic hernia (CDH) is a relatively common and genetically heterogeneous structural birth defect associated with high mortality and morbidity. We describe eight unrelated families with an X-linked condition characterized by diaphragm defects, variable anterior body-wall anomalies, and/or facial dysmorphism. Using linkage analysis and exome or genome sequencing, we found that missense variants in plastin 3 (PLS3), a gene encoding an actin bundling protein, co-segregate with disease in all families. Loss-of-function variants in PLS3 have been previously associated with X-linked osteoporosis (MIM: 300910), so we used in silico protein modeling and a mouse model to address these seemingly disparate clinical phenotypes. The missense variants in individuals with CDH are located within the actin-binding domains of the protein but are not predicted to affect protein structure, whereas the variants in individuals with osteoporosis are predicted to result in loss of function. A mouse knockin model of a variant identified in one of the CDH-affected families, c.1497G>C (p.Trp499Cys), shows partial perinatal lethality and recapitulates the key findings of the human phenotype, including diaphragm and abdominal-wall defects. Both the mouse model and one adult human male with a CDH-associated PLS3 variant were observed to have increased rather than decreased bone mineral density. Together, these clinical and functional data in humans and mice reveal that specific missense variants affecting the actin-binding domains of PLS3 might have a gain-of-function effect and cause a Mendelian congenital disorder.

%B Am J Hum Genet %V 110 %P 1787-1803 %8 2023 Oct 05 %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/37751738?dopt=Abstract %R 10.1016/j.ajhg.2023.09.002 %0 Journal Article %J HGG Adv %D 2023 %T Rare variant enrichment analysis supports as a contributory driver gene in the etiology of Mayer-Rokitansky-Küster-Hauser syndrome. %A Jolly, Angad %A Du, Haowei %A Borel, Christelle %A Chen, Na %A Zhao, Sen %A Grochowski, Christopher M %A Duan, Ruizhi %A Fatih, Jawid M %A Dawood, Moez %A Salvi, Sejal %A Jhangiani, Shalini N %A Donna M Muzny %A Koch, André %A Rouskas, Konstantinos %A Glentis, Stavros %A Deligeoroglou, Efthymios %A Bacopoulou, Flora %A Wise, Carol A %A Dietrich, Jennifer E %A Van den Veyver, Ignatia B %A Dimas, Antigone S %A Brucker, Sara %A Sutton, V Reid %A Richard A Gibbs %A Antonarakis, Stylianos E %A Wu, Nan %A Coban-Akdemir, Zeynep H %A Zhu, Lan %A Posey, Jennifer E %A Lupski, James R %K 46, XX Disorders of Sex Development %K Female %K Humans %K Urogenital Abnormalities %K Uterus %X

Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome is characterized by aplasia of the female reproductive tract; the syndrome can include renal anomalies, absence or dysgenesis, and skeletal anomalies. While functional models have elucidated several candidate genes, only (MIM: 603490) variants have been definitively associated with a subtype of MRKH with hyperandrogenism (MIM: 158330). DNA from 148 clinically diagnosed MRKH probands across 144 unrelated families and available family members from North America, Europe, and South America were exome sequenced (ES) and by family-based genomics analyzed for rare likely deleterious variants. A replication cohort consisting of 442 Han Chinese individuals with MRKH was used to further reproduce findings in diverse genetic backgrounds. Proband and OMIM phenotypes annotated using the Human Phenotype Ontology were analyzed to quantitatively delineate the phenotypic spectrum associated with variant alleles found in our MRKH cohort and those previously published. This study reports 18 novel variant alleles, 16 within a multiethnic MRKH cohort and two within a congenital scoliosis cohort. Cohort-wide analyses for a burden of rare variants within a single gene identified likely damaging variants in (MIM: 617782), a known disease gene for renal hypoplasia and uterine abnormalities (MIM: 617805), in 16 of 590 MRKH probands. variant alleles, including a CNV null allele, were found in 8 MRKH type 1 probands and 8 MRKH type II probands. This study used quantitative phenotypic analyses in a worldwide multiethnic cohort to identify and strengthen the association of to isolated uterine agenesis (MRKH type I) and syndromic MRKH type II.

%B HGG Adv %V 4 %P 100188 %8 2023 Jul 13 %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/37124138?dopt=Abstract %R 10.1016/j.xhgg.2023.100188 %0 Journal Article %J J Med Genet %D 2023 %T Recurring germline mosaicism in a family due to reversion of an inherited derivative chromosome 8 from an 8;21 translocation with interstitial telomeric sequences. %A Bi, Weimin %A Bo Yuan %A Liu, Pengfei %A Murry, Jaclyn B %A Xiang Qin %A Xia, Fan %A Quach, Thao %A Cooper, Lance M %A Wiszniewska, Joanna %A Hixson, Patricia %A Peacock, Sandra %A Tonk, Vijay S %A Huff, Robert W %A Ortega, Veronica %A James R Lupski %A Steven E Scherer %A Littlejohn, Rebecca Okashah %A Velagaleti, Gopalrao V N %A Roeder, Elizabeth R %A Cheung, Sau Wai %K Chromosome Aberrations %K Chromosomes, Human, Pair 8 %K Germ Cells %K Humans %K In Situ Hybridization, Fluorescence %K Karyotyping %K Mosaicism %K Ring Chromosomes %K Translocation, Genetic %X

BACKGROUND: Mosaicism for chromosomal structural abnormalities, other than marker or ring chromosomes, is rarely inherited.

METHODS: We performed cytogenetics studies and breakpoint analyses on a family with transmission of mosaicism for a derivative chromosome 8 (der(8)), resulting from an unbalanced translocation between the long arms of chromosomes 8 and 21 over three generations.

RESULTS: The proband and his maternal half-sister had mosaicism for a der(8) cell line leading to trisomy of the distal 21q, and both had Down syndrome phenotypic features. Mosaicism for a cell line with the der(8) and a normal cell line was also detected in a maternal half-cousin. The der(8) was inherited from the maternal grandmother who had four abnormal cell lines containing the der(8), in addition to a normal cell line. One maternal half-aunt had the der(8) and an isodicentric chromosome 21 (idic(21)). Sequencing studies revealed microhomologies at the junctures of the der(8) and idic(21) in the half-aunt, suggesting a replicative mechanism in the rearrangement formation. Furthermore, interstitial telomeric sequences (ITS) were identified in the juncture between chromosomes 8 and 21 in the der(8).

CONCLUSION: Mosaicism in the proband, his half-sister and half-cousin resulting from loss of chromosome 21 material from the der(8) appears to be a postzygotic event due to the genomic instability of ITS and associated with selective growth advantage of normal cells. The reversion of the inherited der(8) to a normal chromosome 8 in this family resembles revertant mosaicism of point mutations. We propose that ITS could mediate recurring revertant mosaicism for some constitutional chromosomal structural abnormalities.

%B J Med Genet %V 60 %P 547-556 %8 2023 Jun %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/36150828?dopt=Abstract %R 10.1136/jmg-2022-108586 %0 Journal Article %J Am J Hum Genet %D 2023 %T SRSF1 haploinsufficiency is responsible for a syndromic developmental disorder associated with intellectual disability. %A Bogaert, Elke %A Garde, Aurore %A Gautier, Thierry %A Rooney, Kathleen %A Duffourd, Yannis %A LeBlanc, Pontus %A van Reempts, Emma %A Tran Mau-Them, Frederic %A Wentzensen, Ingrid M %A Au, Kit Sing %A Richardson, Kate %A Northrup, Hope %A Gatinois, Vincent %A Geneviève, David %A Louie, Raymond J %A Lyons, Michael J %A Laulund, Lone Walentin %A Brasch-Andersen, Charlotte %A Maxel Juul, Trine %A El It, Fatima %A Marle, Nathalie %A Callier, Patrick %A Relator, Raissa %A Haghshenas, Sadegheh %A McConkey, Haley %A Kerkhof, Jennifer %A Cesario, Claudia %A Novelli, Antonio %A Brunetti-Pierri, Nicola %A Pinelli, Michele %A Pennamen, Perrine %A Naudion, Sophie %A Legendre, Marine %A Courdier, Cécile %A Trimouille, Aurelien %A Fenzy, Martine Doco %A Pais, Lynn %A Yeung, Alison %A Nugent, Kimberly %A Roeder, Elizabeth R %A Mitani, Tadahiro %A Posey, Jennifer E %A Calame, Daniel %A Yonath, Hagith %A Rosenfeld, Jill A %A Musante, Luciana %A Faletra, Flavio %A Montanari, Francesca %A Sartor, Giovanna %A Vancini, Alessandra %A Seri, Marco %A Besmond, Claude %A Poirier, Karine %A Hubert, Laurence %A Hemelsoet, Dimitri %A Munnich, Arnold %A James R Lupski %A Philippe, Christophe %A Thauvin-Robinet, Christel %A Faivre, Laurence %A Sadikovic, Bekim %A Govin, Jérôme %A Dermaut, Bart %A Vitobello, Antonio %K Child %K Developmental Disabilities %K Female %K Haploinsufficiency %K Humans %K Intellectual Disability %K Male %K Mutation, Missense %K Neurodevelopmental Disorders %K Phenotype %X

SRSF1 (also known as ASF/SF2) is a non-small nuclear ribonucleoprotein (non-snRNP) that belongs to the arginine/serine (R/S) domain family. It recognizes and binds to mRNA, regulating both constitutive and alternative splicing. The complete loss of this proto-oncogene in mice is embryonically lethal. Through international data sharing, we identified 17 individuals (10 females and 7 males) with a neurodevelopmental disorder (NDD) with heterozygous germline SRSF1 variants, mostly de novo, including three frameshift variants, three nonsense variants, seven missense variants, and two microdeletions within region 17q22 encompassing SRSF1. Only in one family, the de novo origin could not be established. All individuals featured a recurrent phenotype including developmental delay and intellectual disability (DD/ID), hypotonia, neurobehavioral problems, with variable skeletal (66.7%) and cardiac (46%) anomalies. To investigate the functional consequences of SRSF1 variants, we performed in silico structural modeling, developed an in vivo splicing assay in Drosophila, and carried out episignature analysis in blood-derived DNA from affected individuals. We found that all loss-of-function and 5 out of 7 missense variants were pathogenic, leading to a loss of SRSF1 splicing activity in Drosophila, correlating with a detectable and specific DNA methylation episignature. In addition, our orthogonal in silico, in vivo, and epigenetics analyses enabled the separation of clearly pathogenic missense variants from those with uncertain significance. Overall, these results indicated that haploinsufficiency of SRSF1 is responsible for a syndromic NDD with ID due to a partial loss of SRSF1-mediated splicing activity.

%B Am J Hum Genet %V 110 %P 790-808 %8 2023 May 04 %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/37071997?dopt=Abstract %R 10.1016/j.ajhg.2023.03.016 %0 Journal Article %J Am J Hum Genet %D 2022 %T Bi-allelic CAMSAP1 variants cause a clinically recognizable neuronal migration disorder. %A Khalaf-Nazzal, Reham %A Fasham, James %A Inskeep, Katherine A %A Blizzard, Lauren E %A Leslie, Joseph S %A Wakeling, Matthew N %A Ubeyratna, Nishanka %A Mitani, Tadahiro %A Griffith, Jennifer L %A Baker, Wisam %A Al-Hijawi, Fida' %A Keough, Karen C %A Gezdirici, Alper %A Pena, Loren %A Spaeth, Christine G %A Turnpenny, Peter D %A Walsh, Joseph R %A Ray, Randall %A Neilson, Amber %A Kouranova, Evguenia %A Cui, Xiaoxia %A Curiel, David T %A Pehlivan, Davut %A Akdemir, Zeynep Coban %A Posey, Jennifer E %A James R Lupski %A Dobyns, William B %A Stottmann, Rolf W %A Crosby, Andrew H %A Baple, Emma L %K Alleles %K Animals %K Classical Lissencephalies and Subcortical Band Heterotopias %K Humans %K Lissencephaly %K Mice %K Mice, Knockout %K Microtubule-Associated Proteins %K Nervous System Malformations %K Phenotype %K Tubulin %X

Non-centrosomal microtubules are essential cytoskeletal filaments that are important for neurite formation, axonal transport, and neuronal migration. They require stabilization by microtubule minus-end-targeting proteins including the CAMSAP family of molecules. Using exome sequencing on samples from five unrelated families, we show that bi-allelic CAMSAP1 loss-of-function variants cause a clinically recognizable, syndromic neuronal migration disorder. The cardinal clinical features of the syndrome include a characteristic craniofacial appearance, primary microcephaly, severe neurodevelopmental delay, cortical visual impairment, and seizures. The neuroradiological phenotype comprises a highly recognizable combination of classic lissencephaly with a posterior more severe than anterior gradient similar to PAFAH1B1(LIS1)-related lissencephaly and severe hypoplasia or absence of the corpus callosum; dysplasia of the basal ganglia, hippocampus, and midbrain; and cerebellar hypodysplasia, similar to the tubulinopathies, a group of monogenic tubulin-associated disorders of cortical dysgenesis. Neural cell rosette lineages derived from affected individuals displayed findings consistent with these phenotypes, including abnormal morphology, decreased cell proliferation, and neuronal differentiation. Camsap1-null mice displayed increased perinatal mortality, and RNAScope studies identified high expression levels in the brain throughout neurogenesis and in facial structures, consistent with the mouse and human neurodevelopmental and craniofacial phenotypes. Together our findings confirm a fundamental role of CAMSAP1 in neuronal migration and brain development and define bi-allelic variants as a cause of a clinically distinct neurodevelopmental disorder in humans and mice.

%B Am J Hum Genet %V 109 %P 2068-2079 %8 2022 Nov 03 %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/36283405?dopt=Abstract %R 10.1016/j.ajhg.2022.09.012 %0 Journal Article %J Brain %D 2022 %T Biallelic variants in SLC38A3 encoding a glutamine transporter cause epileptic encephalopathy. %A Marafi, Dana %A Fatih, Jawid M %A Kaiyrzhanov, Rauan %A Ferla, Matteo P %A Gijavanekar, Charul %A Al-Maraghi, Aljazi %A Liu, Ning %A Sites, Emily %A Alsaif, Hessa S %A Al-Owain, Mohammad %A Zakkariah, Mohamed %A El-Anany, Ehab %A Guliyeva, Ulviyya %A Guliyeva, Sughra %A Gaba, Colette %A Haseeb, Ateeq %A Alhashem, Amal M %A Danish, Enam %A Karageorgou, Vasiliki %A Beetz, Christian %A Subhi, Alaa A %A Mullegama, Sureni V %A Torti, Erin %A Sebastin, Monisha %A Breilyn, Margo Sheck %A Duberstein, Susan %A Abdel-Hamid, Mohamed S %A Mitani, Tadahiro %A Du, Haowei %A Rosenfeld, Jill A %A Jhangiani, Shalini N %A Coban Akdemir, Zeynep %A Richard A Gibbs %A Taylor, Jenny C %A Fakhro, Khalid A %A Hunter, Jill V %A Pehlivan, Davut %A Zaki, Maha S %A Gleeson, Joseph G %A Maroofian, Reza %A Houlden, Henry %A Posey, Jennifer E %A Sutton, V Reid %A Alkuraya, Fowzan S %A Sarah H Elsea %A James R Lupski %K Epilepsy, Generalized %K Glutamine %K Histidine %K Humans %K Metabolome %K Nitrogen %K Sodium-Calcium Exchanger %X

The solute carrier (SLC) superfamily encompasses >400 transmembrane transporters involved in the exchange of amino acids, nutrients, ions, metals, neurotransmitters and metabolites across biological membranes. SLCs are highly expressed in the mammalian brain; defects in nearly 100 unique SLC-encoding genes (OMIM: https://www.omim.org) are associated with rare Mendelian disorders including developmental and epileptic encephalopathy and severe neurodevelopmental disorders. Exome sequencing and family-based rare variant analyses on a cohort with neurodevelopmental disorders identified two siblings with developmental and epileptic encephalopathy and a shared deleterious homozygous splicing variant in SLC38A3. The gene encodes SNAT3, a sodium-coupled neutral amino acid transporter and a principal transporter of the amino acids asparagine, histidine, and glutamine, the latter being the precursor for the neurotransmitters GABA and glutamate. Additional subjects with a similar developmental and epileptic encephalopathy phenotype and biallelic predicted-damaging SLC38A3 variants were ascertained through GeneMatcher and collaborations with research and clinical molecular diagnostic laboratories. Untargeted metabolomic analysis was performed to identify novel metabolic biomarkers. Ten individuals from seven unrelated families from six different countries with deleterious biallelic variants in SLC38A3 were identified. Global developmental delay, intellectual disability, hypotonia, and absent speech were common features while microcephaly, epilepsy, and visual impairment were present in the majority. Epilepsy was drug-resistant in half. Metabolomic analysis revealed perturbations of glutamate, histidine, and nitrogen metabolism in plasma, urine, and CSF of selected subjects, potentially representing biomarkers of disease. Our data support the contention that SLC38A3 is a novel disease gene for developmental and epileptic encephalopathy and illuminate the likely pathophysiology of the disease as perturbations in glutamine homeostasis.

%B Brain %V 145 %P 909-924 %8 2022 Apr 29 %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/34605855?dopt=Abstract %R 10.1093/brain/awab369 %0 Journal Article %J Ann Neurol %D 2022 %T Biallelic Variants in the Ectonucleotidase ENTPD1 Cause a Complex Neurodevelopmental Disorder with Intellectual Disability, Distinct White Matter Abnormalities, and Spastic Paraplegia. %A Calame, Daniel G %A Herman, Isabella %A Maroofian, Reza %A Marshall, Aren E %A Donis, Karina Carvalho %A Fatih, Jawid M %A Mitani, Tadahiro %A Du, Haowei %A Grochowski, Christopher M %A Sousa, Sergio B %A Gijavanekar, Charul %A Bakhtiari, Somayeh %A Ito, Yoko A %A Rocca, Clarissa %A Hunter, Jill V %A Sutton, V Reid %A Emrick, Lisa T %A Boycott, Kym M %A Lossos, Alexander %A Fellig, Yakov %A Prus, Eugenia %A Kalish, Yosef %A Meiner, Vardiella %A Suerink, Manon %A Ruivenkamp, Claudia %A Muirhead, Kayla %A Saadi, Nebal W %A Zaki, Maha S %A Bouman, Arjan %A Barakat, Tahsin Stefan %A Skidmore, David L %A Osmond, Matthew %A Silva, Thiago Oliveira %A Murphy, David %A Karimiani, Ehsan Ghayoor %A Jamshidi, Yalda %A Jaddoa, Asaad Ghanim %A Tajsharghi, Homa %A Jin, Sheng Chih %A Abbaszadegan, Mohammad Reza %A Ebrahimzadeh-Vesal, Reza %A Hosseini, Susan %A Alavi, Shahryar %A Bahreini, Amir %A Zarean, Elahe %A Salehi, Mohammad Mehdi %A Al-Sannaa, Nouriya Abbas %A Zifarelli, Giovanni %A Bauer, Peter %A Robson, Simon C %A Coban-Akdemir, Zeynep %A Travaglini, Lorena %A Nicita, Francesco %A Jhangiani, Shalini N %A Richard A Gibbs %A Posey, Jennifer E %A Kruer, Michael C %A Kernohan, Kristin D %A Morales Saute, Jonas A %A Houlden, Henry %A Vanderver, Adeline %A Sarah H Elsea %A Pehlivan, Davut %A Marafi, Dana %A James R Lupski %K Apyrase %K Dysarthria %K Humans %K Intellectual Disability %K Mutation %K Paraplegia %K Pedigree %K Phenotype %K Spastic Paraplegia, Hereditary %K White Matter %X

OBJECTIVE: Human genomics established that pathogenic variation in diverse genes can underlie a single disorder. For example, hereditary spastic paraplegia is associated with >80 genes, with frequently only few affected individuals described for each gene. Herein, we characterize a large cohort of individuals with biallelic variation in ENTPD1, a gene previously linked to spastic paraplegia 64 (Mendelian Inheritance in Man # 615683).

METHODS: Individuals with biallelic ENTPD1 variants were recruited worldwide. Deep phenotyping and molecular characterization were performed.

RESULTS: A total of 27 individuals from 17 unrelated families were studied; additional phenotypic information was collected from published cases. Twelve novel pathogenic ENTPD1 variants are described (NM 001776.6): c.398_399delinsAA; p.(Gly133Glu), c.540del; p.(Thr181Leufs*18), c.640del; p.(Gly216Glufs*75), c.185 T > G; p.(Leu62*), c.1531 T > C; p.(*511Glnext*100), c.967C > T; p.(Gln323*), c.414-2_414-1del, and c.146 A > G; p.(Tyr49Cys) including 4 recurrent variants c.1109 T > A; p.(Leu370*), c.574-6_574-3del, c.770_771del; p.(Gly257Glufs*18), and c.1041del; p.(Ile348Phefs*19). Shared disease traits include childhood onset, progressive spastic paraplegia, intellectual disability (ID), dysarthria, and white matter abnormalities. In vitro assays demonstrate that ENTPD1 expression and function are impaired and that c.574-6_574-3del causes exon skipping. Global metabolomics demonstrate ENTPD1 deficiency leads to impaired nucleotide, lipid, and energy metabolism.

INTERPRETATION: The ENTPD1 locus trait consists of childhood disease onset, ID, progressive spastic paraparesis, dysarthria, dysmorphisms, and white matter abnormalities, with some individuals showing neurocognitive regression. Investigation of an allelic series of ENTPD1 (1) expands previously described features of ENTPD1-related neurological disease, (2) highlights the importance of genotype-driven deep phenotyping, (3) documents the need for global collaborative efforts to characterize rare autosomal recessive disease traits, and (4) provides insights into disease trait neurobiology. ANN NEUROL 2022;92:304-321.

%B Ann Neurol %V 92 %P 304-321 %8 2022 Aug %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/35471564?dopt=Abstract %R 10.1002/ana.26381 %0 Journal Article %J Genet Med %D 2022 %T Centers for Mendelian Genomics: A decade of facilitating gene discovery. %A Baxter, Samantha M %A Posey, Jennifer E %A Lake, Nicole J %A Sobreira, Nara %A Chong, Jessica X %A Buyske, Steven %A Blue, Elizabeth E %A Chadwick, Lisa H %A Coban-Akdemir, Zeynep H %A Doheny, Kimberly F %A Davis, Colleen P %A Lek, Monkol %A Wellington, Christopher %A Jhangiani, Shalini N %A Gerstein, Mark %A Richard A Gibbs %A Lifton, Richard P %A MacArthur, Daniel G %A Matise, Tara C %A James R Lupski %A Valle, David %A Bamshad, Michael J %A Hamosh, Ada %A Mane, Shrikant %A Nickerson, Deborah A %A Rehm, Heidi L %A O'Donnell-Luria, Anne %K Exome %K Exome Sequencing %K Genetic Association Studies %K Genomics %K Humans %K Phenotype %X

PURPOSE: Mendelian disease genomic research has undergone a massive transformation over the past decade. With increasing availability of exome and genome sequencing, the role of Mendelian research has expanded beyond data collection, sequencing, and analysis to worldwide data sharing and collaboration.

METHODS: Over the past 10 years, the National Institutes of Health-supported Centers for Mendelian Genomics (CMGs) have played a major role in this research and clinical evolution.

RESULTS: We highlight the cumulative gene discoveries facilitated by the program, biomedical research leveraged by the approach, and the larger impact on the research community. Beyond generating a list of gene-phenotype relationships and participating in widespread data sharing, the CMGs have created resources, tools, and training for the larger community to foster understanding of genes and genome variation. The CMGs have participated in a wide range of data sharing activities, including deposition of all eligible CMG data into the Analysis, Visualization, and Informatics Lab-space (AnVIL), sharing candidate genes through the Matchmaker Exchange and the CMG website, and sharing variants in Genotypes to Mendelian Phenotypes (Geno2MP) and VariantMatcher.

CONCLUSION: The work is far from complete; strengthening communication between research and clinical realms, continued development and sharing of knowledge and tools, and improving access to richly characterized data sets are all required to diagnose the remaining molecularly undiagnosed patients.

%B Genet Med %V 24 %P 784-797 %8 2022 Apr %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/35148959?dopt=Abstract %R 10.1016/j.gim.2021.12.005 %0 Journal Article %J HGG Adv %D 2022 %T CRISPR/Cas9-induced gene conversion between paralogs. %A Yanovsky-Dagan, Shira %A Frumkin, Ayala %A James R Lupski %A Harel, Tamar %X

Paralogs and pseudogenes are abundant within the human genome, and can mediate non-allelic homologous recombination (NAHR) or gene conversion events. The locus contains three paralogs situated in tandem, and is therefore prone to NAHR-mediated deletions and duplications associated with severe neurological phenotypes. To study this locus further, we aimed to generate biallelic loss-of-function variants in by CRISPR/Cas9 genome editing. Unexpectedly, two of the generated clones underwent gene conversion, as evidenced by replacement of the targeted sequence of by a donor sequence from its paralog We highlight the complexity of CRISPR/Cas9 design, end-product formation, and recombination repair mechanisms for CRISPR/Cas9 delivery as a nucleic acid molecular therapy when targeting genes that have paralogs or pseudogenes, and advocate meticulous evaluation of resultant clones in model organisms. In addition, we suggest that endogenous gene conversion may be used to repair missense variants in genes with paralogs or pseudogenes.

%B HGG Adv %V 3 %P 100092 %8 2022 Apr 14 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/35199044?dopt=Abstract %R 10.1016/j.xhgg.2022.100092 %0 Journal Article %J Am J Med Genet A %D 2022 %T De novo heterozygous variants in SLC30A7 are a candidate cause for Joubert syndrome. %A Penon-Portmann, Monica %A Eldomery, Mohammad K %A Potocki, Lorraine %A Marafi, Dana %A Posey, Jennifer E %A Coban-Akdemir, Zeynep %A Harel, Tamar %A Grochowski, Christopher M %A Loucks, Hailey %A Devine, Walter Patrick %A Van Ziffle, Jessica %A Doherty, Dan %A James R Lupski %A Shieh, Joseph T %K Abnormalities, Multiple %K Ataxia %K Cation Transport Proteins %K Cerebellum %K Eye Abnormalities %K Female %K Hedgehog Proteins %K Humans %K Kidney Diseases, Cystic %K Megalencephaly %K Polydactyly %K Proteomics %K Retina %K Zinc %X

Joubert syndrome (JS), a well-established ciliopathy, is characterized by the distinctive molar tooth sign on brain MRI, ataxia, and neurodevelopmental features. Other manifestations can include polydactyly, accessory frenula, renal, or liver disease. Here, we report individuals meeting criteria for JS with de novo heterozygous variants in SLC30A7 (Chr1p21.2). The first individual is a female with history of unilateral postaxial polydactyly, classic molar tooth sign on MRI, macrocephaly, ataxia, ocular motor apraxia, neurodevelopmental delay, and precocious puberty. Exome sequencing detected a de novo heterozygous missense variant in SLC30A7: NM_133496.5: c.407 T > C, (p.Val136Ala). The second individual had bilateral postaxial polydactyly, molar tooth sign, macrocephaly, developmental delay, and an extra oral frenulum. A de novo deletion-insertion variant in SLC30A7, c.490_491delinsAG (p.His164Ser) was found. Both de novo variants affect highly conserved residues. Variants were not identified in known Joubert genes for either case. SLC30A7 has not yet been associated with a human phenotype. The SLC30 family of zinc transporters, like SLC30A7, permit cellular efflux of zinc, and although it is expressed in the brain its functions remain unknown. Published data from proteomic studies support SLC30A7 interaction with TCTN3, another protein associated with JS. The potential involvement of such genes in primary cilia suggest a role in Sonic Hedgehog signaling. SLC30A7 is a candidate JS-associated gene. Future work could be directed toward further characterization of SLC30A7 variants and understanding its function.

%B Am J Med Genet A %V 188 %P 2360-2366 %8 2022 Aug %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/35751429?dopt=Abstract %R 10.1002/ajmg.a.62872 %0 Journal Article %J Hum Mol Genet %D 2022 %T De novo variants in EMC1 lead to neurodevelopmental delay and cerebellar degeneration and affect glial function in Drosophila. %A Chung, Hyung-Lok %A Rump, Patrick %A Lu, Di %A Glassford, Megan R %A Mok, Jung-Wan %A Fatih, Jawid %A Basal, Adily %A Marcogliese, Paul C %A Kanca, Oguz %A Rapp, Michele %A Fock, Johanna M %A Kamsteeg, Erik-Jan %A James R Lupski %A Larson, Austin %A Haninbal, Mark C %A Bellen, Hugo %A Harel, Tamar %K Animals %K Basic Helix-Loop-Helix Transcription Factors %K Cerebellar Diseases %K Drosophila %K Drosophila Proteins %K Intellectual Disability %K Membrane Proteins %K Nervous System Malformations %K Neurodegenerative Diseases %K Neurodevelopmental Disorders %K Neuroglia %K Repressor Proteins %X

BACKGROUND: The endoplasmic reticulum (ER)-membrane protein complex (EMC) is a multi-protein transmembrane complex composed of 10 subunits that functions as a membrane-protein chaperone. Variants in EMC1 lead to neurodevelopmental delay and cerebellar degeneration. Multiple families with biallelic variants have been published, yet to date, only a single report of a monoallelic variant has been described, and functional evidence is sparse.

METHODS: Exome sequencing was used to investigate the genetic cause underlying severe developmental delay in three unrelated children. EMC1 variants were modeled in Drosophila, using loss-of-function (LoF) and overexpression studies. Glial-specific and neuronal-specific assays were used to determine whether the dysfunction was specific to one cell type.

RESULTS: Exome sequencing identified de novo variants in EMC1 in three individuals affected by global developmental delay, hypotonia, seizures, visual impairment and cerebellar atrophy. All variants were located at Pro582 or Pro584. Drosophila studies indicated that imbalance of EMC1-either overexpression or knockdown-results in pupal lethality and suggest that the tested homologous variants are LoF alleles. In addition, glia-specific gene dosage, overexpression or knockdown, of EMC1 led to lethality, whereas neuron-specific alterations were tolerated.

DISCUSSION: We establish de novo monoallelic EMC1 variants as causative of a neurological disease trait by providing functional evidence in a Drosophila model. The identified variants failed to rescue the lethality of a null allele. Variations in dosage of the wild-type EMC1, specifically in glia, lead to pupal lethality, which we hypothesize results from the altered stoichiometry of the multi-subunit protein complex EMC.

%B Hum Mol Genet %V 31 %P 3231-3244 %8 2022 Sep 29 %G eng %N 19 %1 https://www.ncbi.nlm.nih.gov/pubmed/35234901?dopt=Abstract %R 10.1093/hmg/ddac053 %0 Journal Article %J HGG Adv %D 2022 %T Developmental genomics of limb malformations: Allelic series in association with gene dosage effects contribute to the clinical variability. %A Duan, Ruizhi %A Hijazi, Hadia %A Gulec, Elif Yilmaz %A Eker, Hatice Koçak %A Costa, Silvia R %A Sahin, Yavuz %A Ocak, Zeynep %A Isikay, Sedat %A Ozalp, Ozge %A Bozdogan, Sevcan %A Aslan, Huseyin %A Elcioglu, Nursel %A Bertola, Debora R %A Gezdirici, Alper %A Du, Haowei %A Fatih, Jawid M %A Grochowski, Christopher M %A Akay, Gulsen %A Jhangiani, Shalini N %A Karaca, Ender %A Gu, Shen %A Coban-Akdemir, Zeynep %A Posey, Jennifer E %A Bayram, Yavuz %A Sutton, V Reid %A Carvalho, Claudia M B %A Pehlivan, Davut %A Richard A Gibbs %A James R Lupski %X

Genetic heterogeneity, reduced penetrance, and variable expressivity, the latter including asymmetric body axis plane presentations, have all been described in families with congenital limb malformations (CLMs). Interfamilial and intrafamilial heterogeneity highlight the complexity of the underlying genetic pathogenesis of these developmental anomalies. Family-based genomics by exome sequencing (ES) and rare variant analyses combined with whole-genome array-based comparative genomic hybridization were implemented to investigate 18 families with limb birth defects. Eleven of 18 (61%) families revealed explanatory variants, including 7 single-nucleotide variant alleles and 3 copy number variants (CNVs), at previously reported "disease trait associated loci": , cluster, , , and . Breakpoint junction analyses for all three CNV alleles revealed mutational signatures consistent with microhomology-mediated break-induced replication, a mechanism facilitated by -mediated rearrangement. Homozygous duplication of was observed in one Turkish kindred and represents a novel contributory genetic mechanism to Gollop-Wolfgang Complex (MIM: 228250), where triplication of the locus has been reported in one family from Japan (i.e., 4n = 2n + 2n versus 4n = 3n + 1n allelic configurations). Genes acting on limb patterning are sensitive to a gene dosage effect and are often associated with an allelic series. We extend an allele-specific gene dosage model to potentially assist, in an adjuvant way, interpretations of interconnections among an allelic series, clinical severity, and reduced penetrance of the -related CLM spectrum.

%B HGG Adv %V 3 %P 100132 %8 2022 Oct 13 %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/36035248?dopt=Abstract %R 10.1016/j.xhgg.2022.100132 %0 Journal Article %J JCI Insight %D 2022 %T An ELF4 hypomorphic variant results in NK cell deficiency. %A Salinas, Sandra Andrea %A Mace, Emily M %A Conte, Matilde I %A Park, Chun Shik %A Li, Yu %A Rosario-Sepulveda, Joshua I %A Mahapatra, Sanjana %A Moore, Emily K %A Hernandez, Evelyn R %A Chinn, Ivan K %A Reed, Abigail E %A Lee, Barclay J %A Frumovitz, Alexander %A Richard A Gibbs %A Posey, Jennifer E %A Forbes Satter, Lisa R %A Thatayatikom, Akaluck %A Allenspach, Eric J %A Wensel, Theodore G %A James R Lupski %A Lacorazza, H Daniel %A Orange, Jordan S %K Animals %K DNA-Binding Proteins %K Humans %K Killer Cells, Natural %K Mice %K Transcription Factors %X

NK cell deficiencies (NKD) are a type of primary immune deficiency in which the major immunologic abnormality affects NK cell number, maturity, or function. Since NK cells contribute to immune defense against virally infected cells, patients with NKD experience higher susceptibility to chronic, recurrent, and fatal viral infections. An individual with recurrent viral infections and mild hypogammaglobulinemia was identified to have an X-linked damaging variant in the transcription factor gene ELF4. The variant does not decrease expression but disrupts ELF4 protein interactions and DNA binding, reducing transcriptional activation of target genes and selectively impairing ELF4 function. Corroborating previous murine models of ELF4 deficiency (Elf4-/-) and using a knockdown human NK cell line, we determined that ELF4 is necessary for normal NK cell development, terminal maturation, and function. Through characterization of the NK cells of the proband, expression of the proband's variant in Elf4-/- mouse hematopoietic precursor cells, and a human in vitro NK cell maturation model, we established this ELF4 variant as a potentially novel cause of NKD.

%B JCI Insight %V 7 %8 2022 Dec 08 %G eng %N 23 %1 https://www.ncbi.nlm.nih.gov/pubmed/36477361?dopt=Abstract %R 10.1172/jci.insight.155481 %0 Journal Article %J Clin Genet %D 2022 %T El-Hattab-Alkuraya syndrome caused by biallelic WDR45B pathogenic variants: Further delineation of the phenotype and genotype. %A Almannai, Mohammed %A Marafi, Dana %A Abdel-Salam, Ghada M H %A Zaki, Maha S %A Duan, Ruizhi %A Calame, Daniel %A Herman, Isabella %A Levesque, Felix %A Elbendary, Hasnaa M %A Hegazy, Ibrahim %A Chung, Wendy K %A Kavus, Haluk %A Saeidi, Kolsoum %A Maroofian, Reza %A AlHashim, Aqeela %A Al-Otaibi, Ali %A Al Madhi, Asma %A Abou Al-Seood, Hager M %A Alasmari, Ali %A Houlden, Henry %A Gleeson, Joseph G %A Hunter, Jill V %A Posey, Jennifer E %A James R Lupski %A El-Hattab, Ayman W %K Atrophy %K Bone Diseases, Metabolic %K Congenital Disorders of Glycosylation %K Homozygote %K Humans %K Microcephaly %K Nervous System Malformations %K Pedigree %K Phenotype %K Quadriplegia %K Seizures %X

Homozygous pathogenic variants in WDR45B were first identified in six subjects from three unrelated families with global development delay, refractory seizures, spastic quadriplegia, and brain malformations. Since the initial report in 2018, no further cases have been described. In this report, we present 12 additional individuals from seven unrelated families and their clinical, radiological, and molecular findings. Six different variants in WDR45B were identified, five of which are novel. Microcephaly and global developmental delay were observed in all subjects, and seizures and spastic quadriplegia in most. Common findings on brain imaging include cerebral atrophy, ex vacuo ventricular dilatation, brainstem volume loss, and symmetric under-opercularization. El-Hattab-Alkuraya syndrome is associated with a consistent phenotype characterized by early onset cerebral atrophy resulting in microcephaly, developmental delay, spastic quadriplegia, and seizures. The phenotype appears to be more severe among individuals with loss-of-function variants whereas those with missense variants were less severely affected suggesting a potential genotype-phenotype correlation in this disorder. A brain imaging pattern emerges which is consistent among individuals with loss-of-function variants and could potentially alert the neuroradiologists or clinician to consider WDR45B-related El-Hattab-Alkuraya syndrome.

%B Clin Genet %V 101 %P 530-540 %8 2022 May %G eng %N 5-6 %1 https://www.ncbi.nlm.nih.gov/pubmed/35322404?dopt=Abstract %R 10.1111/cge.14132 %0 Journal Article %J Genet Med %D 2022 %T Elucidating the clinical spectrum and molecular basis of HYAL2 deficiency. %A Fasham, James %A Lin, Siying %A Ghosh, Promita %A Radio, Francesca Clementina %A Farrow, Emily G %A Thiffault, Isabelle %A Kussman, Jennifer %A Zhou, Dihong %A Hemming, Rick %A Zahka, Kenneth %A Chioza, Barry A %A Rawlins, Lettie E %A Wenger, Olivia K %A Gunning, Adam C %A Pizzi, Simone %A Onesimo, Roberta %A Zampino, Giuseppe %A Barker, Emily %A Osawa, Natasha %A Rodriguez, Megan Christine %A Neuhann, Teresa M %A Zackai, Elaine H %A Keena, Beth %A Capasso, Jenina %A Levin, Alex V %A Bhoj, Elizabeth %A Li, Dong %A Hakonarson, Hakon %A Wentzensen, Ingrid M %A Jackson, Adam %A Chandler, Kate E %A Coban-Akdemir, Zeynep H %A Posey, Jennifer E %A Banka, Siddharth %A James R Lupski %A Sheppard, Sarah E %A Tartaglia, Marco %A Triggs-Raine, Barbara %A Crosby, Andrew H %A Baple, Emma L %K Alleles %K Animals %K Cell Adhesion Molecules %K Cleft Lip %K Cleft Palate %K Genetic Association Studies %K GPI-Linked Proteins %K Humans %K Hyaluronoglucosaminidase %K Mice %K Phenotype %X

PURPOSE: We previously defined biallelic HYAL2 variants causing a novel disorder in 2 families, involving orofacial clefting, facial dysmorphism, congenital heart disease, and ocular abnormalities, with Hyal2 knockout mice displaying similar phenotypes. In this study, we better define the phenotype and pathologic disease mechanism.

METHODS: Clinical and genomic investigations were undertaken alongside molecular studies, including immunoblotting and immunofluorescence analyses of variant/wild-type human HYAL2 expressed in mouse fibroblasts, and in silico modeling of putative pathogenic variants.

RESULTS: Ten newly identified individuals with this condition were investigated, and they were associated with 9 novel pathogenic variants. Clinical studies defined genotype-phenotype correlations and confirmed a recognizable craniofacial phenotype in addition to myopia, cleft lip/palate, and congenital cardiac anomalies as the most consistent manifestations of the condition. In silico modeling of missense variants identified likely deleterious effects on protein folding. Consistent with this, functional studies indicated that these variants cause protein instability and a concomitant cell surface absence of HYAL2 protein.

CONCLUSION: These studies confirm an association between HYAL2 alterations and syndromic cleft lip/palate, provide experimental evidence for the pathogenicity of missense alleles, enable further insights into the pathomolecular basis of the disease, and delineate the core and variable clinical outcomes of the condition.

%B Genet Med %V 24 %P 631-644 %8 2022 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/34906488?dopt=Abstract %R 10.1016/j.gim.2021.10.014 %0 Journal Article %J NPJ Genom Med %D 2022 %T Expanding the mutation and phenotype spectrum of MYH3-associated skeletal disorders. %A Zhao, Sen %A Zhang, Yuanqiang %A Hallgrimsdottir, Sigrun %A Zuo, Yuzhi %A Li, Xiaoxin %A Batkovskyte, Dominyka %A Liu, Sen %A Lindelöf, Hillevi %A Wang, Shengru %A Hammarsjö, Anna %A Yang, Yang %A Ye, Yongyu %A Wang, Lianlei %A Yan, Zihui %A Lin, Jiachen %A Yu, Chenxi %A Chen, Zefu %A Niu, Yuchen %A Wang, Huizi %A Zhao, Zhi %A Liu, Pengfei %A Qiu, Guixing %A Posey, Jennifer E %A Wu, Zhihong %A James R Lupski %A Micule, Ieva %A Anderlid, Britt-Marie %A Voss, Ulrika %A Sulander, Dennis %A Kuchinskaya, Ekaterina %A Nordgren, Ann %A Nilsson, Ola %A Zhang, Terry Jianguo %A Grigelioniene, Giedre %A Wu, Nan %X

Pathogenic variants in MYH3 cause distal arthrogryposis type 2A and type 2B3 as well as contractures, pterygia and spondylocarpotarsal fusion syndromes types 1A and 1B. These disorders are ultra-rare and their natural course and phenotypic variability are not well described. In this study, we summarize the clinical features and genetic findings of 17 patients from 10 unrelated families with vertebral malformations caused by dominant or recessive pathogenic variants in MYH3. Twelve novel pathogenic variants in MYH3 (NM_002470.4) were identified: three of them were de novo or inherited in autosomal dominant way and nine were inherited in autosomal recessive way. The patients had vertebral segmentation anomalies accompanied with variable joint contractures, short stature and dysmorphic facial features. There was a significant phenotypic overlap between dominant and recessive MYH3-associated conditions regarding the degree of short stature as well as the number of vertebral fusions. All monoallelic variants caused significantly decreased SMAD3 phosphorylation, which is consistent with the previously proposed pathogenic mechanism of impaired canonical TGF-β signaling. Most of the biallelic variants were predicted to be protein-truncating, while one missense variant c.4244T>G,p.(Leu1415Arg), which was inherited in an autosomal recessive way, was found to alter the phosphorylation level of p38, suggesting an inhibition of the non-canonical pathway of TGF-β signaling. In conclusion, the identification of 12 novel pathogenic variants and overlapping phenotypes in 17 affected individuals from 10 unrelated families expands the mutation and phenotype spectrum of MYH3-associated skeletal disorders. We show that disturbances of canonical or non-canonical TGF-β signaling pathways are involved in pathogenesis of MYH3-associated skeletal fusion (MASF) syndrome.

%B NPJ Genom Med %V 7 %P 11 %8 2022 Feb 15 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/35169139?dopt=Abstract %R 10.1038/s41525-021-00273-x %0 Journal Article %J Am J Med Genet A %D 2022 %T Expanding the phenotypic and allelic spectrum of SMG8: Clinical observations reveal overlap with SMG9-associated disease trait. %A Abdel-Salam, Ghada M H %A Duan, Ruizhi %A Abdel-Hamid, Mohamed S %A Sayed, Inas S M %A Jhangiani, Shalini N %A Ziad Khan %A Du, Haowei %A Richard A Gibbs %A Posey, Jennifer E %A Marafi, Dana %A James R Lupski %K Alleles %K Homozygote %K Humans %K Intracellular Signaling Peptides and Proteins %K Nonsense Mediated mRNA Decay %K Phenotype %K Phosphorylation %X

SMG8 (MIM *617315) is a regulatory subunit involved in nonsense-mediated mRNA decay (NMD), a cellular protective pathway that regulates mRNA transcription, transcript stability, and degrades transcripts containing premature stop codons. SMG8 binds SMG9 and SMG1 to form the SMG1C complex and inhibit the kinase activity of SMG1. Biallelic deleterious variants in SMG9 are known to cause a heart and brain malformation syndrome (HBMS; MIM #616920), whereas biallelic deleterious variants in SMG8 were recently described to cause a novel neurodevelopmental disorder (NDD) with dysmorphic facies and cataracts, now defined as Alzahrani-Kuwahara syndrome (ALKUS: MIM #619268). Only eight subjects from four families with ALKUS have been described to date. Through research reanalysis of a nondiagnostic clinical exome, we identified a subject from a fifth unrelated family with a homozygous deleterious variant in SMG8 and features consistent with ALKUS. Interestingly, the subject also had unilateral microphthalmia, a clinical feature that has been described in SMG9-related disorder. Our study expands the phenotypic spectrum of SMG8-related disorder, demonstrates an overlapping phenotype between SMG8- and SMG9-related rare disease traits, provides further evidence for the SMG8 and SMG9 protein interactions, and highlights the importance of revisiting nondiagnostic exome data to identify and affirm emerging novel genes for rare disease traits.

%B Am J Med Genet A %V 188 %P 648-657 %8 2022 Feb %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/34761517?dopt=Abstract %R 10.1002/ajmg.a.62561 %0 Journal Article %J Genet Med %D 2022 %T Functional characteristics of a broad spectrum of TBX6 variants in Mayer-Rokitansky-Küster-Hauser syndrome. %A Ma, Congcong %A Chen, Na %A Jolly, Angad %A Zhao, Sen %A Coban-Akdemir, Zeynep %A Tian, Weijie %A Kang, Jia %A Ye, Yang %A Wang, Yuan %A Koch, André %A Zhang, Yuanqiang %A Qin, Chenglu %A Bonilla, Ximena %A Borel, Christelle %A Rall, Katharina %A Chen, Zefu %A Jhangiani, Shalini %A Niu, Yuchen %A Li, Xiaoxin %A Qiu, Guixing %A Zhang, Shuyang %A Luo, Guangnan %A Wu, Zhihong %A Bacopoulou, Flora %A Deligeoroglou, Efthymios %A Zhang, Terry Jianguo %A Rosenberg, Carla %A Richard A Gibbs %A Dietrich, Jennifer E %A Dimas, Antigone S %A Liu, Pengfei %A Antonarakis, Stylianos E %A Brucker, Sara Y %A Posey, Jennifer E %A James R Lupski %A Wu, Nan %A Zhu, Lan %K 46, XX Disorders of Sex Development %K Congenital Abnormalities %K Female %K Humans %K Mullerian Ducts %K RNA, Messenger %K T-Box Domain Proteins %K Vagina %X

PURPOSE: Mayer-Rokitansky-Küster-Hauser syndrome (MRKHS) is characterized by congenital absence of the uterus, cervix, and the upper part of the vagina in females. Whole-gene deletion and loss-of-function variants in TBX6 have been identified in association with MRKHS. We aimed to expand the spectrum of TBX6 variants in MRKHS and explore the biological effect of the variant alleles.

METHODS: Rare variants in TBX6 were called from a combined multiethnic cohort of 622 probands with MRKHS who underwent exome sequencing or genome sequencing. Multiple in vitro functional experiments were performed, including messenger RNA analysis, western blotting, transcriptional activity assay, and immunofluorescence staining.

RESULTS: We identified 16 rare variants in TBX6 from the combined cohort, including 1 protein-truncating variant reported in our previous study and 15 variants with unknown effects. By comparing the prevalence of TBX6 variants in the Chinese MRKHS cohort vs 1038 female controls, we observed a significant mutational burden of TBX6 in affected individuals (P = .0004, odds ratio = 5.25), suggesting a causal role of TBX6 variants in MRKHS. Of the 15 variants with uncertain effects, 7 were shown to induce a loss-of-function effect through various mechanisms. The c.423G>A (p.Leu141=) and c.839+5G>A variants impaired the normal splicing of TBX6 messenger RNA, c.422T>C (p.Leu141Pro) and c.745G>A (p.Val249Met) led to decreased protein expression, c.10C>T (p.Pro4Ser) and c.400G>A (p.Glu134Lys) resulted in perturbed transcriptional activity, and c.356G>A (p.Arg119His) caused protein mislocalization. We observed incomplete penetrance and variable expressivity in families carrying deleterious variants, which indicates a more complex genetic mechanism than classical Mendelian inheritance.

CONCLUSION: Our study expands the mutational spectrum of TBX6 in MRKHS and delineates the molecular pathogenesis of TBX6 variants, supporting the association between deleterious variants in TBX6 and MRKHS.

%B Genet Med %V 24 %P 2262-2273 %8 2022 Nov %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/36112137?dopt=Abstract %R 10.1016/j.gim.2022.08.012 %0 Journal Article %J J Allergy Clin Immunol %D 2022 %T Genetic errors of immunity distinguish pediatric nonmalignant lymphoproliferative disorders. %A Forbes, Lisa R %A Eckstein, Olive S %A Gulati, Nitya %A Peckham-Gregory, Erin C %A Ozuah, Nmazuo W %A Lubega, Joseph %A El-Mallawany, Nader K %A Agrusa, Jennifer E %A Poli, M Cecilia %A Vogel, Tiphanie P %A Chaimowitz, Natalia S %A Rider, Nicholas L %A Mace, Emily M %A Orange, Jordan S %A Caldwell, Jason W %A Aldave-Becerra, Juan C %A Jolles, Stephen %A Saettini, Francesco %A Chong, Hey J %A Stray-Pedersen, Asbjorg %A Heslop, Helen E %A Kamdar, Kala Y %A Rouce, R Helen %A Donna M Muzny %A Jhangiani, Shalini N %A Richard A Gibbs %A Coban-Akdemir, Zeynep H %A James R Lupski %A McClain, Kenneth L %A Allen, Carl E %A Chinn, Ivan K %K Adolescent %K Autoimmunity %K Child %K Child, Preschool %K Exome Sequencing %K Female %K Genetic Association Studies %K Genetic Testing %K Herpesvirus 4, Human %K Humans %K Immunity %K Infant %K Lymphoproliferative Disorders %K Male %K Young Adult %X

BACKGROUND: Pediatric nonmalignant lymphoproliferative disorders (PLPDs) are clinically and genetically heterogeneous. Long-standing immune dysregulation and lymphoproliferation in children may be life-threatening, and a paucity of data exists to guide evaluation and treatment of children with PLPD.

OBJECTIVE: The primary objective of this study was to ascertain the spectrum of genomic immunologic defects in PLPD. Secondary objectives included characterization of clinical outcomes and associations between genetic diagnoses and those outcomes.

METHODS: PLPD was defined by persistent lymphadenopathy, lymph organ involvement, or lymphocytic infiltration for more than 3 months, with or without chronic or significant Epstein-Barr virus (EBV) infection. Fifty-one subjects from 47 different families with PLPD were analyzed using whole exome sequencing.

RESULTS: Whole exome sequencing identified likely genetic errors of immunity in 51% to 62% of families (53% to 65% of affected children). Presence of a genetic etiology was associated with younger age and hemophagocytic lymphohistiocytosis. Ten-year survival for the cohort was 72.4%, and patients with viable genetic diagnoses had a higher survival rate (82%) compared to children without a genetic explanation (48%, P = .03). Survival outcomes for individuals with EBV-associated disease and no genetic explanation were particularly worse than outcomes for subjects with EBV-associated disease and a genetic explanation (17% vs 90%; P = .002). Ascertainment of a molecular diagnosis provided targetable treatment options for up to 18 individuals and led to active management changes for 12 patients.

CONCLUSIONS: PLPD defines children at high risk for mortality, and whole exome sequencing informs clinical risks and therapeutic opportunities for this diagnosis.

%B J Allergy Clin Immunol %V 149 %P 758-766 %8 2022 Feb %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/34329649?dopt=Abstract %R 10.1016/j.jaci.2021.07.015 %0 Journal Article %J Hum Mutat %D 2022 %T Long read sequencing and expression studies of AHDC1 deletions in Xia-Gibbs syndrome reveal a novel genetic regulatory mechanism. %A Chander, Varuna %A Mahmoud, Medhat %A Jianhong Hu %A Dardas, Zain %A Grochowski, Christopher M %A Dawood, Moez %A Khayat, Michael M %A Li, He %A Li, Shoudong %A Jhangiani, Shalini %A Korchina, Viktoriya %A Shen, Hua %A Weissenberger, George %A Meng, Qingchang %A Marie-Claude Gingras %A Donna M Muzny %A Harshavardhan Doddapaneni %A Posey, Jennifer E %A James R Lupski %A Aniko Sabo %A David R Murdock %A Fritz J Sedlazeck %A Richard A Gibbs %K Abnormalities, Multiple %K DNA-Binding Proteins %K Endoribonucleases %K Humans %K Intellectual Disability %K Musculoskeletal Abnormalities %K Neurodevelopmental Disorders %K Phosphoprotein Phosphatases %K Qa-SNARE Proteins %K RNA-Binding Proteins %K Sphingomyelin Phosphodiesterase %X

Xia-Gibbs syndrome (XGS; MIM# 615829) is a rare mendelian disorder characterized by Development Delay (DD), intellectual disability (ID), and hypotonia. Individuals with XGS typically harbor de novo protein-truncating mutations in the AT-Hook DNA binding motif containing 1 (AHDC1) gene, although some missense mutations can also cause XGS. Large de novo heterozygous deletions that encompass the AHDC1 gene have also been ascribed as diagnostic for the disorder, without substantial evidence to support their pathogenicity. We analyzed 19 individuals with large contiguous deletions involving AHDC1, along with other genes. One individual bore the smallest known contiguous AHDC1 deletion (∼350 Kb), encompassing eight other genes within chr1p36.11 (Feline Gardner-Rasheed, IFI6, FAM76A, STX12, PPP1R8, THEMIS2, RPA2, SMPDL3B) and terminating within the first intron of AHDC1. The breakpoint junctions and phase of the deletion were identified using both short and long read sequencing (Oxford Nanopore). Quantification of RNA expression patterns in whole blood revealed that AHDC1 exhibited a mono-allelic expression pattern with no deficiency in overall AHDC1 expression levels, in contrast to the other deleted genes, which exhibited a 50% reduction in mRNA expression. These results suggest that AHDC1 expression in this individual is compensated by a novel regulatory mechanism and advances understanding of mutational and regulatory mechanisms in neurodevelopmental disorders.

%B Hum Mutat %V 43 %P 2033-2053 %8 2022 Dec %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/36054313?dopt=Abstract %R 10.1002/humu.24461 %0 Journal Article %J Dev Cell %D 2022 %T Loss of non-motor kinesin KIF26A causes congenital brain malformations via dysregulated neuronal migration and axonal growth as well as apoptosis. %A Qian, Xuyu %A DeGennaro, Ellen M %A Talukdar, Maya %A Akula, Shyam K %A Lai, Abbe %A Shao, Diane D %A Gonzalez, Dilenny %A Marciano, Jack H %A Smith, Richard S %A Hylton, Norma K %A Yang, Edward %A Bazan, J Fernando %A Barrett, Lee %A Yeh, Rebecca C %A Hill, R Sean %A Beck, Samantha G %A Otani, Aoi %A Angad, Jolly %A Mitani, Tadahiro %A Posey, Jennifer E %A Pehlivan, Davut %A Calame, Daniel %A Aydin, Hatip %A Yesilbas, Osman %A Parks, Kendall C %A Argilli, Emanuela %A England, Eleina %A Im, Kiho %A Taranath, Ajay %A Scott, Hamish S %A Barnett, Christopher P %A Arts, Peer %A Sherr, Elliott H %A James R Lupski %A Walsh, Christopher A %K Animals %K Apoptosis %K Brain %K Focal Adhesion Protein-Tyrosine Kinases %K Humans %K Kinesins %K Mice %K Neurons %X

Kinesins are canonical molecular motors but can also function as modulators of intracellular signaling. KIF26A, an unconventional kinesin that lacks motor activity, inhibits growth-factor-receptor-bound protein 2 (GRB2)- and focal adhesion kinase (FAK)-dependent signal transduction, but its functions in the brain have not been characterized. We report a patient cohort with biallelic loss-of-function variants in KIF26A, exhibiting a spectrum of congenital brain malformations. In the developing brain, KIF26A is preferentially expressed during early- and mid-gestation in excitatory neurons. Combining mice and human iPSC-derived organoid models, we discovered that loss of KIF26A causes excitatory neuron-specific defects in radial migration, localization, dendritic and axonal growth, and apoptosis, offering a convincing explanation of the disease etiology in patients. Single-cell RNA sequencing in KIF26A knockout organoids revealed transcriptional changes in MAPK, MYC, and E2F pathways. Our findings illustrate the pathogenesis of KIF26A loss-of-function variants and identify the surprising versatility of this non-motor kinesin.

%B Dev Cell %V 57 %P 2381-2396.e13 %8 2022 Oct 24 %G eng %N 20 %1 https://www.ncbi.nlm.nih.gov/pubmed/36228617?dopt=Abstract %R 10.1016/j.devcel.2022.09.011 %0 Journal Article %J Genome Med %D 2022 %T The multiple de novo copy number variant (MdnCNV) phenomenon presents with peri-zygotic DNA mutational signatures and multilocus pathogenic variation. %A Du, Haowei %A Jolly, Angad %A Grochowski, Christopher M %A Bo Yuan %A Dawood, Moez %A Jhangiani, Shalini N %A Li, He %A Donna M Muzny %A Fatih, Jawid M %A Coban-Akdemir, Zeynep %A Carlin, Mary Esther %A Scheuerle, Angela E %A Witzl, Karin %A Posey, Jennifer E %A Pendleton, Matthew %A Harrington, Eoghan %A Juul, Sissel %A Hastings, P J %A Bi, Weimin %A Richard A Gibbs %A Fritz J Sedlazeck %A James R Lupski %A Carvalho, Claudia M B %A Liu, Pengfei %K Comparative Genomic Hybridization %K DNA %K DNA Copy Number Variations %K DNA-Binding Proteins %K Genomic Instability %K Humans %K Mutation %K Nucleotides %K Transcription Factors %X

BACKGROUND: The multiple de novo copy number variant (MdnCNV) phenotype is described by having four or more constitutional de novo CNVs (dnCNVs) arising independently throughout the human genome within one generation. It is a rare peri-zygotic mutational event, previously reported to be seen once in every 12,000 individuals referred for genome-wide chromosomal microarray analysis due to congenital abnormalities. These rare families provide a unique opportunity to understand the genetic factors of peri-zygotic genome instability and the impact of dnCNV on human diseases.

METHODS: Chromosomal microarray analysis (CMA), array-based comparative genomic hybridization, short- and long-read genome sequencing (GS) were performed on the newly identified MdnCNV family to identify de novo mutations including dnCNVs, de novo single-nucleotide variants (dnSNVs), and indels. Short-read GS was performed on four previously published MdnCNV families for dnSNV analysis. Trio-based rare variant analysis was performed on the newly identified individual and four previously published MdnCNV families to identify potential genetic etiologies contributing to the peri-zygotic genomic instability. Lin semantic similarity scores informed quantitative human phenotype ontology analysis on three MdnCNV families to identify gene(s) driving or contributing to the clinical phenotype.

RESULTS: In the newly identified MdnCNV case, we revealed eight de novo tandem duplications, each ~ 1 Mb, with microhomology at 6/8 breakpoint junctions. Enrichment of de novo single-nucleotide variants (SNV; 6/79) and de novo indels (1/12) was found within 4 Mb of the dnCNV genomic regions. An elevated post-zygotic SNV mutation rate was observed in MdnCNV families. Maternal rare variant analyses identified three genes in distinct families that may contribute to the MdnCNV phenomenon. Phenotype analysis suggests that gene(s) within dnCNV regions contribute to the observed proband phenotype in 3/3 cases. CNVs in two cases, a contiguous gene duplication encompassing PMP22 and RAI1 and another duplication affecting NSD1 and SMARCC2, contribute to the clinically observed phenotypic manifestations.

CONCLUSIONS: Characteristic features of dnCNVs reported here are consistent with a microhomology-mediated break-induced replication (MMBIR)-driven mechanism during the peri-zygotic period. Maternal genetic variants in DNA repair genes potentially contribute to peri-zygotic genomic instability. Variable phenotypic features were observed across a cohort of three MdnCNV probands, and computational quantitative phenotyping revealed that two out of three had evidence for the contribution of more than one genetic locus to the proband's phenotype supporting the hypothesis of de novo multilocus pathogenic variation (MPV) in those families.

%B Genome Med %V 14 %P 122 %8 2022 Oct 27 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/36303224?dopt=Abstract %R 10.1186/s13073-022-01123-w %0 Journal Article %J Brain %D 2022 %T Niacin therapy improves outcome and normalizes metabolic abnormalities in an NAXD-deficient patient. %A Manor, Joshua %A Calame, Daniel G %A Gijavanekar, Charul %A Tran, Alyssa %A Fatih, Jawid M %A Lalani, Seema R %A Mizerik, Elizabeth %A Parnes, Mered %A Mehta, Vidya P %A Adesina, Adekunle M %A James R Lupski %A Scaglia, Fernando %A Sarah H Elsea %K Cholesterol, HDL %K Humans %K Niacin %B Brain %V 145 %P e36-e40 %8 2022 Jun 03 %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/35231119?dopt=Abstract %R 10.1093/brain/awac065 %0 Journal Article %J HGG Adv %D 2022 %T Novel pathogenic variants and quantitative phenotypic analyses of Robinow syndrome: WNT signaling perturbation and phenotypic variability. %A Zhang, Chaofan %A Jolly, Angad %A Shayota, Brian J %A Mazzeu, Juliana F %A Du, Haowei %A Dawood, Moez %A Soper, Patricia Celestino %A Ramalho de Lima, Ariadne %A Ferreira, Barbara Merfort %A Coban-Akdemir, Zeynep %A White, Janson %A Shears, Deborah %A Thomson, Fraser Robert %A Douglas, Sarah Louise %A Wainwright, Andrew %A Bailey, Kathryn %A Wordsworth, Paul %A Oldridge, Mike %A Lester, Tracy %A Calder, Alistair D %A Dumic, Katja %A Banka, Siddharth %A Donnai, Dian %A Jhangiani, Shalini N %A Potocki, Lorraine %A Chung, Wendy K %A Mora, Sara %A Northrup, Hope %A Ashfaq, Myla %A Rosenfeld, Jill A %A Mason, Kati %A Pollack, Lynda C %A McConkie-Rosell, Allyn %A Kelly, Wei %A McDonald, Marie %A Hauser, Natalie S %A Leahy, Peter %A Powell, Cynthia M %A Boy, Raquel %A Honjo, Rachel Sayuri %A Kok, Fernando %A Martelli, Lucia R %A Filho, Vicente Odone %A Donna M Muzny %A Richard A Gibbs %A Posey, Jennifer E %A Liu, Pengfei %A James R Lupski %A Sutton, V Reid %A Carvalho, Claudia M B %X

Robinow syndrome (RS) is a genetically heterogeneous disorder with six genes that converge on the WNT/planar cell polarity (PCP) signaling pathway implicated (, , , , , and ). RS is characterized by skeletal dysplasia and distinctive facial and physical characteristics. To further explore the genetic heterogeneity, paralog contribution, and phenotypic variability of RS, we investigated a cohort of 22 individuals clinically diagnosed with RS from 18 unrelated families. Pathogenic or likely pathogenic variants in genes associated with RS or RS phenocopies were identified in all 22 individuals, including the first variant to be reported in . We retrospectively collected medical records of 16 individuals from this cohort and extracted clinical descriptions from 52 previously published cases. We performed Human Phenotype Ontology (HPO) based quantitative phenotypic analyses to dissect allele-specific phenotypic differences. Individuals with variants clustered into two groups with demonstrable phenotypic differences between those with missense and truncating alleles. Probands with biallelic variants clustered together with the majority of probands carrying , , and variants, demonstrating no phenotypic distinction between the -autosomal recessive and dominant forms of RS. While phenotypically similar diseases on the RS differential matched through HPO analysis, clustering using phenotype similarity score placed RS-associated phenotypes in a unique cluster containing , , and apart from non-RS-associated paralogs. Through human phenotype analyses of this RS cohort and OMIM clinical synopses of Mendelian disease, this study begins to tease apart specific biologic roles for non-canonical WNT-pathway proteins.

%B HGG Adv %V 3 %P 100074 %8 2022 Jan 13 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/35047859?dopt=Abstract %R 10.1016/j.xhgg.2021.100074 %0 Journal Article %J Am J Med Genet A %D 2022 %T Novel RETREG1 (FAM134B) founder allele is linked to HSAN2B and renal disease in a Turkish family. %A Taşdelen, Elifcan %A Calame, Daniel G %A Akay, Gulsen %A Mitani, Tadahiro %A Fatih, Jawid M %A Herman, Isabella %A Du, Haowei %A Coban-Akdemir, Zeynep %A Marafi, Dana %A Jhangiani, Shalini N %A Posey, Jennifer E %A Richard A Gibbs %A Altıparmak, Taylan %A Kutlay, Nüket Yürür %A James R Lupski %A Pehlivan, Davut %K Alleles %K Hereditary Sensory and Autonomic Neuropathies %K Humans %K Intracellular Signaling Peptides and Proteins %K Membrane Proteins %K Osteomyelitis %K Pedigree %K Renal Insufficiency %X

Hereditary sensory and autonomic neuropathy type 2B (HSAN2B) is a rare autosomal recessive peripheral neuropathy caused by biallelic variants in RETREG1 (formerly FAM134B). HSAN2B is characterized by sensory impairment resulting in skin ulcerations, amputations, and osteomyelitis as well as variable weakness, spasticity, and autonomic dysfunction. Here, we report four affected individuals with recurrent osteomyelitis, ulceration, and amputation of hands and feet, sensory neuropathy, hyperhidrosis, urinary incontinence, and renal failure from a family without any known shared parental ancestry. Due to the history of chronic recurrent multifocal osteomyelitis and microcytic anemia, a diagnosis of Majeed syndrome was considered; however, sequencing of LPIN2 was negative. Family-based exome sequencing (ES) revealed a novel homozygous ultrarare RETREG1 variant NM_001034850.2:c.321G>A;p.Trp107Ter. Electrophysiological studies of the proband demonstrated axonal sensorimotor neuropathy predominantly in the lower extremities. Consistent with the lack of shared ancestry, the coefficient of inbreeding calculated from ES data was low (F = 0.002), but absence of heterozygosity (AOH) analysis demonstrated a 7.2 Mb AOH block surrounding the variant consistent with a founder allele. Two of the four affected individuals had unexplained renal failure which has not been reported in HSAN2B cases to date. Therefore, this report describes a novel RETREG1 founder allele and suggests renal failure may be an unrecognized feature of the RETREG1-disease spectrum.

%B Am J Med Genet A %V 188 %P 2153-2161 %8 2022 Jul %G eng %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/35332675?dopt=Abstract %R 10.1002/ajmg.a.62727 %0 Journal Article %J Hum Mutat %D 2022 %T Phenotypic and mutational spectrum of ROR2-related Robinow syndrome. %A Lima, Ariadne R %A Ferreira, Barbara M %A Zhang, Chaofan %A Jolly, Angad %A Du, Haowei %A White, Janson J %A Dawood, Moez %A Lins, Tulio C %A Chiabai, Marcela A %A van Beusekom, Ellen %A Cordoba, Mara S %A Caldas Rosa, Erica C C %A Kayserili, Hulya %A Kimonis, Virginia %A Wu, Erica %A Mellado, Cecilia %A Aggarwal, Vineet %A Richieri-Costa, Antonio %A Brunoni, Décio %A Canó, Talyta M %A Jorge, Alexander A L %A Kim, Chong A %A Honjo, Rachel %A Bertola, Debora R %A Dandalo-Girardi, Raissa M %A Bayram, Yavuz %A Gezdirici, Alper %A Yilmaz-Gulec, Elif %A Gumus, Evren %A Yilmaz, Gülay C %A Okamoto, Nobuhiko %A Ohashi, Hirofumi %A Coban-Akdemir, Zeynep %A Mitani, Tadahiro %A Jhangiani, Shalini N %A Donna M Muzny %A Regattieri, Neysa A P %A Pogue, Robert %A Pereira, Rinaldo W %A Otto, Paulo A %A Richard A Gibbs %A Ali, Bassam R %A van Bokhoven, Hans %A Brunner, Han G %A Sutton, V Reid %A James R Lupski %A Vianna-Morgante, Angela M %A Carvalho, Claudia M B %A Mazzeu, Juliana F %K Craniofacial Abnormalities %K Dwarfism %K Genes, Recessive %K Humans %K Limb Deformities, Congenital %K Male %K Phenotype %K Receptor Tyrosine Kinase-like Orphan Receptors %K Urogenital Abnormalities %X

Robinow syndrome is characterized by a triad of craniofacial dysmorphisms, disproportionate-limb short stature, and genital hypoplasia. A significant degree of phenotypic variability seems to correlate with different genes/loci. Disturbances of the noncanonical WNT-pathway have been identified as the main cause of the syndrome. Biallelic variants in ROR2 cause an autosomal recessive form of the syndrome with distinctive skeletal findings. Twenty-two patients with a clinical diagnosis of autosomal recessive Robinow syndrome were screened for variants in ROR2 using multiple molecular approaches. We identified 25 putatively pathogenic ROR2 variants, 16 novel, including single nucleotide variants and exonic deletions. Detailed phenotypic analyses revealed that all subjects presented with a prominent forehead, hypertelorism, short nose, abnormality of the nasal tip, brachydactyly, mesomelic limb shortening, short stature, and genital hypoplasia in male patients. A total of 19 clinical features were present in more than 75% of the subjects, thus pointing to an overall uniformity of the phenotype. Disease-causing variants in ROR2, contribute to a clinically recognizable autosomal recessive trait phenotype with multiple skeletal defects. A comprehensive quantitative clinical evaluation of this cohort delineated the phenotypic spectrum of ROR2-related Robinow syndrome. The identification of exonic deletion variant alleles further supports the contention of a loss-of-function mechanism in the etiology of the syndrome.

%B Hum Mutat %V 43 %P 900-918 %8 2022 Jul %G eng %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/35344616?dopt=Abstract %R 10.1002/humu.24375 %0 Journal Article %J Am J Med Genet A %D 2022 %T Quantitative dissection of multilocus pathogenic variation in an Egyptian infant with severe neurodevelopmental disorder resulting from multiple molecular diagnoses. %A Herman, Isabella %A Jolly, Angad %A Du, Haowei %A Dawood, Moez %A Abdel-Salam, Ghada M H %A Marafi, Dana %A Mitani, Tadahiro %A Calame, Daniel G %A Coban-Akdemir, Zeynep %A Fatih, Jawid M %A Hegazy, Ibrahim %A Jhangiani, Shalini N %A Richard A Gibbs %A Pehlivan, Davut %A Posey, Jennifer E %A James R Lupski %K Animals %K Calpain %K Egypt %K Exome Sequencing %K Humans %K Infant %K Muscle Proteins %K Muscular Dystrophies, Limb-Girdle %K Mutation %K Neurodevelopmental Disorders %K Phenotype %X

Genomic sequencing and clinical genomics have demonstrated that substantial subsets of atypical and/or severe disease presentations result from multilocus pathogenic variation (MPV) causing blended phenotypes. In an infant with a severe neurodevelopmental disorder, four distinct molecular diagnoses were found by exome sequencing (ES). The blended phenotype that includes brain malformation, dysmorphism, and hypotonia was dissected using the Human Phenotype Ontology (HPO). ES revealed variants in CAPN3 (c.259C > G:p.L87V), MUSK (c.1781C > T:p.A594V), NAV2 (c.1996G > A:p.G666R), and ZC4H2 (c.595A > C:p.N199H). CAPN3, MUSK, and ZC4H2 are established disease genes linked to limb-girdle muscular dystrophy (OMIM# 253600), congenital myasthenia (OMIM# 616325), and Wieacker-Wolff syndrome (WWS; OMIM# 314580), respectively. NAV2 is a retinoic-acid responsive novel disease gene candidate with biological roles in neurite outgrowth and cerebellar dysgenesis in mouse models. Using semantic similarity, we show that no gene identified by ES individually explains the proband phenotype, but rather the totality of the clinically observed disease is explained by the combination of disease-contributing effects of the identified genes. These data reveal that multilocus pathogenic variation can result in a blended phenotype with each gene affecting a different part of the nervous system and nervous system-muscle connection. We provide evidence from this n = 1 study that in patients with MPV and complex blended phenotypes resulting from multiple molecular diagnoses, quantitative HPO analysis can allow for dissection of phenotypic contribution of both established disease genes and novel disease gene candidates not yet proven to cause human disease.

%B Am J Med Genet A %V 188 %P 735-750 %8 2022 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/34816580?dopt=Abstract %R 10.1002/ajmg.a.62565 %0 Journal Article %J Genet Med %D 2022 %T Retrospective analysis of a clinical exome sequencing cohort reveals the mutational spectrum and identifies candidate disease-associated loci for BAFopathies. %A Chen, Chun-An %A Lattier, John %A Zhu, Wenmiao %A Rosenfeld, Jill %A Wang, Lei %A Scott, Tiana M %A Du, Haowei %A Patel, Vipulkumar %A Dang, Anh %A Magoulas, Pilar %A Streff, Haley %A Sebastian, Jessica %A Svihovec, Shayna %A Curry, Kathryn %A Delgado, Mauricio R %A Hanchard, Neil A %A Lalani, Seema %A Marom, Ronit %A Madan-Khetarpal, Suneeta %A Saenz, Margarita %A Dai, Hongzheng %A Meng, Linyan %A Xia, Fan %A Bi, Weimin %A Liu, Pengfei %A Posey, Jennifer E %A Scott, Daryl A %A James R Lupski %A Eng, Christine M %A Xiao, Rui %A Bo Yuan %K Abnormalities, Multiple %K Actins %K Chromosomal Proteins, Non-Histone %K DNA-Binding Proteins %K Exome %K Hand Deformities, Congenital %K Humans %K Micrognathism %K Retrospective Studies %X

PURPOSE: BRG1/BRM-associated factor (BAF) complex is a chromatin remodeling complex that plays a critical role in gene regulation. Defects in the genes encoding BAF subunits lead to BAFopathies, a group of neurodevelopmental disorders with extensive locus and phenotypic heterogeneity.

METHODS: We retrospectively analyzed data from 16,243 patients referred for clinical exome sequencing (ES) with a focus on the BAF complex. We applied a genotype-first approach, combining predicted genic constraints to propose candidate BAFopathy genes.

RESULTS: We identified 127 patients carrying pathogenic variants, likely pathogenic variants, or de novo variants of unknown clinical significance in 11 known BAFopathy genes. Those include 34 patients molecularly diagnosed using ES reanalysis with new gene-disease evidence (n = 21) or variant reclassifications in known BAFopathy genes (n = 13). We also identified de novo or predicted loss-of-function variants in 4 candidate BAFopathy genes, including ACTL6A, BICRA (implicated in Coffin-Siris syndrome during this study), PBRM1, and SMARCC1.

CONCLUSION: We report the mutational spectrum of BAFopathies in an ES cohort. A genotype-driven and pathway-based reanalysis of ES data identified new evidence for candidate genes involved in BAFopathies. Further mechanistic and phenotypic characterization of additional patients are warranted to confirm their roles in human disease and to delineate their associated phenotypic spectrums.

%B Genet Med %V 24 %P 364-373 %8 2022 Feb %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/34906496?dopt=Abstract %R 10.1016/j.gim.2021.09.017 %0 Journal Article %J Am J Hum Genet %D 2022 %T A reverse genetics and genomics approach to gene paralog function and disease: Myokymia and the juxtaparanode. %A Marafi, Dana %A Kozar, Nina %A Duan, Ruizhi %A Bradley, Stephen %A Yokochi, Kenji %A Al Mutairi, Fuad %A Saadi, Nebal Waill %A Whalen, Sandra %A Brunet, Theresa %A Kotzaeridou, Urania %A Choukair, Daniela %A Keren, Boris %A Nava, Caroline %A Kato, Mitsuhiro %A Arai, Hiroshi %A Froukh, Tawfiq %A Faqeih, Eissa Ali %A AlAsmari, Ali M %A Saleh, Mohammed M %A Pinto E Vairo, Filippo %A Pichurin, Pavel N %A Klee, Eric W %A Schmitz, Christopher T %A Grochowski, Christopher M %A Mitani, Tadahiro %A Herman, Isabella %A Calame, Daniel G %A Fatih, Jawid M %A Du, Haowei %A Coban-Akdemir, Zeynep %A Pehlivan, Davut %A Jhangiani, Shalini N %A Richard A Gibbs %A Miyatake, Satoko %A Matsumoto, Naomichi %A Wagstaff, Laura J %A Posey, Jennifer E %A James R Lupski %A Meijer, Dies %A Wagner, Matias %K Animals %K Autoantibodies %K Axons %K Genomics %K Humans %K Intracellular Signaling Peptides and Proteins %K Mammals %K Mice %K Myokymia %K Nerve Tissue Proteins %K Phenotype %K Reverse Genetics %X

The leucine-rich glioma-inactivated (LGI) family consists of four highly conserved paralogous genes, LGI1-4, that are highly expressed in mammalian central and/or peripheral nervous systems. LGI1 antibodies are detected in subjects with autoimmune limbic encephalitis and peripheral nerve hyperexcitability syndromes (PNHSs) such as Isaacs and Morvan syndromes. Pathogenic variations of LGI1 and LGI4 are associated with neurological disorders as disease traits including familial temporal lobe epilepsy and neurogenic arthrogryposis multiplex congenita 1 with myelin defects, respectively. No human disease has been reported associated with either LGI2 or LGI3. We implemented exome sequencing and family-based genomics to identify individuals with deleterious variants in LGI3 and utilized GeneMatcher to connect practitioners and researchers worldwide to investigate the clinical and electrophysiological phenotype in affected subjects. We also generated Lgi3-null mice and performed peripheral nerve dissection and immunohistochemistry to examine the juxtaparanode LGI3 microarchitecture. As a result, we identified 16 individuals from eight unrelated families with loss-of-function (LoF) bi-allelic variants in LGI3. Deep phenotypic characterization showed LGI3 LoF causes a potentially clinically recognizable PNHS trait characterized by global developmental delay, intellectual disability, distal deformities with diminished reflexes, visible facial myokymia, and distinctive electromyographic features suggestive of motor nerve instability. Lgi3-null mice showed reduced and mis-localized Kv1 channel complexes in myelinated peripheral axons. Our data demonstrate bi-allelic LoF variants in LGI3 cause a clinically distinguishable disease trait of PNHS, most likely caused by disturbed Kv1 channel distribution in the absence of LGI3.

%B Am J Hum Genet %V 109 %P 1713-1723 %8 2022 Sep 01 %G eng %N 9 %1 https://www.ncbi.nlm.nih.gov/pubmed/35948005?dopt=Abstract %R 10.1016/j.ajhg.2022.07.006 %0 Journal Article %J Genome Med %D 2022 %T Sequencing individual genomes with recurrent genomic disorder deletions: an approach to characterize genes for autosomal recessive rare disease traits. %A Bo Yuan %A Schulze, Katharina V %A Assia Batzir, Nurit %A Sinson, Jefferson %A Dai, Hongzheng %A Zhu, Wenmiao %A Bocanegra, Francia %A Fong, Chin-To %A Holder, Jimmy %A Nguyen, Joanne %A Schaaf, Christian P %A Yang, Yaping %A Bi, Weimin %A Eng, Christine %A Shaw, Chad %A James R Lupski %A Liu, Pengfei %K Base Sequence %K Genomics %K Homologous Recombination %K Humans %K Rare Diseases %K Retrospective Studies %X

BACKGROUND: In medical genetics, discovery and characterization of disease trait contributory genes and alleles depends on genetic reasoning, study design, and patient ascertainment; we suggest a segmental haploid genetics approach to enhance gene discovery and molecular diagnostics.

METHODS: We constructed a genome-wide map for nonallelic homologous recombination (NAHR)-mediated recurrent genomic deletions and used this map to estimate population frequencies of NAHR deletions based on large-scale population cohorts and region-specific studies. We calculated recessive disease carrier burden using high-quality pathogenic or likely pathogenic variants from ClinVar and gnomAD. We developed a NIRD (NAHR deletion Impact to Recessive Disease) score for recessive disorders by quantifying the contribution of NAHR deletion to the overall allele load that enumerated all pairwise combinations of disease-causing alleles; we used a Punnett square approach based on an assumption of random mating. Literature mining was conducted to identify all reported patients with defects in a gene with a high NIRD score; meta-analysis was performed on these patients to estimate the representation of NAHR deletions in recessive traits from contemporary human genomics studies. Retrospective analyses of extant clinical exome sequencing (cES) were performed for novel rare recessive disease trait gene and allele discovery from individuals with NAHR deletions.

RESULTS: We present novel genomic insights regarding the genome-wide impact of NAHR recurrent segmental variants on recessive disease burden; we demonstrate the utility of NAHR recurrent deletions to enhance discovery in the challenging context of autosomal recessive (AR) traits and biallelic variation. Computational results demonstrate new mutations mediated by NAHR, involving recurrent deletions at 30 genomic regions, likely drive recessive disease burden for over 74% of loci within these segmental deletions or at least 2% of loci genome-wide. Meta-analyses on 170 literature-reported patients implicate that NAHR deletions are depleted from the ascertained pool of AR trait alleles. Exome reanalysis of personal genomes from subjects harboring recurrent deletions uncovered new disease-contributing variants in genes including COX10, ERCC6, PRRT2, and OTUD7A.

CONCLUSIONS: Our results demonstrate that genomic sequencing of personal genomes with NAHR deletions could dramatically improve allele and gene discovery and enhance clinical molecular diagnosis. Moreover, results suggest NAHR events could potentially enable human haploid genetic screens as an approach to experimental inquiry into disease biology.

%B Genome Med %V 14 %P 113 %8 2022 Sep 30 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/36180924?dopt=Abstract %R 10.1186/s13073-022-01113-y %0 Journal Article %J Am J Hum Genet %D 2022 %T TCEAL1 loss-of-function results in an X-linked dominant neurodevelopmental syndrome and drives the neurological disease trait in Xq22.2 deletions. %A Hijazi, Hadia %A Reis, Linda M %A Pehlivan, Davut %A Bernstein, Jonathan A %A Muriello, Michael %A Syverson, Erin %A Bonner, Devon %A Estiar, Mehrdad A %A Gan-Or, Ziv %A Rouleau, Guy A %A Lyulcheva, Ekaterina %A Greenhalgh, Lynn %A Tessarech, Marine %A Colin, Estelle %A Guichet, Agnès %A Bonneau, Dominique %A van Jaarsveld, R H %A Lachmeijer, A M A %A Ruaud, Lyse %A Levy, Jonathan %A Tabet, Anne-Claude %A Ploski, Rafal %A Rydzanicz, Małgorzata %A Kępczyński, Łukasz %A Połatyńska, Katarzyna %A Li, Yidan %A Fatih, Jawid M %A Marafi, Dana %A Rosenfeld, Jill A %A Coban-Akdemir, Zeynep %A Bi, Weimin %A Richard A Gibbs %A Hobson, Grace M %A Hunter, Jill V %A Carvalho, Claudia M B %A Posey, Jennifer E %A Semina, Elena V %A James R Lupski %K Autistic Disorder %K Female %K Humans %K Intellectual Disability %K Male %K Muscle Hypotonia %K Phenotype %K Syndrome %K Transcription Factors %X

An Xq22.2 region upstream of PLP1 has been proposed to underly a neurological disease trait when deleted in 46,XX females. Deletion mapping revealed that heterozygous deletions encompassing the smallest region of overlap (SRO) spanning six Xq22.2 genes (BEX3, RAB40A, TCEAL4, TCEAL3, TCEAL1, and MORF4L2) associate with an early-onset neurological disease trait (EONDT) consisting of hypotonia, intellectual disability, neurobehavioral abnormalities, and dysmorphic facial features. None of the genes within the SRO have been associated with monogenic disease in OMIM. Through local and international collaborations facilitated by GeneMatcher and Matchmaker Exchange, we have identified and herein report seven de novo variants involving TCEAL1 in seven unrelated families: three hemizygous truncating alleles; one hemizygous missense allele; one heterozygous TCEAL1 full gene deletion; one heterozygous contiguous deletion of TCEAL1, TCEAL3, and TCEAL4; and one heterozygous frameshift variant allele. Variants were identified through exome or genome sequencing with trio analysis or through chromosomal microarray. Comparison with previously reported Xq22 deletions encompassing TCEAL1 identified a more-defined syndrome consisting of hypotonia, abnormal gait, developmental delay/intellectual disability especially affecting expressive language, autistic-like behavior, and mildly dysmorphic facial features. Additional features include strabismus, refractive errors, variable nystagmus, gastroesophageal reflux, constipation, dysmotility, recurrent infections, seizures, and structural brain anomalies. An additional maternally inherited hemizygous missense allele of uncertain significance was identified in a male with hypertonia and spasticity without syndromic features. These data provide evidence that TCEAL1 loss of function causes a neurological rare disease trait involving significant neurological impairment with features overlapping the EONDT phenotype in females with the Xq22 deletion.

%B Am J Hum Genet %V 109 %P 2270-2282 %8 2022 Dec 01 %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/36368327?dopt=Abstract %R 10.1016/j.ajhg.2022.10.007 %0 Journal Article %J Nature %D 2022 %T TLR7 gain-of-function genetic variation causes human lupus. %A Brown, Grant J %A Cañete, Pablo F %A Wang, Hao %A Medhavy, Arti %A Bones, Josiah %A Roco, Jonathan A %A He, Yuke %A Qin, Yuting %A Cappello, Jean %A Ellyard, Julia I %A Bassett, Katharine %A Shen, Qian %A Burgio, Gaetan %A Zhang, Yaoyuan %A Turnbull, Cynthia %A Meng, Xiangpeng %A Wu, Phil %A Cho, Eun %A Miosge, Lisa A %A Andrews, T Daniel %A Field, Matt A %A Tvorogov, Denis %A Lopez, Angel F %A Babon, Jeffrey J %A López, Cristina Aparicio %A Gónzalez-Murillo, África %A Garulo, Daniel Clemente %A Pascual, Virginia %A Levy, Tess %A Mallack, Eric J %A Calame, Daniel G %A Lotze, Timothy %A James R Lupski %A Ding, Huihua %A Ullah, Tomalika R %A Walters, Giles D %A Koina, Mark E %A Cook, Matthew C %A Shen, Nan %A de Lucas Collantes, Carmen %A Corry, Ben %A Gantier, Michael P %A Athanasopoulos, Vicki %A Vinuesa, Carola G %K Animals %K Autoimmunity %K B-Lymphocytes %K Cyclic GMP %K Gain of Function Mutation %K Guanosine %K Humans %K Lupus Erythematosus, Systemic %K Mice %K Myeloid Differentiation Factor 88 %K Toll-Like Receptor 7 %X

Although circumstantial evidence supports enhanced Toll-like receptor 7 (TLR7) signalling as a mechanism of human systemic autoimmune disease, evidence of lupus-causing TLR7 gene variants is lacking. Here we describe human systemic lupus erythematosus caused by a TLR7 gain-of-function variant. TLR7 is a sensor of viral RNA, and binds to guanosine-. We identified a de novo, previously undescribed missense TLR7 variant in a child with severe lupus and additional variants in other patients with lupus. The TLR7 variant selectively increased sensing of guanosine and 2',3'-cGMP, and was sufficient to cause lupus when introduced into mice. We show that enhanced TLR7 signalling drives aberrant survival of B cell receptor (BCR)-activated B cells, and in a cell-intrinsic manner, accumulation of CD11c age-associated B cells and germinal centre B cells. Follicular and extrafollicular helper T cells were also increased but these phenotypes were cell-extrinsic. Deficiency of MyD88 (an adaptor protein downstream of TLR7) rescued autoimmunity, aberrant B cell survival, and all cellular and serological phenotypes. Despite prominent spontaneous germinal-centre formation in Tlr7 mice, autoimmunity was not ameliorated by germinal-centre deficiency, suggesting an extrafollicular origin of pathogenic B cells. We establish the importance of TLR7 and guanosine-containing self-ligands for human lupus pathogenesis, which paves the way for therapeutic TLR7 or MyD88 inhibition.

%B Nature %V 605 %P 349-356 %8 2022 May %G eng %N 7909 %1 https://www.ncbi.nlm.nih.gov/pubmed/35477763?dopt=Abstract %R 10.1038/s41586-022-04642-z %0 Journal Article %J Hum Mutat %D 2022 %T Variant-level matching for diagnosis and discovery: Challenges and opportunities. %A Rodrigues, Eliete da S %A Griffith, Sean %A Martin, Renan %A Antonescu, Corina %A Posey, Jennifer E %A Coban-Akdemir, Zeynep %A Jhangiani, Shalini N %A Doheny, Kimberly F %A James R Lupski %A Valle, David %A Bamshad, Michael J %A Hamosh, Ada %A Sheffer, Assaf %A Chong, Jessica X %A Einhorn, Yaron %A Cupak, Miro %A Sobreira, Nara %K Databases, Genetic %K Exome %K Genomics %K Humans %K Information Dissemination %K Phenotype %X

Here we describe MyGene2, Geno2MP, VariantMatcher, and Franklin; databases that provide variant-level information and phenotypic features to researchers, clinicians, healthcare providers and patients. Following the footsteps of the Matchmaker Exchange project that connects exome, genome, and phenotype databases at the gene level, these databases have as one goal to facilitate connection to one another using Data Connect, a standard for discovery and search of biomedical data from the Global Alliance for Genomics and Health (GA4GH).

%B Hum Mutat %V 43 %P 782-790 %8 2022 Jun %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/35191117?dopt=Abstract %R 10.1002/humu.24359 %0 Journal Article %J Blood %D 2021 %T Absent B cells, agammaglobulinemia, and hypertrophic cardiomyopathy in folliculin-interacting protein 1 deficiency. %A Saettini, Francesco %A Poli, Cecilia %A Vengoechea, Jaime %A Bonanomi, Sonia %A Orellana, Julio C %A Fazio, Grazia %A Rodriguez, Fred H %A Noguera, Loreani P %A Booth, Claire %A Jarur-Chamy, Valentina %A Shams, Marissa %A Iascone, Maria %A Vukic, Maja %A Gasperini, Serena %A Quadri, Manuel %A Barroeta Seijas, Amairelys %A Rivers, Elizabeth %A Mauri, Mario %A Badolato, Raffaele %A Cazzaniga, Gianni %A Bugarin, Cristina %A Gaipa, Giuseppe %A Kroes, Wilma G M %A Moratto, Daniele %A van Oostaijen-Ten Dam, Monique M %A Baas, Frank %A van der Maarel, Silvère %A Piazza, Rocco %A Coban-Akdemir, Zeynep H %A James R Lupski %A Bo Yuan %A Chinn, Ivan K %A Daxinger, Lucia %A Biondi, Andrea %K Adult %K Agammaglobulinemia %K Animals %K B-Lymphocytes %K Cardiomyopathy, Hypertrophic %K Carrier Proteins %K Child %K Child, Preschool %K Chromosomes, Human, Pair 5 %K Codon, Nonsense %K Consanguinity %K Crohn Disease %K Developmental Disabilities %K Disease Models, Animal %K Disease Susceptibility %K DNA Copy Number Variations %K Female %K Heart Defects, Congenital %K Humans %K Immunologic Deficiency Syndromes %K Infections %K Loss of Function Mutation %K Lymphopenia %K Male %K Mice %K Neutropenia %K Pedigree %K Uniparental Disomy %K Whole Exome Sequencing %X

Agammaglobulinemia is the most profound primary antibody deficiency that can occur due to an early termination of B-cell development. We here investigated 3 novel patients, including the first known adult, from unrelated families with agammaglobulinemia, recurrent infections, and hypertrophic cardiomyopathy (HCM). Two of them also presented with intermittent or severe chronic neutropenia. We identified homozygous or compound-heterozygous variants in the gene for folliculin interacting protein 1 (FNIP1), leading to loss of the FNIP1 protein. B-cell metabolism, including mitochondrial numbers and activity and phosphatidylinositol 3-kinase/AKT pathway, was impaired. These defects recapitulated the Fnip1-/- animal model. Moreover, we identified either uniparental disomy or copy-number variants (CNVs) in 2 patients, expanding the variant spectrum of this novel inborn error of immunity. The results indicate that FNIP1 deficiency can be caused by complex genetic mechanisms and support the clinical utility of exome sequencing and CNV analysis in patients with broad phenotypes, including agammaglobulinemia and HCM. FNIP1 deficiency is a novel inborn error of immunity characterized by early and severe B-cell development defect, agammaglobulinemia, variable neutropenia, and HCM. Our findings elucidate a functional and relevant role of FNIP1 in B-cell development and metabolism and potentially neutrophil activity.

%B Blood %V 137 %P 493-499 %8 2021 01 28 %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/32905580?dopt=Abstract %R 10.1182/blood.2020006441 %0 Journal Article %J Genet Med %D 2021 %T Biallelic and monoallelic variants in PLXNA1 are implicated in a novel neurodevelopmental disorder with variable cerebral and eye anomalies. %A Dworschak, Gabriel C %A Punetha, Jaya %A Kalanithy, Jeshurun C %A Mingardo, Enrico %A Erdem, Haktan B %A Akdemir, Zeynep C %A Karaca, Ender %A Mitani, Tadahiro %A Marafi, Dana %A Fatih, Jawid M %A Jhangiani, Shalini N %A Hunter, Jill V %A Dakal, Tikam Chand %A Dhabhai, Bhanupriya %A Dabbagh, Omar %A Alsaif, Hessa S %A Alkuraya, Fowzan S %A Maroofian, Reza %A Houlden, Henry %A Efthymiou, Stephanie %A Dominik, Natalia %A Salpietro, Vincenzo %A Sultan, Tipu %A Haider, Shahzad %A Bibi, Farah %A Thiele, Holger %A Hoefele, Julia %A Riedhammer, Korbinian M %A Wagner, Matias %A Guella, Ilaria %A Demos, Michelle %A Keren, Boris %A Buratti, Julien %A Charles, Perrine %A Nava, Caroline %A Héron, Delphine %A Heide, Solveig %A Valkanas, Elise %A Waddell, Leigh B %A Jones, Kristi J %A Oates, Emily C %A Cooper, Sandra T %A MacArthur, Daniel %A Syrbe, Steffen %A Ziegler, Andreas %A Platzer, Konrad %A Okur, Volkan %A Chung, Wendy K %A O'Shea, Sarah A %A Alcalay, Roy %A Fahn, Stanley %A Mark, Paul R %A Guerrini, Renzo %A Vetro, Annalisa %A Hudson, Beth %A Schnur, Rhonda E %A Hoganson, George E %A Burton, Jennifer E %A McEntagart, Meriel %A Lindenberg, Tobias %A Yilmaz, Öznur %A Odermatt, Benjamin %A Pehlivan, Davut %A Posey, Jennifer E %A James R Lupski %A Reutter, Heiko %K Animals %K Eye Abnormalities %K Genetic Association Studies %K Humans %K Nerve Tissue Proteins %K Neurodevelopmental Disorders %K Phenotype %K Receptors, Cell Surface %K Zebrafish %X

PURPOSE: To investigate the effect of PLXNA1 variants on the phenotype of patients with autosomal dominant and recessive inheritance patterns and to functionally characterize the zebrafish homologs plxna1a and plxna1b during development.

METHODS: We assembled ten patients from seven families with biallelic or de novo PLXNA1 variants. We describe genotype-phenotype correlations, investigated the variants by structural modeling, and used Morpholino knockdown experiments in zebrafish to characterize the embryonic role of plxna1a and plxna1b.

RESULTS: Shared phenotypic features among patients include global developmental delay (9/10), brain anomalies (6/10), and eye anomalies (7/10). Notably, seizures were predominantly reported in patients with monoallelic variants. Structural modeling of missense variants in PLXNA1 suggests distortion in the native protein. Our zebrafish studies enforce an embryonic role of plxna1a and plxna1b in the development of the central nervous system and the eye.

CONCLUSION: We propose that different biallelic and monoallelic variants in PLXNA1 result in a novel neurodevelopmental syndrome mainly comprising developmental delay, brain, and eye anomalies. We hypothesize that biallelic variants in the extracellular Plexin-A1 domains lead to impaired dimerization or lack of receptor molecules, whereas monoallelic variants in the intracellular Plexin-A1 domains might impair downstream signaling through a dominant-negative effect.

%B Genet Med %V 23 %P 1715-1725 %8 2021 Sep %G eng %N 9 %1 https://www.ncbi.nlm.nih.gov/pubmed/34054129?dopt=Abstract %R 10.1038/s41436-021-01196-9 %0 Journal Article %J Genet Med %D 2021 %T Biallelic loss-of-function variants in the splicing regulator NSRP1 cause a severe neurodevelopmental disorder with spastic cerebral palsy and epilepsy. %A Calame, Daniel G %A Bakhtiari, Somayeh %A Logan, Rachel %A Coban-Akdemir, Zeynep %A Du, Haowei %A Mitani, Tadahiro %A Fatih, Jawid M %A Hunter, Jill V %A Herman, Isabella %A Pehlivan, Davut %A Jhangiani, Shalini N %A Person, Richard %A Schnur, Rhonda E %A Jin, Sheng Chih %A Bilguvar, Kaya %A Posey, Jennifer E %A Koh, Sookyong %A Firouzabadi, Saghar G %A Alehabib, Elham %A Tafakhori, Abbas %A Esmkhani, Sahra %A Richard A Gibbs %A Noureldeen, Mahmoud M %A Zaki, Maha S %A Marafi, Dana %A Darvish, Hossein %A Kruer, Michael C %A James R Lupski %K Cerebral Palsy %K Epilepsy %K Humans %K Microcephaly %K Neurodevelopmental Disorders %K Nuclear Proteins %K Pedigree %K RNA Splicing %X

PURPOSE: Alternative splicing plays a critical role in mouse neurodevelopment, regulating neurogenesis, cortical lamination, and synaptogenesis, yet few human neurodevelopmental disorders are known to result from pathogenic variation in splicing regulator genes. Nuclear Speckle Splicing Regulator Protein 1 (NSRP1) is a ubiquitously expressed splicing regulator not known to underlie a Mendelian disorder.

METHODS: Exome sequencing and rare variant family-based genomics was performed as a part of the Baylor-Hopkins Center for Mendelian Genomics Initiative. Additional families were identified via GeneMatcher.

RESULTS: We identified six patients from three unrelated families with homozygous loss-of-function variants in NSRP1. Clinical features include developmental delay, epilepsy, variable microcephaly (Z-scores -0.95 to -5.60), hypotonia, and spastic cerebral palsy. Brain abnormalities included simplified gyral pattern, underopercularization, and/or vermian hypoplasia. Molecular analysis identified three pathogenic NSRP1 predicted loss-of-function variant alleles: c.1359_1362delAAAG (p.Glu455AlafsTer20), c.1272dupG (p.Lys425GlufsTer5), and c.52C>T (p.Gln18Ter). The two frameshift variants result in a premature termination codon in the last exon, and the mutant transcripts are predicted to escape nonsense mediated decay and cause loss of a C-terminal nuclear localization signal required for NSRP1 function.

CONCLUSION: We establish NSRP1 as a gene for a severe autosomal recessive neurodevelopmental disease trait characterized by developmental delay, epilepsy, microcephaly, and spastic cerebral palsy.

%B Genet Med %V 23 %P 2455-2460 %8 2021 Dec %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/34385670?dopt=Abstract %R 10.1038/s41436-021-01291-x %0 Journal Article %J Neurol Genet %D 2021 %T Biallelic Pathogenic Variants in Associated With Congenital Myopathy. %A Calame, Daniel G %A Fatih, Jawid %A Herman, Isabella %A Akdemir, Zeynep Coban %A Du, Haowei %A Jhangiani, Shalini N %A Richard A Gibbs %A Marafi, Dana %A Pehlivan, Davut %A Posey, Jennifer E %A Lotze, Timothy %A Mancias, Pedro %A Bhattacharjee, Meenakshi Bidwai %A James R Lupski %X

OBJECTIVE: Pathogenic variants in , the gene encoding fast skeletal muscle troponin T, were first described in autosomal dominant distal arthrogryposis type 2B2. Recently, a homozygous splice site variant, c.681+1G>A, was identified in a patient with nemaline myopathy and distal arthrogryposis. Here, we describe the second individual with congenital myopathy associated with biallelic variants.

METHODS: Clinical exome sequencing data from a patient with molecularly undiagnosed congenital myopathy underwent research reanalysis. Clinical and histopathologic data were collected and compared with the single reported patient with -related congenital myopathy.

RESULTS: A homozygous variant, c.481-1G>A, was identified. This variant alters a consensus splice acceptor and is predicted to affect splicing by multiple prediction tools. Both the patient reported here and the previously published patient exhibited limb, bulbar, and respiratory muscle weakness from birth, which improved over time. Other shared features include history of polyhydramnios, hypotonia, scoliosis, and high-arched palate. Distal arthrogryposis and nemaline rods, findings reported in the first patient with -related congenital myopathy, were not observed in the patient reported here.

CONCLUSIONS: This report provides further evidence for the association of biallelic variants with severe recessive congenital myopathy with or without nemaline rods and distal arthrogryposis. sequencing and copy number analysis should be incorporated into the workup of congenital myopathies.

%B Neurol Genet %V 7 %P e589 %8 2021 Jun %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/33977145?dopt=Abstract %R 10.1212/NXG.0000000000000589 %0 Journal Article %J Front Genet %D 2021 %T Chromoanagenesis Event Underlies a Pericentric and Multiple Paracentric Inversions in a Single Chromosome Causing Coffin-Siris Syndrome. %A Grochowski, Christopher M %A Krepischi, Ana C V %A Eisfeldt, Jesper %A Du, Haowei %A Bertola, Debora R %A Oliveira, Danyllo %A Costa, Silvia S %A James R Lupski %A Lindstrand, Anna %A Carvalho, Claudia M B %X

Chromoanagenesis is a descriptive term that encompasses classes of catastrophic mutagenic processes that generate localized and complex chromosome rearrangements in both somatic and germline genomes. Herein, we describe a 5-year-old female presenting with a constellation of clinical features consistent with a clinical diagnosis of Coffin-Siris syndrome 1 (CSS1). Initial G-banded karyotyping detected a 90-Mb pericentric and a 47-Mb paracentric inversion on a single chromosome. Subsequent analysis of short-read whole-genome sequencing data and genomic optical mapping revealed additional inversions, all clustered on chromosome 6, one of them disrupting for which haploinsufficiency leads to the CSS1 disease trait (MIM:135900). The aggregate structural variant data show that the resolved, the resolved derivative chromosome architecture presents four inversions, one pericentric and three paracentric, involving six breakpoint junctions in what appears to be a shuffling of genomic material on this chromosome. Each junction was resolved to nucleotide-level resolution with mutational signatures suggestive of non-homologous end joining. The disruption of the gene is shown to occur between the fourth and fifth exon of the canonical transcript with subsequent qPCR studies confirming a decrease in expression in the patient versus healthy controls. Deciphering the underlying genomic architecture of chromosomal rearrangements and complex structural variants may require multiple technologies and can be critical to elucidating the molecular etiology of a patient's clinical phenotype or resolving unsolved Mendelian disease cases.

%B Front Genet %V 12 %P 708348 %8 2021 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/34512724?dopt=Abstract %R 10.3389/fgene.2021.708348 %0 Journal Article %J Am J Med Genet A %D 2021 %T Clan genomics: From OMIM phenotypic traits to genes and biology. %A James R Lupski %K Computational Biology %K Databases, Genetic %K Genetic Diseases, Inborn %K Genetics, Medical %K Genomics %K Humans %K Phenotype %X

Clinical characterization of a patient phenotype has been the quintessential approach for elucidating a differential diagnosis and a hypothesis to explore a potential clinical diagnosis. This has resulted in a language of medicine and a semantic ontology, with both specialty- and subspecialty-specific lexicons, that can be challenging to translate and interpret. There is no 'Rosetta Stone' of clinical medicine such as the genetic code that can assist translation and interpretation of the language of genetics. Nevertheless, the information content embodied within a clinical diagnosis can guide management, therapeutic intervention, and potentially prognostic outlook of disease enabling anticipatory guidance for patients and families. Clinical genomics is now established firmly in medical practice. The granularity and informative content of a personal genome is immense. Yet, we are limited in our utility of much of that personal genome information by the lack of functional characterization of the overwhelming majority of computationally annotated genes in the haploid human reference genome sequence. Whereas DNA and the genetic code have provided a 'Rosetta Stone' to translate genetic variant information, clinical medicine, and clinical genomics provide the context to understand human biology and disease. A path forward will integrate deep phenotyping, such as available in a clinical synopsis in the Online Mendelian Inheritance in Man (OMIM) entries, with personal genome analyses.

%B Am J Med Genet A %V 185 %P 3294-3313 %8 2021 Nov %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/34405553?dopt=Abstract %R 10.1002/ajmg.a.62434 %0 Journal Article %J Hum Mutat %D 2021 %T Clinical, neuroimaging, and molecular spectrum of TECPR2-associated hereditary sensory and autonomic neuropathy with intellectual disability. %A Neuser, Sonja %A Brechmann, Barbara %A Heimer, Gali %A Brösse, Ines %A Schubert, Susanna %A O'Grady, Lauren %A Zech, Michael %A Srivastava, Siddharth %A Sweetser, David A %A Dincer, Yasemin %A Mall, Volker %A Winkelmann, Juliane %A Behrends, Christian %A Darras, Basil T %A Graham, Robert J %A Jayakar, Parul %A Byrne, Barry %A Bar-Aluma, Bat El %A Haberman, Yael %A Szeinberg, Amir %A Aldhalaan, Hesham M %A Hashem, Mais %A Al Tenaiji, Amal %A Ismayl, Omar %A Al Nuaimi, Asma E %A Maher, Karima %A Ibrahim, Shahnaz %A Khan, Fatima %A Houlden, Henry %A Ramakumaran, Vijayalakshmi S %A Pagnamenta, Alistair T %A Posey, Jennifer E %A James R Lupski %A Tan, Wen-Hann %A ElGhazali, Gehad %A Herman, Isabella %A Muñoz, Tatiana %A Repetto, Gabriela M %A Seitz, Angelika %A Krumbiegel, Mandy %A Poli, Maria Cecilia %A Kini, Usha %A Efthymiou, Stephanie %A Meiler, Jens %A Maroofian, Reza %A Alkuraya, Fowzan S %A Abou Jamra, Rami %A Popp, Bernt %A Ben-Zeev, Bruria %A Ebrahimi-Fakhari, Darius %K Adolescent %K Carrier Proteins %K Child %K Child, Preschool %K Cohort Studies %K Cross-Sectional Studies %K Family %K Female %K Hereditary Sensory and Autonomic Neuropathies %K Humans %K Infant %K Intellectual Disability %K Magnetic Resonance Imaging %K Male %K Models, Molecular %K Mutation, Missense %K Nerve Tissue Proteins %K Neuroimaging %K Pedigree %K Phenotype %K Protein Conformation %X

Bi-allelic TECPR2 variants have been associated with a complex syndrome with features of both a neurodevelopmental and neurodegenerative disorder. Here, we provide a comprehensive clinical description and variant interpretation framework for this genetic locus. Through international collaboration, we identified 17 individuals from 15 families with bi-allelic TECPR2-variants. We systemically reviewed clinical and molecular data from this cohort and 11 cases previously reported. Phenotypes were standardized using Human Phenotype Ontology terms. A cross-sectional analysis revealed global developmental delay/intellectual disability, muscular hypotonia, ataxia, hyporeflexia, respiratory infections, and central/nocturnal hypopnea as core manifestations. A review of brain magnetic resonance imaging scans demonstrated a thin corpus callosum in 52%. We evaluated 17 distinct variants. Missense variants in TECPR2 are predominantly located in the N- and C-terminal regions containing β-propeller repeats. Despite constituting nearly half of disease-associated TECPR2 variants, classifying missense variants as (likely) pathogenic according to ACMG criteria remains challenging. We estimate a pathogenic variant carrier frequency of 1/1221 in the general and 1/155 in the Jewish Ashkenazi populations. Based on clinical, neuroimaging, and genetic data, we provide recommendations for variant reporting, clinical assessment, and surveillance/treatment of individuals with TECPR2-associated disorder. This sets the stage for future prospective natural history studies.

%B Hum Mutat %V 42 %P 762-776 %8 2021 Jun %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/33847017?dopt=Abstract %R 10.1002/humu.24206 %0 Journal Article %J Am J Med Genet A %D 2021 %T Clinical presentation and evolution of Xia-Gibbs syndrome due to p.Gly375ArgfsTer3 variant in a patient from DR Congo (Central Africa). %A Mubungu, Gerrye %A Makay, Prince %A Boujemla, Bouchra %A Yanda, Stephane %A Posey, Jennifer E %A James R Lupski %A Bours, Vincent %A Lukusa, Prosper %A Devriendt, Koenraad %A Lumaka, Aimé %K Abnormalities, Multiple %K Agenesis of Corpus Callosum %K Attention Deficit Disorder with Hyperactivity %K Child %K Democratic Republic of the Congo %K Developmental Disabilities %K DNA-Binding Proteins %K Exome Sequencing %K Face %K Frameshift Mutation %K Humans %K Intellectual Disability %K Language Development Disorders %K Male %K Mitral Valve Insufficiency %K Palate %K Syndrome %K Talipes Cavus %X

Xia-Gibbs syndrome (XGS) is a very rare genetic condition. The clinical spectrum is very broad and variable. The phenotype and evolution in a Congolese boy with XGS have been reported. At 6 years he had speech delay, drooling, marked hyperactivity, attention deficit, aggressive behavior, and intellectual disability. Dysmorphological evaluation revealed strabismus, mild unilateral ptosis, uplifted ear lobes, flat philtrum, thin upper lip vermillion, high arched palate, and flat feet. Patient-only whole exome sequencing identified a known pathogenic frameshift variant in the AHDC1 gene [NM_001029882.3(AHDC1):c.1122dupC;(p.Gly375ArgfsTer3)]. The clinical follow-up revealed the deterioration of his fine motor skills and significant cerebellar phenotype including tremor, pes cavus, and gait instability at the age of 12 years. This patient was compared with three previously reported patients with the same variant but did not identify a consistent pattern in the evolution of symptoms with age.

%B Am J Med Genet A %V 185 %P 990-994 %8 2021 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/33372375?dopt=Abstract %R 10.1002/ajmg.a.62049 %0 Journal Article %J NPJ Genom Med %D 2021 %T De novo variants in H3-3A and H3-3B are associated with neurodevelopmental delay, dysmorphic features, and structural brain abnormalities. %A Okur, Volkan %A Chen, Zefu %A Vossaert, Liesbeth %A Peacock, Sandra %A Rosenfeld, Jill %A Zhao, Lina %A Du, Haowei %A Calamaro, Emily %A Gerard, Amanda %A Zhao, Sen %A Kelsay, Jill %A Lahr, Ashley %A Mighton, Chloe %A Porter, Hillary M %A Siemon, Amy %A Silver, Josh %A Svihovec, Shayna %A Fong, Chin-To %A Grant, Christina L %A Lerner-Ellis, Jordan %A Manickam, Kandamurugu %A Madan-Khetarpal, Suneeta %A McCandless, Shawn E %A Morel, Chantal F %A Schaefer, G Bradley %A Berry-Kravis, Elizabeth M %A Gates, Ryan %A Gomez-Ospina, Natalia %A Qiu, Guixing %A Zhang, Terry Jianguo %A Wu, Zhihong %A Meng, Linyan %A Liu, Pengfei %A Scott, Daryl A %A James R Lupski %A Eng, Christine M %A Wu, Nan %A Bo Yuan %X

The histone H3 variant H3.3, encoded by two genes H3-3A and H3-3B, can replace canonical isoforms H3.1 and H3.2. H3.3 is important in chromatin compaction, early embryonic development, and lineage commitment. The role of H3.3 in somatic cancers has been studied extensively, but its association with a congenital disorder has emerged just recently. Here we report eleven de novo missense variants and one de novo stop-loss variant in H3-3A (n = 6) and H3-3B (n = 6) from Baylor Genetics exome cohort (n = 11) and Matchmaker Exchange (n = 1), of which detailed phenotyping was conducted for 10 individuals (H3-3A = 4 and H3-3B = 6) that showed major phenotypes including global developmental delay, short stature, failure to thrive, dysmorphic facial features, structural brain abnormalities, hypotonia, and visual impairment. Three variant constructs (p.R129H, p.M121I, and p.I52N) showed significant decrease in protein expression, while one variant (p.R41C) accumulated at greater levels than wild-type control. One H3.3 variant construct (p.R129H) was found to have stronger interaction with the chaperone death domain-associated protein 6.

%B NPJ Genom Med %V 6 %P 104 %8 2021 Dec 07 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/34876591?dopt=Abstract %R 10.1038/s41525-021-00268-8 %0 Journal Article %J Ann Clin Transl Neurol %D 2021 %T Deep clinicopathological phenotyping identifies a previously unrecognized pathogenic EMD splice variant. %A Calame, Daniel G %A Fatih, Jawid M %A Herman, Isabella %A Coban-Akdemir, Zeynep %A Du, Haowei %A Mitani, Tadahiro %A Jhangiani, Shalini N %A Marafi, Dana %A Richard A Gibbs %A Posey, Jennifer E %A Mehta, Vidya P %A Mohila, Carrie A %A Abid, Farida %A Lotze, Timothy E %A Pehlivan, Davut %A Adesina, Adekunle M %A James R Lupski %K Adult %K Exome Sequencing %K Humans %K Male %K Membrane Proteins %K Muscle, Skeletal %K Muscular Dystrophy, Emery-Dreifuss %K Nuclear Proteins %K Young Adult %X

Exome sequencing (ES) has revolutionized rare disease management, yet only ~25%-30% of patients receive a molecular diagnosis. A limiting factor is the quality of available phenotypic data. Here, we describe how deep clinicopathological phenotyping yielded a molecular diagnosis for a 19-year-old proband with muscular dystrophy and negative clinical ES. Deep phenotypic analysis identified two critical data points: (1) the absence of emerin protein in muscle biopsy and (2) clinical features consistent with Emery-Dreifuss muscular dystrophy. Sequencing data analysis uncovered an ultra-rare, intronic variant in EMD, the gene encoding emerin. The variant, NM_000117.3: c.188-6A > G, is predicted to impact splicing by in silico tools. This case thus illustrates how better integration of clinicopathologic data into ES analysis can enhance diagnostic yield with implications for clinical practice.

%B Ann Clin Transl Neurol %V 8 %P 2052-2058 %8 2021 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/34524739?dopt=Abstract %R 10.1002/acn3.51454 %0 Journal Article %J Genet Med %D 2021 %T Delineating the molecular and phenotypic spectrum of the SETD1B-related syndrome. %A Weerts, Marjolein J A %A Lanko, Kristina %A Guzmán-Vega, Francisco J %A Jackson, Adam %A Ramakrishnan, Reshmi %A Cardona-Londoño, Kelly J %A Peña-Guerra, Karla A %A van Bever, Yolande %A van Paassen, Barbara W %A Kievit, Anneke %A van Slegtenhorst, Marjon %A Allen, Nicholas M %A Kehoe, Caroline M %A Robinson, Hannah K %A Pang, Lewis %A Banu, Selina H %A Zaman, Mashaya %A Efthymiou, Stephanie %A Houlden, Henry %A Järvelä, Irma %A Lauronen, Leena %A Määttä, Tuomo %A Schrauwen, Isabelle %A Leal, Suzanne M %A Ruivenkamp, Claudia A L %A Barge-Schaapveld, Daniela Q C M %A Peeters-Scholte, Cacha M P C D %A Galehdari, Hamid %A Mazaheri, Neda %A Sisodiya, Sanjay M %A Harrison, Victoria %A Sun, Angela %A Thies, Jenny %A Pedroza, Luis Alberto %A Lara-Taranchenko, Yana %A Chinn, Ivan K %A James R Lupski %A Garza-Flores, Alexandra %A McGlothlin, Jeffery %A Yang, Lin %A Huang, Shaoping %A Wang, Xiaodong %A Jewett, Tamison %A Rosso, Gretchen %A Lin, Xi %A Mohammed, Shehla %A Merritt, J Lawrence %A Mirzaa, Ghayda M %A Timms, Andrew E %A Scheck, Joshua %A Elting, Mariet W %A Polstra, Abeltje M %A Schenck, Lauren %A Ruzhnikov, Maura R Z %A Vetro, Annalisa %A Montomoli, Martino %A Guerrini, Renzo %A Koboldt, Daniel C %A Mosher, Theresa Mihalic %A Pastore, Matthew T %A McBride, Kim L %A Peng, Jing %A Pan, Zou %A Willemsen, Marjolein %A Koning, Susanne %A Turnpenny, Peter D %A de Vries, Bert B A %A Gilissen, Christian %A Pfundt, Rolph %A Lees, Melissa %A Braddock, Stephen R %A Klemp, Kara C %A Vansenne, Fleur %A van Gijn, Marielle E %A Quindipan, Catherine %A Deardorff, Matthew A %A Hamm, J Austin %A Putnam, Abbey M %A Baud, Rebecca %A Walsh, Laurence %A Lynch, Sally A %A Baptista, Julia %A Person, Richard E %A Monaghan, Kristin G %A Crunk, Amy %A Keller-Ramey, Jennifer %A Reich, Adi %A Elloumi, Houda Zghal %A Alders, Marielle %A Kerkhof, Jennifer %A McConkey, Haley %A Haghshenas, Sadegheh %A Maroofian, Reza %A Sadikovic, Bekim %A Banka, Siddharth %A Arold, Stefan T %A Barakat, Tahsin Stefan %K Epilepsy %K Histone-Lysine N-Methyltransferase %K Humans %K Intellectual Disability %K Male %K Neurodevelopmental Disorders %K Phenotype %K Seizures %X

PURPOSE: Pathogenic variants in SETD1B have been associated with a syndromic neurodevelopmental disorder including intellectual disability, language delay, and seizures. To date, clinical features have been described for 11 patients with (likely) pathogenic SETD1B sequence variants. This study aims to further delineate the spectrum of the SETD1B-related syndrome based on characterizing an expanded patient cohort.

METHODS: We perform an in-depth clinical characterization of a cohort of 36 unpublished individuals with SETD1B sequence variants, describing their molecular and phenotypic spectrum. Selected variants were functionally tested using in vitro and genome-wide methylation assays.

RESULTS: Our data present evidence for a loss-of-function mechanism of SETD1B variants, resulting in a core clinical phenotype of global developmental delay, language delay including regression, intellectual disability, autism and other behavioral issues, and variable epilepsy phenotypes. Developmental delay appeared to precede seizure onset, suggesting SETD1B dysfunction impacts physiological neurodevelopment even in the absence of epileptic activity. Males are significantly overrepresented and more severely affected, and we speculate that sex-linked traits could affect susceptibility to penetrance and the clinical spectrum of SETD1B variants.

CONCLUSION: Insights from this extensive cohort will facilitate the counseling regarding the molecular and phenotypic landscape of newly diagnosed patients with the SETD1B-related syndrome.

%B Genet Med %V 23 %P 2122-2137 %8 2021 Nov %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/34345025?dopt=Abstract %R 10.1038/s41436-021-01246-2 %0 Journal Article %J J Med Genet %D 2021 %T Diagnostic yield and clinical impact of exome sequencing in early-onset scoliosis (EOS). %A Zhao, Sen %A Zhang, Yuanqiang %A Chen, Weisheng %A Li, Weiyu %A Wang, Shengru %A Wang, Lianlei %A Zhao, Yanxue %A Lin, Mao %A Ye, Yongyu %A Lin, Jiachen %A Zheng, Yu %A Liu, Jiaqi %A Zhao, Hengqiang %A Yan, Zihui %A Yang, Yongxin %A Huang, Yingzhao %A Lin, Guanfeng %A Chen, Zefu %A Zhang, Zhen %A Liu, Sen %A Jin, Lichao %A Wang, Zhaoyang %A Chen, Jingdan %A Niu, Yuchen %A Li, Xiaoxin %A Wu, Yong %A Wang, Yipeng %A Du, Renqian %A Gao, Na %A Zhao, Hong %A Yang, Ying %A Liu, Ying %A Tian, Ye %A Li, Wenli %A Zhao, Yu %A Liu, Jia %A Yu, Bin %A Zhang, Na %A Yu, Keyi %A Yang, Xu %A Li, Shugang %A Xu, Yuan %A Hu, Jianhua %A Liu, Zhe %A Shen, Jianxiong %A Zhang, Shuyang %A Su, Jianzhong %A Khanshour, Anas M %A Kidane, Yared H %A Ramo, Brandon %A Rios, Jonathan J %A Liu, Pengfei %A Sutton, V Reid %A Posey, Jennifer E %A Wu, Zhihong %A Qiu, Guixing %A Wise, Carol A %A Zhang, Feng %A James R Lupski %A Zhang, Jianguo %A Wu, Nan %K Adolescent %K Adult %K Age of Onset %K Child, Preschool %K China %K Cohort Studies %K Exome %K Exome Sequencing %K Female %K Genetic Predisposition to Disease %K Humans %K Male %K Retrospective Studies %K Scoliosis %X

BACKGROUND: Early-onset scoliosis (EOS), defined by an onset age of scoliosis less than 10 years, conveys significant health risk to affected children. Identification of the molecular aetiology underlying patients with EOS could provide valuable information for both clinical management and prenatal screening.

METHODS: In this study, we consecutively recruited a cohort of 447 Chinese patients with operative EOS. We performed exome sequencing (ES) screening on these individuals and their available family members (totaling 670 subjects). Another cohort of 13 patients with idiopathic early-onset scoliosis (IEOS) from the USA who underwent ES was also recruited.

RESULTS: After ES data processing and variant interpretation, we detected molecular diagnostic variants in 92 out of 447 (20.6%) Chinese patients with EOS, including 8 patients with molecular confirmation of their clinical diagnosis and 84 patients with molecular diagnoses of previously unrecognised diseases underlying scoliosis. One out of 13 patients with IEOS from the US cohort was molecularly diagnosed. The age at presentation, the number of organ systems involved and the Cobb angle were the three top features predictive of a molecular diagnosis.

CONCLUSION: ES enabled the molecular diagnosis/classification of patients with EOS. Specific clinical features/feature pairs are able to indicate the likelihood of gaining a molecular diagnosis through ES.

%B J Med Genet %V 58 %P 41-47 %8 2021 Jan %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/32381727?dopt=Abstract %R 10.1136/jmedgenet-2019-106823 %0 Journal Article %J Parkinsonism Relat Disord %D 2021 %T Dominant mitochondrial membrane protein-associated neurodegeneration (MPAN) variants cluster within a specific C19orf12 isoform. %A Rickman, Olivia J %A Salter, Claire G %A Gunning, Adam C %A Fasham, James %A Voutsina, Nikol %A Leslie, Joseph S %A McGavin, Lucy %A Cross, Harold E %A Posey, Jennifer E %A Akdemir, Zeynep Coban %A Jhangiani, Shalini N %A James R Lupski %A Baple, Emma L %A Crosby, Andrew H %K Amish %K Humans %K Iron Metabolism Disorders %K Loss of Function Mutation %K Magnetic Resonance Imaging %K Membrane Proteins %K Mitochondrial Membranes %K Mitochondrial Proteins %K Neuroaxonal Dystrophies %K Pedigree %K Protein Isoforms %X

Mitochondria membrane protein-associated neurodegeneration (MPAN) neurodegenerative disorder is typically associated with biallelic C19orf12 variants. Here we describe a new and review candidate previous monoallelic de novo C19orf12 variants to define loss of function mutations located in the putative non-membrane spanning C19orf12 isoform as the potential basis of monoallelic MPAN.

%B Parkinsonism Relat Disord %V 82 %P 84-86 %8 2021 Jan %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/33260061?dopt=Abstract %R 10.1016/j.parkreldis.2020.10.041 %0 Journal Article %J J Genet Genomics %D 2021 %T Exome sequencing reveals genetic architecture in patients with isolated or syndromic short stature. %A Fan, Xin %A Zhao, Sen %A Yu, Chenxi %A Wu, Di %A Yan, Zihui %A Fan, Lijun %A Song, Yanning %A Wang, Yi %A Li, Chuan %A Ming, Yue %A Gui, Baoheng %A Niu, Yuchen %A Li, Xiaoxin %A Yang, Xinzhuang %A Luo, Shiyu %A Zhang, Qiang %A Zhao, Xiuli %A Pan, Hui %A Li, Mei %A Xia, Weibo %A Qiu, Guixing %A Liu, Pengfei %A Zhang, Shuyang %A Zhang, Jianguo %A Wu, Zhihong %A James R Lupski %A Posey, Jennifer E %A Chen, Shaoke %A Gong, Chunxiu %A Wu, Nan %K Adolescent %K Alleles %K Child %K Child, Preschool %K China %K Disease Management %K DNA Copy Number Variations %K Dwarfism %K Exome %K Exome Sequencing %K Female %K Genetic Association Studies %K Genetic Predisposition to Disease %K Genetic Testing %K Genotype %K Humans %K Male %K Mutation %K Odds Ratio %K Phenotype %K Polymorphism, Single Nucleotide %K Syndrome %X

Short stature is among the most common endocrinological disease phenotypes of childhood and may occur as an isolated finding or in conjunction with other clinical manifestations. Although the diagnostic utility of clinical genetic testing in short stature has been implicated, the genetic architecture and the utility of genomic studies such as exome sequencing (ES) in a sizable cohort of patients with short stature have not been investigated systematically. In this study, we recruited 561 individuals with short stature from two centers in China during a 4-year period. We performed ES for all patients and available parents. All patients were retrospectively divided into two groups: an isolated short stature group (group I, n = 257) and an apparently syndromic short stature group (group II, n = 304). Causal variants were identified in 135 of 561 (24.1%) patients. In group I, 29 of 257 (11.3%) of the patients were solved by variants in 24 genes. In group II, 106 of 304 (34.9%) patients were solved by variants in 57 genes. Genes involved in fundamental cellular process played an important role in the genetic architecture of syndromic short stature. Distinct genetic architectures and pathophysiological processes underlie isolated and syndromic short stature.

%B J Genet Genomics %V 48 %P 396-402 %8 2021 May 20 %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/34006472?dopt=Abstract %R 10.1016/j.jgg.2021.02.008 %0 Journal Article %J Hum Genet %D 2021 %T Exome sequencing reveals predominantly de novo variants in disorders with intellectual disability (ID) in the founder population of Finland. %A Järvelä, Irma %A Määttä, Tuomo %A Acharya, Anushree %A Leppälä, Juha %A Jhangiani, Shalini N %A Arvio, Maria %A Siren, Auli %A Kankuri-Tammilehto, Minna %A Kokkonen, Hannaleena %A Palomäki, Maarit %A Varilo, Teppo %A Fang, Mary %A Hadley, Trevor D %A Jolly, Angad %A Linnankivi, Tarja %A Paetau, Ritva %A Saarela, Anni %A Kälviäinen, Reetta %A Olme, Jan %A Nouel-Saied, Liz M %A Cornejo-Sanchez, Diana M %A Llaci, Lorida %A James R Lupski %A Posey, Jennifer E %A Leal, Suzanne M %A Schrauwen, Isabelle %K Exome %K Exome Sequencing %K Family %K Female %K Finland %K Genes, Recessive %K Genetic Predisposition to Disease %K Genotype %K Homozygote %K Humans %K Intellectual Disability %K Male %K Pedigree %X

The genetics of autosomal recessive intellectual disability (ARID) has mainly been studied in consanguineous families, however, founder populations may also be of interest to study intellectual disability (ID) and the contribution of ARID. Here, we used a genotype-driven approach to study the genetic landscape of ID in the founder population of Finland. A total of 39 families with syndromic and non-syndromic ID were analyzed using exome sequencing, which revealed a variant in a known ID gene in 27 families. Notably, 75% of these variants in known ID genes were de novo or suspected de novo (64% autosomal dominant; 11% X-linked) and 25% were inherited (14% autosomal recessive; 7% X-linked; and 4% autosomal dominant). A dual molecular diagnosis was suggested in two families (5%). Via additional analysis and molecular testing, we identified three cases with an abnormal molecular karyotype, including chr21q22.12q22.2 uniparental disomy with a mosaic interstitial 2.7 Mb deletion covering DYRK1A and KCNJ6. Overall, a pathogenic or likely pathogenic variant was identified in 64% (25/39) of the families. Last, we report an alternate inheritance model for 3 known ID genes (UBA7, DDX47, DHX58) and discuss potential candidate genes for ID, including SYPL1 and ERGIC3 with homozygous founder variants and de novo variants in POLR2F and DNAH3. In summary, similar to other European populations, de novo variants were the most common variants underlying ID in the studied Finnish population, with limited contribution of ARID to ID etiology, though mainly driven by founder and potential founder variation in the latter case.

%B Hum Genet %V 140 %P 1011-1029 %8 2021 Jul %G eng %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/33710394?dopt=Abstract %R 10.1007/s00439-021-02268-1 %0 Journal Article %J Am J Hum Genet %D 2021 %T Exome variant discrepancies due to reference-genome differences. %A Li, He %A Dawood, Moez %A Khayat, Michael M %A Farek, Jesse R %A Jhangiani, Shalini N %A Khan, Ziad M %A Mitani, Tadahiro %A Coban-Akdemir, Zeynep %A James R Lupski %A Eric Venner %A Posey, Jennifer E %A Aniko Sabo %A Richard A Gibbs %K Cohort Studies %K Exome %K Genetic Diseases, Inborn %K Genome, Human %K Humans %K Polymorphism, Single Nucleotide %K Reference Values %X

Despite release of the GRCh38 human reference genome more than seven years ago, GRCh37 remains more widely used by most research and clinical laboratories. To date, no study has quantified the impact of utilizing different reference assemblies for the identification of variants associated with rare and common diseases from large-scale exome-sequencing data. By calling variants on both the GRCh37 and GRCh38 references, we identified single-nucleotide variants (SNVs) and insertion-deletions (indels) in 1,572 exomes from participants with Mendelian diseases and their family members. We found that a total of 1.5% of SNVs and 2.0% of indels were discordant when different references were used. Notably, 76.6% of the discordant variants were clustered within discrete discordant reference patches (DISCREPs) comprising only 0.9% of loci targeted by exome sequencing. These DISCREPs were enriched for genomic elements including segmental duplications, fix patch sequences, and loci known to contain alternate haplotypes. We identified 206 genes significantly enriched for discordant variants, most of which were in DISCREPs and caused by multi-mapped reads on the reference assembly that lacked the variant call. Among these 206 genes, eight are implicated in known Mendelian diseases and 53 are associated with common phenotypes from genome-wide association studies. In addition, variant interpretations could also be influenced by the reference after lifting-over variant loci to another assembly. Overall, we identified genes and genomic loci affected by reference assembly choice, including genes associated with Mendelian disorders and complex human diseases that require careful evaluation in both research and clinical applications.

%B Am J Hum Genet %V 108 %P 1239-1250 %8 2021 Jul 01 %G eng %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/34129815?dopt=Abstract %R 10.1016/j.ajhg.2021.05.011 %0 Journal Article %J Genome Med %D 2021 %T Functional interpretation of ATAD3A variants in neuro-mitochondrial phenotypes. %A Yap, Zheng Yie %A Park, Yo Han %A Wortmann, Saskia B %A Gunning, Adam C %A Ezer, Shlomit %A Lee, Sukyeong %A Duraine, Lita %A Wilichowski, Ekkehard %A Wilson, Kate %A Mayr, Johannes A %A Wagner, Matias %A Li, Hong %A Kini, Usha %A Black, Emily Davis %A Monaghan, Kristin G %A James R Lupski %A Ellard, Sian %A Westphal, Dominik S %A Harel, Tamar %A Yoon, Wan Hee %K Adolescent %K Alleles %K Amino Acid Sequence %K Animals %K ATPases Associated with Diverse Cellular Activities %K Autophagy %K Computer Simulation %K Drosophila %K Female %K Genetic Variation %K Humans %K Infant %K Infant, Newborn %K Locomotion %K Male %K Membrane Proteins %K Mitochondria %K Mitochondrial Proteins %K Mitophagy %K Mutation, Missense %K Neurogenesis %K Neurons %K Pedigree %K Phenotype %K Polymorphism, Single Nucleotide %K Young Adult %X

BACKGROUND: ATPase family AAA-domain containing protein 3A (ATAD3A) is a nuclear-encoded mitochondrial membrane-anchored protein involved in diverse processes including mitochondrial dynamics, mitochondrial DNA organization, and cholesterol metabolism. Biallelic deletions (null), recessive missense variants (hypomorph), and heterozygous missense variants or duplications (antimorph) in ATAD3A lead to neurological syndromes in humans.

METHODS: To expand the mutational spectrum of ATAD3A variants and to provide functional interpretation of missense alleles in trans to deletion alleles, we performed exome sequencing for identification of single nucleotide variants (SNVs) and copy number variants (CNVs) in ATAD3A in individuals with neurological and mitochondrial phenotypes. A Drosophila Atad3a Gal4 knockin-null allele was generated using CRISPR-Cas9 genome editing technology to aid the interpretation of variants.

RESULTS: We report 13 individuals from 8 unrelated families with biallelic ATAD3A variants. The variants included four missense variants inherited in trans to loss-of-function alleles (p.(Leu77Val), p.(Phe50Leu), p.(Arg170Trp), p.(Gly236Val)), a homozygous missense variant p.(Arg327Pro), and a heterozygous non-frameshift indel p.(Lys568del). Affected individuals exhibited findings previously associated with ATAD3A pathogenic variation, including developmental delay, hypotonia, congenital cataracts, hypertrophic cardiomyopathy, and cerebellar atrophy. Drosophila studies indicated that Phe50Leu, Gly236Val, Arg327Pro, and Lys568del are severe loss-of-function alleles leading to early developmental lethality. Further, we showed that Phe50Leu, Gly236Val, and Arg327Pro cause neurogenesis defects. On the contrary, Leu77Val and Arg170Trp are partial loss-of-function alleles that cause progressive locomotion defects and whose expression leads to an increase in autophagy and mitophagy in adult muscles.

CONCLUSION: Our findings expand the allelic spectrum of ATAD3A variants and exemplify the use of a functional assay in Drosophila to aid variant interpretation.

%B Genome Med %V 13 %P 55 %8 2021 Apr 12 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/33845882?dopt=Abstract %R 10.1186/s13073-021-00873-3 %0 Journal Article %J HGG Adv %D 2021 %T Germline mutation in : a heterogeneous, multi-systemic developmental disorder characterized by transcriptional dysregulation. %A Hansen, Adam W %A Arora, Payal %A Khayat, Michael M %A Smith, Leah J %A Lewis, Andrea M %A Rossetti, Linda Z %A Jayaseelan, Joy %A Cristian, Ingrid %A Haynes, Devon %A DiTroia, Stephanie %A Meeks, Naomi %A Delgado, Mauricio R %A Rosenfeld, Jill A %A Pais, Lynn %A White, Susan M %A Meng, Qingchang %A Pehlivan, Davut %A Liu, Pengfei %A Marie-Claude Gingras %A Wangler, Michael F %A Donna M Muzny %A James R Lupski %A Kaplan, Craig D %A Richard A Gibbs %X

germline variation in was recently reported to associate with a neurodevelopmental disorder. We report twelve individuals harboring putatively pathogenic or inherited variants in , detail their phenotypes, and map all known variants to the domain structure of and crystal structure of RNA polymerase II. Affected individuals were ascertained from a local data lake, pediatric genetics clinic, and an online community of families of affected individuals. These include six affected by missense variants (including one previously reported individual), four clinical laboratory samples affected by missense variation with unknown inheritance-with yeast functional assays further supporting altered function-one affected by a in-frame deletion, and one affected by a C-terminal frameshift variant inherited from a largely asymptomatic mother. Recurrently observed phenotypes include ataxia, joint hypermobility, short stature, skin abnormalities, congenital cardiac abnormalities, immune system abnormalities, hip dysplasia, and short Achilles tendons. We report a significantly higher occurrence of epilepsy (8/12, 66.7%) than previously reported (3/15, 20%) (p value = 0.014196; chi-square test) and a lower occurrence of hypotonia (8/12, 66.7%) than previously reported (14/15, 93.3%) (p value = 0.076309). -related developmental disorders likely represent a spectrum of related, multi-systemic developmental disorders, driven by distinct mechanisms, converging at a single locus.

%B HGG Adv %V 2 %8 2021 Jan 14 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/33665635?dopt=Abstract %R 10.1016/j.xhgg.2020.100014 %0 Journal Article %J Genet Med %D 2021 %T Haploinsufficiency of ARFGEF1 is associated with developmental delay, intellectual disability, and epilepsy with variable expressivity. %A Thomas, Quentin %A Gautier, Thierry %A Marafi, Dana %A Besnard, Thomas %A Willems, Marjolaine %A Moutton, Sebastien %A Isidor, Bertand %A Cogné, Benjamin %A Conrad, Solène %A Tenconi, Romano %A Iascone, Maria %A Sorlin, Arthur %A Masurel, Alice %A Dabir, Tabib %A Jackson, Adam %A Banka, Siddharth %A Delanne, Julian %A James R Lupski %A Saadi, Nebal Waill %A Alkuraya, Fowzan S %A Zahrani, Fatema Al %A Agrawal, Pankaj B %A England, Eleina %A Madden, Jill A %A Posey, Jennifer E %A Burglen, Lydie %A Rodriguez, Diana %A Chevarin, Martin %A Nguyen, Sylvie %A Mau-Them, Frédéric Tran %A Duffourd, Yannis %A Garret, Philippine %A Bruel, Ange-Line %A Callier, Patrick %A Marle, Nathalie %A Denommé-Pichon, Anne-Sophie %A Duplomb, Laurence %A Philippe, Christophe %A Thauvin-Robinet, Christel %A Govin, Jérôme %A Faivre, Laurence %A Vitobello, Antonio %K Epilepsy %K Guanine Nucleotide Exchange Factors %K Haploinsufficiency %K Heterozygote %K Humans %K Intellectual Disability %X

PURPOSE: ADP ribosylation factor guanine nucleotide exchange factors (ARFGEFs) are a family of proteins implicated in cellular trafficking between the Golgi apparatus and the plasma membrane through vesicle formation. Among them is ARFGEF1/BIG1, a protein involved in axon elongation, neurite development, and polarization processes. ARFGEF1 has been previously suggested as a candidate gene for different types of epilepsies, although its implication in human disease has not been well characterized.

METHODS: International data sharing, in silico predictions, and in vitro assays with minigene study, western blot analyses, and RNA sequencing.

RESULTS: We identified 13 individuals with heterozygous likely pathogenic variants in ARFGEF1. These individuals displayed congruent clinical features of developmental delay, behavioral problems, abnormal findings on brain magnetic resonance image (MRI), and epilepsy for almost half of them. While nearly half of the cohort carried de novo variants, at least 40% of variants were inherited from mildly affected parents who were clinically re-evaluated by reverse phenotyping. Our in silico predictions and in vitro assays support the contention that ARFGEF1-related conditions are caused by haploinsufficiency, and are transmitted in an autosomal dominant fashion with variable expressivity.

CONCLUSION: We provide evidence that loss-of-function variants in ARFGEF1 are implicated in sporadic and familial cases of developmental delay with or without epilepsy.

%B Genet Med %V 23 %P 1901-1911 %8 2021 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/34113008?dopt=Abstract %R 10.1038/s41436-021-01218-6 %0 Journal Article %J Am J Hum Genet %D 2021 %T High prevalence of multilocus pathogenic variation in neurodevelopmental disorders in the Turkish population. %A Mitani, Tadahiro %A Isikay, Sedat %A Gezdirici, Alper %A Gulec, Elif Yilmaz %A Punetha, Jaya %A Fatih, Jawid M %A Herman, Isabella %A Akay, Gulsen %A Du, Haowei %A Calame, Daniel G %A Ayaz, Akif %A Tos, Tulay %A Yesil, Gozde %A Aydin, Hatip %A Geckinli, Bilgen %A Elcioglu, Nursel %A Candan, Sukru %A Sezer, Ozlem %A Erdem, Haktan Bagis %A Gul, Davut %A Demiral, Emine %A Elmas, Muhsin %A Yesilbas, Osman %A Kilic, Betul %A Gungor, Serdal %A Ceylan, Ahmet C %A Bozdogan, Sevcan %A Ozalp, Ozge %A Cicek, Salih %A Aslan, Huseyin %A Yalcintepe, Sinem %A Topcu, Vehap %A Bayram, Yavuz %A Grochowski, Christopher M %A Jolly, Angad %A Dawood, Moez %A Duan, Ruizhi %A Jhangiani, Shalini N %A Harshavardhan Doddapaneni %A Jianhong Hu %A Donna M Muzny %A Marafi, Dana %A Akdemir, Zeynep Coban %A Karaca, Ender %A Carvalho, Claudia M B %A Richard A Gibbs %A Posey, Jennifer E %A James R Lupski %A Pehlivan, Davut %K Adolescent %K Adult %K Child %K Child, Preschool %K Cohort Studies %K Exome Sequencing %K Female %K Genomics %K Humans %K Infant %K Infant, Newborn %K Male %K Middle Aged %K Mutation %K Neurodevelopmental Disorders %K Pedigree %K Phenotype %K Prevalence %K Turkey %K Young Adult %X

Neurodevelopmental disorders (NDDs) are clinically and genetically heterogenous; many such disorders are secondary to perturbation in brain development and/or function. The prevalence of NDDs is > 3%, resulting in significant sociocultural and economic challenges to society. With recent advances in family-based genomics, rare-variant analyses, and further exploration of the Clan Genomics hypothesis, there has been a logarithmic explosion in neurogenetic "disease-associated genes" molecular etiology and biology of NDDs; however, the majority of NDDs remain molecularly undiagnosed. We applied genome-wide screening technologies, including exome sequencing (ES) and whole-genome sequencing (WGS), to identify the molecular etiology of 234 newly enrolled subjects and 20 previously unsolved Turkish NDD families. In 176 of the 234 studied families (75.2%), a plausible and genetically parsimonious molecular etiology was identified. Out of 176 solved families, deleterious variants were identified in 218 distinct genes, further documenting the enormous genetic heterogeneity and diverse perturbations in human biology underlying NDDs. We propose 86 candidate disease-trait-associated genes for an NDD phenotype. Importantly, on the basis of objective and internally established variant prioritization criteria, we identified 51 families (51/176 = 28.9%) with multilocus pathogenic variation (MPV), mostly driven by runs of homozygosity (ROHs) - reflecting genomic segments/haplotypes that are identical-by-descent. Furthermore, with the use of additional bioinformatic tools and expansion of ES to additional family members, we established a molecular diagnosis in 5 out of 20 families (25%) who remained undiagnosed in our previously studied NDD cohort emanating from Turkey.

%B Am J Hum Genet %V 108 %P 1981-2005 %8 2021 Oct 07 %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/34582790?dopt=Abstract %R 10.1016/j.ajhg.2021.08.009 %0 Journal Article %J Hum Genet %D 2021 %T IFIH1 loss-of-function variants contribute to very early-onset inflammatory bowel disease. %A Cananzi, Mara %A Wohler, Elizabeth %A Marzollo, Antonio %A Colavito, Davide %A You, Jing %A Jing, Huie %A Bresolin, Silvia %A Gaio, Paola %A Martin, Renan %A Mescoli, Claudia %A Bade, Sangeeta %A Posey, Jennifer E %A Dalle Carbonare, Maurizio %A Tung, Wesley %A Jhangiani, Shalini N %A Bosa, Luca %A Zhang, Yu %A Filho, Joselito Sobreira %A Gabelli, Maria %A Kellermayer, Richard %A Kader, Howard A %A Oliva-Hemker, Maria %A Perilongo, Giorgio %A James R Lupski %A Biffi, Alessandra %A Valle, David %A Leon, Alberta %A de Macena Sobreira, Nara Lygia %A Su, Helen C %A Guerrerio, Anthony L %K Child, Preschool %K Female %K Humans %K Infant %K Inflammatory Bowel Diseases %K Interferon-Induced Helicase, IFIH1 %K Italy %K Loss of Function Mutation %K Male %K Whole Genome Sequencing %X

Genetic defects of innate immunity impairing intestinal bacterial sensing are linked to the development of Inflammatory Bowel Disease (IBD). Although much evidence supports a role of the intestinal virome in gut homeostasis, most studies focus on intestinal viral composition rather than on host intestinal viral sensitivity. To demonstrate the association between the development of Very Early Onset IBD (VEOIBD) and variants in the IFIH1 gene which encodes MDA5, a key cytosolic sensor for viral nucleic acids. Whole exome sequencing (WES) was performed in two independent cohorts of children with VEOIBD enrolled in Italy (n = 18) and USA (n = 24). Luciferase reporter assays were employed to assess MDA5 activity. An enrichment analysis was performed on IFIH1 comparing 42 VEOIBD probands with 1527 unrelated individuals without gastrointestinal or immunological issues. We identified rare, likely loss-of-function (LoF), IFIH1 variants in eight patients with VEOIBD from a combined cohort of 42 children. One subject, carrying a homozygous truncating variant resulting in complete LoF, experienced neonatal-onset, pan-gastrointestinal, IBD-like enteropathy plus multiple infectious episodes. The remaining seven subjects, affected by VEOIBD without immunodeficiency, were carriers of one LoF variant in IFIH1. Among these, two patients also carried a second hypomorphic variant, with partial function apparent when MDA5 was weakly stimulated. Furthermore, IFIH1 variants were significantly enriched in children with VEOIBD as compared to controls (p = 0.007). Complete and partial MDA5 deficiency is associated with VEOIBD with variable penetrance and expressivity, suggesting a role for impaired intestinal viral sensing in IBD pathogenesis.

%B Hum Genet %V 140 %P 1299-1312 %8 2021 Sep %G eng %N 9 %1 https://www.ncbi.nlm.nih.gov/pubmed/34185153?dopt=Abstract %R 10.1007/s00439-021-02300-4 %0 Journal Article %J Front Pediatr %D 2021 %T Immune Dysregulation Mimicking Systemic Lupus Erythematosus in a Patient With Lysinuric Protein Intolerance: Case Report and Review of the Literature. %A Contreras, Josefina Longeri %A Ladino, Mabel A %A Aránguiz, Katherine %A Mendez, Gonzalo P %A Coban-Akdemir, Zeynep %A Bo Yuan %A Richard A Gibbs %A Burrage, Lindsay C %A James R Lupski %A Chinn, Ivan K %A Vogel, Tiphanie P %A Orange, Jordan S %A Poli, M Cecilia %X

Lysinuric protein intolerance (LPI) is an inborn error of metabolism caused by defective transport of cationic amino acids in epithelial cells of intestines, kidneys and other tissues as well as non-epithelial cells including macrophages. LPI is caused by biallelic, pathogenic variants in . The clinical phenotype of LPI includes failure to thrive and multi-system disease including hematologic, neurologic, pulmonary and renal manifestations. Individual presentations are extremely variable, often leading to misdiagnosis or delayed diagnosis. Here we describe a patient that clinically presented with immune dysregulation in the setting of early-onset systemic lupus erythematosus (SLE), including renal involvement, in whom an LPI diagnosis was suspected post-mortem based on exome sequencing analysis. A review of the literature was performed to provide an overview of the clinical spectrum and immune mechanisms involved in this disease. The precise mechanism by which ineffective amino acid transport triggers systemic inflammatory features is not yet understood. However, LPI should be considered in the differential diagnosis of early-onset SLE, particularly in the absence of response to immunosuppressive therapy.

%B Front Pediatr %V 9 %P 673957 %8 2021 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/34095032?dopt=Abstract %R 10.3389/fped.2021.673957 %0 Journal Article %J Am J Hum Genet %D 2021 %T Loss of C2orf69 defines a fatal autoinflammatory syndrome in humans and zebrafish that evokes a glycogen-storage-associated mitochondriopathy. %A Wong, Hui Hui %A Seet, Sze Hwee %A Maier, Michael %A Gurel, Ayse %A Traspas, Ricardo Moreno %A Lee, Cheryl %A Zhang, Shan %A Talim, Beril %A Loh, Abigail Y T %A Chia, Crystal Y %A Teoh, Tze Shin %A Sng, Danielle %A Rensvold, Jarred %A Unal, Sule %A Shishkova, Evgenia %A Cepni, Ece %A Nathan, Fatima M %A Sirota, Fernanda L %A Liang, Chao %A Yarali, Nese %A Simsek-Kiper, Pelin O %A Mitani, Tadahiro %A Ceylaner, Serdar %A Arman-Bilir, Ozlem %A Mbarek, Hamdi %A Gumruk, Fatma %A Efthymiou, Stephanie %A Uğurlu Çi Men, Deniz %A Georgiadou, Danai %A Sotiropoulou, Kortessa %A Houlden, Henry %A Paul, Franziska %A Pehlivan, Davut %A Lainé, Candice %A Chai, Guoliang %A Ali, Nur Ain %A Choo, Siew Chin %A Keng, Soh Sok %A Boisson, Bertrand %A Yılmaz, Elanur %A Xue, Shifeng %A Coon, Joshua J %A Ly, Thanh Thao Nguyen %A Gilani, Naser %A Hasbini, Dana %A Kayserili, Hulya %A Zaki, Maha S %A Isfort, Robert J %A Ordonez, Natalia %A Tripolszki, Kornelia %A Bauer, Peter %A Rezaei, Nima %A Seyedpour, Simin %A Khotaei, Ghamar Taj %A Bascom, Charles C %A Maroofian, Reza %A Chaabouni, Myriam %A Alsubhi, Afaf %A Eyaid, Wafaa %A Isikay, Sedat %A Gleeson, Joseph G %A James R Lupski %A Casanova, Jean-Laurent %A Pagliarini, David J %A Akarsu, Nurten A %A Maurer-Stroh, Sebastian %A Cetinkaya, Arda %A Bertoli-Avella, Aida %A Mathuru, Ajay S %A Ho, Lena %A Bard, Frederic A %A Reversade, Bruno %K Animals %K Biological Evolution %K Cell Line %K CRISPR-Cas Systems %K Encephalitis %K Female %K Genes, Recessive %K Glycogen %K Humans %K Inflammation %K Male %K Membrane Proteins %K Mitochondrial Diseases %K Pedigree %K Seizures %K Zebrafish %X

Human C2orf69 is an evolutionarily conserved gene whose function is unknown. Here, we report eight unrelated families from which 20 children presented with a fatal syndrome consisting of severe autoinflammation and progredient leukoencephalopathy with recurrent seizures; 12 of these subjects, whose DNA was available, segregated homozygous loss-of-function C2orf69 variants. C2ORF69 bears homology to esterase enzymes, and orthologs can be found in most eukaryotic genomes, including that of unicellular phytoplankton. We found that endogenous C2ORF69 (1) is loosely bound to mitochondria, (2) affects mitochondrial membrane potential and oxidative respiration in cultured neurons, and (3) controls the levels of the glycogen branching enzyme 1 (GBE1) consistent with a glycogen-storage-associated mitochondriopathy. We show that CRISPR-Cas9-mediated inactivation of zebrafish C2orf69 results in lethality by 8 months of age due to spontaneous epileptic seizures, which is preceded by persistent brain inflammation. Collectively, our results delineate an autoinflammatory Mendelian disorder of C2orf69 deficiency that disrupts the development/homeostasis of the immune and central nervous systems.

%B Am J Hum Genet %V 108 %P 1301-1317 %8 2021 Jul 01 %G eng %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/34038740?dopt=Abstract %R 10.1016/j.ajhg.2021.05.003 %0 Journal Article %J Ann Neurol %D 2021 %T MED27 Variants Cause Developmental Delay, Dystonia, and Cerebellar Hypoplasia. %A Meng, Linyan %A Isohanni, Pirjo %A Shao, Yunru %A Graham, Brett H %A Hickey, Scott E %A Brooks, Stephanie %A Suomalainen, Anu %A Joset, Pascal %A Steindl, Katharina %A Rauch, Anita %A Hackenberg, Annette %A High, Frances A %A Armstrong-Javors, Amy %A Mencacci, Niccolò E %A Gonzàlez-Latapi, Paulina %A Kamel, Walaa A %A Al-Hashel, Jasem Y %A Bustos, Bernabé I %A Hernandez, Alejandro V %A Krainc, Dimitri %A Lubbe, Steven J %A Van Esch, Hilde %A De Luca, Chiara %A Ballon, Katleen %A Ravelli, Claudia %A Burglen, Lydie %A Qebibo, Leila %A Calame, Daniel G %A Mitani, Tadahiro %A Marafi, Dana %A Pehlivan, Davut %A Saadi, Nebal W %A Sahin, Yavuz %A Maroofian, Reza %A Efthymiou, Stephanie %A Houlden, Henry %A Maqbool, Shazia %A Rahman, Fatima %A Gu, Shen %A Posey, Jennifer E %A James R Lupski %A Hunter, Jill V %A Wangler, Michael F %A Carroll, Christopher J %A Yang, Yaping %K Adolescent %K Adult %K Amino Acid Sequence %K Cataract %K Cerebellum %K Child %K Child, Preschool %K Developmental Disabilities %K Dystonia %K Epilepsy %K Exome Sequencing %K Genetic Variation %K Humans %K Infant %K Mediator Complex %K Nervous System Malformations %K Phenotype %X

The Mediator multiprotein complex functions as a regulator of RNA polymerase II-catalyzed gene transcription. In this study, exome sequencing detected biallelic putative disease-causing variants in MED27, encoding Mediator complex subunit 27, in 16 patients from 11 families with a novel neurodevelopmental syndrome. Patient phenotypes are highly homogeneous, including global developmental delay, intellectual disability, axial hypotonia with distal spasticity, dystonic movements, and cerebellar hypoplasia. Seizures and cataracts were noted in severely affected individuals. Identification of multiple patients with biallelic MED27 variants supports the critical role of MED27 in normal human neural development, particularly for the cerebellum. ANN NEUROL 2021;89:828-833.

%B Ann Neurol %V 89 %P 828-833 %8 2021 Apr %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/33443317?dopt=Abstract %R 10.1002/ana.26019 %0 Journal Article %J HGG Adv %D 2021 %T missense mutations in Xia-Gibbs syndrome. %A Khayat, Michael M %A Jianhong Hu %A Jiang, Yunyun %A Li, He %A Chander, Varuna %A Dawood, Moez %A Hansen, Adam W %A Li, Shoudong %A Friedman, Jennifer %A Cross, Laura %A Bijlsma, Emilia K %A Ruivenkamp, Claudia A L %A Sansbury, Francis H %A Innis, Jeffrey W %A O'Shea, Jessica Omark %A Meng, Qingchang %A Rosenfeld, Jill A %A McWalter, Kirsty %A Wangler, Michael F %A James R Lupski %A Posey, Jennifer E %A David R Murdock %A Richard A Gibbs %X

Xia-Gibbs syndrome (XGS; MIM: 615829) is a phenotypically heterogeneous neurodevelopmental disorder (NDD) caused by newly arising mutations in the AT-Hook DNA-Binding Motif-Containing 1 () gene that are predicted to lead to truncated AHDC1 protein synthesis. More than 270 individuals have been diagnosed with XGS worldwide. Despite the absence of an independent assay for AHDC1 protein function to corroborate potential functional consequences of rare variant genetic findings, there are also reports of individuals with XGS-like trait manifestations who have missense mutations and who have been provided a molecular diagnosis of the disorder. To investigate a potential contribution of missense mutations to XGS, we mapped the missense mutations from 10 such individuals to the AHDC1 conserved protein domain structure and detailed the observed phenotypes. Five newly identified individuals were ascertained from a local XGS Registry, and an additional five were taken from external reports or databases, including one publication. Where clinical data were available, individuals with missense mutations all displayed phenotypes consistent with those observed in individuals with truncating mutations, including delayed motor milestones, intellectual disability (ID), hypotonia, and speech delay. A subset of the 10 reported missense mutations cluster in two regions of the AHDC1 protein with known conserved domains, likely representing functional motifs. Variants outside the clustered regions score lower for computational prediction of their likely damaging effects. Overall, missense variants in are likely diagnostic of XGS when analysis of their position relative to conserved regions is considered together with disease trait manifestations.

%B HGG Adv %V 2 %8 2021 Oct 14 %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/34950897?dopt=Abstract %R 10.1016/j.xhgg.2021.100049 %0 Journal Article %J Am J Med Genet A %D 2021 %T Neurodevelopmental disorder in an Egyptian family with a biallelic ALKBH8 variant. %A Saad, Ahmed K %A Marafi, Dana %A Mitani, Tadahiro %A Du, Haowei %A Rafat, Karima %A Fatih, Jawid M %A Jhangiani, Shalini N %A Coban-Akdemir, Zeynep %A Richard A Gibbs %A Pehlivan, Davut %A Hunter, Jill V %A Posey, Jennifer E %A Zaki, Maha S %A James R Lupski %K Adolescent %K AlkB Homolog 8, tRNA Methyltransferase %K Brain %K Child %K Child, Preschool %K Female %K Genetic Predisposition to Disease %K Humans %K Infant %K Magnetic Resonance Imaging %K Male %K Neurodevelopmental Disorders %K Pedigree %X

Alkylated DNA repair protein AlkB homolog 8 (ALKBH8) is a member of the AlkB family of dioxygenases. ALKBH8 is a methyltransferase of the highly variable wobble nucleoside position in the anticodon loop of tRNA and thus plays a critical role in tRNA modification by preserving codon recognition and preventing errors in amino acid incorporation during translation. Moreover, its activity catalyzes uridine modifications that are proposed to be critical for accurate protein translation. Previously, two distinct homozygous truncating variants in the final exon of ALKBH8 were described in two unrelated large Saudi Arabian kindreds with intellectual developmental disorder and autosomal recessive 71 (MRT71) syndrome (MIM# 618504). Here, we report a third family-of Egyptian descent-harboring a novel homozygous frame-shift variant in the last exon of ALKBH8. Two affected siblings in this family exhibit global developmental delay and intellectual disability as shared characteristic features of MRT71 syndrome, and we further characterize their observed dysmorphic features and brain MRI findings. This description of a third family with a truncating ALKBH8 variant from a distinct population broadens the phenotypic and genotypic spectrum of MRT71 syndrome, affirms that perturbations in tRNA biogenesis can contribute to neurogenetic disease traits, and firmly establishes ALKBH8 as a novel neurodevelopmental disease gene.

%B Am J Med Genet A %V 185 %P 1288-1293 %8 2021 Apr %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/33544954?dopt=Abstract %R 10.1002/ajmg.a.62100 %0 Journal Article %J Hum Mol Genet %D 2021 %T NMIHBA results from hypomorphic PRUNE1 variants that lack short-chain exopolyphosphatase activity. %A Nistala, Harikiran %A Dronzek, John %A Gonzaga-Jauregui, Claudia %A Chim, Shek Man %A Rajamani, Saathyaki %A Nuwayhid, Samer %A Delgado, Dennis %A Burke, Elizabeth %A Karaca, Ender %A Franklin, Matthew C %A Sarangapani, Prasad %A Podgorski, Michael %A Tang, Yajun %A Dominguez, Melissa G %A Withers, Marjorie %A Deckelbaum, Ron A %A Scheonherr, Christopher J %A Gahl, William A %A Malicdan, May C %A Zambrowicz, Brian %A Gale, Nicholas W %A Richard A Gibbs %A Chung, Wendy K %A James R Lupski %A Economides, Aris N %K Acid Anhydride Hydrolases %K Alleles %K Animals %K Child, Preschool %K Female %K Humans %K Infant %K Intellectual Disability %K Male %K Mice %K Microcephaly %K Muscle Hypotonia %K Mutation %K Neurodevelopmental Disorders %K Pedigree %K Phenotype %K Phosphoric Monoester Hydrolases %X

Neurodevelopmental disorder with microcephaly, hypotonia and variable brain anomalies (NMIHBA) is an autosomal recessive neurodevelopmental and neurodegenerative disorder characterized by global developmental delay and severe intellectual disability. Microcephaly, progressive cortical atrophy, cerebellar hypoplasia and delayed myelination are neurological hallmarks in affected individuals. NMIHBA is caused by biallelic variants in PRUNE1 encoding prune exopolyphosphatase 1. We provide in-depth clinical description of two affected siblings harboring compound heterozygous variant alleles, c.383G > A (p.Arg128Gln), c.520G > T (p.Gly174*) in PRUNE1. To gain insights into disease biology, we biochemically characterized missense variants within the conserved N-terminal aspartic acid-histidine-histidine (DHH) motif and provide evidence that they result in the destabilization of protein structure and/or loss of exopolyphosphatase activity. Genetic ablation of Prune1 results in midgestational lethality in mice, associated with perturbations to embryonic growth and vascular development. Our findings suggest that NMIHBA results from hypomorphic variant alleles in humans and underscore the potential key role of PRUNE1 exopolyphoshatase activity in neurodevelopment.

%B Hum Mol Genet %V 29 %P 3516-3531 %8 2021 Jan 06 %G eng %N 21 %1 https://www.ncbi.nlm.nih.gov/pubmed/33105479?dopt=Abstract %R 10.1093/hmg/ddaa237 %0 Journal Article %J Am J Med Genet A %D 2021 %T A novel homozygous SLC13A5 whole-gene deletion generated by Alu/Alu-mediated rearrangement in an Iraqi family with epileptic encephalopathy. %A Duan, Ruizhi %A Saadi, Nebal Waill %A Grochowski, Christopher M %A Bhadila, Ghalia %A Faridoun, Afnan %A Mitani, Tadahiro %A Du, Haowei %A Fatih, Jawid M %A Jhangiani, Shalini N %A Akdemir, Zeynep C %A Richard A Gibbs %A Pehlivan, Davut %A Posey, Jennifer E %A Marafi, Dana %A James R Lupski %K Alu Elements %K Child, Preschool %K Chromosomes, Human, Pair 17 %K DNA Copy Number Variations %K Epilepsy, Generalized %K Exome Sequencing %K Female %K Homozygote %K Humans %K Infant %K Intellectual Disability %K Male %K Mutation %K Pedigree %K Sequence Deletion %K Symporters %X

Biallelic loss-of-function (LoF) of SLC13A5 (solute carrier family 13, member 5) induced deficiency in sodium/citrate transporter (NaCT) causes autosomal recessive developmental epileptic encephalopathy 25 with hypoplastic amelogenesis imperfecta (DEE25; MIM #615905). Many pathogenic SLC13A5 single nucleotide variants (SNVs) and small indels have been described; however, no cases with copy number variants (CNVs) have been sufficiently investigated. We describe a consanguineous Iraqi family harboring an 88.5 kb homozygous deletion including SLC13A5 in Chr17p13.1. The three affected male siblings exhibit neonatal-onset epilepsy with fever-sensitivity, recurrent status epilepticus, global developmental delay/intellectual disability (GDD/ID), and other variable neurological findings as shared phenotypical features of DEE25. Two of the three affected subjects exhibit hypoplastic amelogenesis imperfecta (AI), while the proband shows no evidence of dental abnormalities or AI at 2 years of age with apparently unaffected primary dentition. Characterization of the genomic architecture at this locus revealed evidence for genomic instability generated by an Alu/Alu-mediated rearrangement; confirmed by break-point junction Sanger sequencing. This multiplex family from a distinct population elucidates the phenotypic consequence of complete LoF of SLC13A5 and illustrates the importance of read-depth-based CNV detection in comprehensive exome sequencing analysis to solve cases that otherwise remain molecularly unsolved.

%B Am J Med Genet A %V 185 %P 1972-1980 %8 2021 Jul %G eng %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/33797191?dopt=Abstract %R 10.1002/ajmg.a.62192 %0 Journal Article %J Am J Med Genet A %D 2021 %T Novel pathogenic genomic variants leading to autosomal dominant and recessive Robinow syndrome. %A Zhang, Chaofan %A Mazzeu, Juliana F %A Eisfeldt, Jesper %A Grochowski, Christopher M %A White, Janson %A Akdemir, Zeynep C %A Jhangiani, Shalini N %A Donna M Muzny %A Richard A Gibbs %A Lindstrand, Anna %A James R Lupski %A Sutton, V Reid %A Carvalho, Claudia M B %K Chromosomes, Human, Pair 17 %K Comparative Genomic Hybridization %K Craniofacial Abnormalities %K Dishevelled Proteins %K Dwarfism %K Exome Sequencing %K Female %K Genes, Dominant %K Genes, Recessive %K Genetic Heterogeneity %K Genetic Predisposition to Disease %K Genomic Structural Variation %K Humans %K Limb Deformities, Congenital %K Male %K Oxidoreductases %K Receptor Tyrosine Kinase-like Orphan Receptors %K Urogenital Abnormalities %K Whole Genome Sequencing %K Wnt Signaling Pathway %X

Robinow syndrome (RS) is a genetically heterogeneous disorder characterized by skeletal dysplasia and a distinctive facial appearance. Previous studies have revealed locus heterogeneity with rare variants in DVL1, DVL3, FZD2, NXN, ROR2, and WNT5A underlying the etiology of RS. The aforementioned "Robinow-associated genes" and their gene products all play a role in the WNT/planar cell polarity signaling pathway. We performed gene-targeted Sanger sequencing, exome sequencing, genome sequencing, and array comparative genomic hybridization on four subjects with a clinical diagnosis of RS who had not had prior DNA testing. Individuals in our cohort were found to carry pathogenic or likely pathogenic variants in three RS related genes: DVL1, ROR2, and NXN. One subject was found to have a nonsense variant (c.817C > T [p.Gln273*]) in NXN in trans with an ~1 Mb telomeric deletion on chromosome 17p containing NXN, which supports our contention that biallelic NXN variant alleles are responsible for a novel autosomal recessive RS locus. These findings provide increased understanding of the role of WNT signaling in skeletal development and maintenance. These data further support the hypothesis that dysregulation of the noncanonical WNT pathway in humans gives rise to RS.

%B Am J Med Genet A %V 185 %P 3593-3600 %8 2021 Dec %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/33048444?dopt=Abstract %R 10.1002/ajmg.a.61908 %0 Journal Article %J Orphanet J Rare Dis %D 2021 %T PhenoDB, GeneMatcher and VariantMatcher, tools for analysis and sharing of sequence data. %A Wohler, Elizabeth %A Martin, Renan %A Griffith, Sean %A Rodrigues, Eliete da S %A Antonescu, Corina %A Posey, Jennifer E %A Coban-Akdemir, Zeynep %A Jhangiani, Shalini N %A Doheny, Kimberly F %A James R Lupski %A Valle, David %A Hamosh, Ada %A Sobreira, Nara %K Computational Biology %K Databases, Genetic %K Genomics %K Humans %K Phenotype %K Software %X

BACKGROUND: With the advent of whole exome (ES) and genome sequencing (GS) as tools for disease gene discovery, rare variant filtering, prioritization and data sharing have become essential components of the search for disease genes and variants potentially contributing to disease phenotypes. The computational storage, data manipulation, and bioinformatic interpretation of thousands to millions of variants identified in ES and GS, respectively, is a challenging task. To aid in that endeavor, we constructed PhenoDB, GeneMatcher and VariantMatcher.

RESULTS: PhenoDB is an accessible, freely available, web-based platform that allows users to store, share, analyze and interpret their patients' phenotypes and variants from ES/GS data. GeneMatcher is accessible to all stakeholders as a web-based tool developed to connect individuals (researchers, clinicians, health care providers and patients) around the globe with interest in the same gene(s), variant(s) or phenotype(s). Finally, VariantMatcher was developed to enable public sharing of variant-level data and phenotypic information from individuals sequenced as part of multiple disease gene discovery projects. Here we provide updates on PhenoDB and GeneMatcher applications and implementation and introduce VariantMatcher.

CONCLUSION: Each of these tools has facilitated worldwide data sharing and data analysis and improved our ability to connect genes to phenotypic traits. Further development of these platforms will expand variant analysis, interpretation, novel disease-gene discovery and facilitate functional annotation of the human genome for clinical genomics implementation and the precision medicine initiative.

%B Orphanet J Rare Dis %V 16 %P 365 %8 2021 Aug 18 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/34407837?dopt=Abstract %R 10.1186/s13023-021-01916-z %0 Journal Article %J Hum Mutat %D 2021 %T Phenotypic and protein localization heterogeneity associated with AHDC1 pathogenic protein-truncating alleles in Xia-Gibbs syndrome. %A Khayat, Michael M %A Li, He %A Chander, Varuna %A Jianhong Hu %A Hansen, Adam W %A Li, Shoudong %A Traynelis, Josh %A Shen, Hua %A Weissenberger, George %A Stossi, Fabio %A Johnson, Hannah L %A James R Lupski %A Posey, Jennifer E %A Aniko Sabo %A Meng, Qingchang %A David R Murdock %A Wangler, Michael %A Richard A Gibbs %K Abnormalities, Multiple %K Alleles %K DNA-Binding Proteins %K Humans %K Intellectual Disability %K Mutation %K Phenotype %K Syndrome %X

Xia-Gibbs syndrome (XGS) is a rare Mendelian disease typically caused by de novo stop-gain or frameshift mutations in the AT-hook DNA binding motif containing 1 (AHDC1) gene. Patients usually present in early infancy with hypotonia and developmental delay and later exhibit intellectual disability (ID). The overall presentation is variable, however, and the emerging clinical picture is still evolving. A detailed phenotypic analysis of 34 XGS individuals revealed five core phenotypes (delayed motor milestones, speech delay, low muscle tone, ID, and hypotonia) in more than 80% of individuals and an additional 12 features that occurred more variably. Seizures and scoliosis were more frequently associated with truncations that arise before the midpoint of the protein although the occurrence of most features could not be predicted by the mutation position. Transient expression of wild type and different patient truncated AHDC1 protein forms in human cell lines revealed abnormal patterns of nuclear localization including a diffuse distribution of a short truncated form and nucleolar aggregation in mid-protein truncated forms. Overall, both the occurrence of variable phenotypes and the different distribution of the expressed protein reflect the heterogeneity of this syndrome.

%B Hum Mutat %V 42 %P 577-591 %8 2021 May %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/33644933?dopt=Abstract %R 10.1002/humu.24190 %0 Journal Article %J Am J Hum Genet %D 2021 %T Response to Biesecker et al. %A Hamosh, Ada %A Amberger, Joanna S %A Bocchini, Carol A %A Bodurtha, Joann %A Bult, Carol J %A Chute, Christopher G %A Cutting, Garry R %A Dietz, Harry C %A Firth, Helen V %A Richard A Gibbs %A Grody, Wayne W %A Haendel, Melissa A %A James R Lupski %A Posey, Jennifer E %A Robinson, Peter N %A Schriml, Lynn M %A Scott, Alan F %A Sobreira, Nara L %A Valle, David %A Wu, Nan %A Rasmussen, Sonja A %K Blepharophimosis %K Facies %K Humans %B Am J Hum Genet %V 108 %P 1807-1808 %8 2021 Sep 02 %G eng %N 9 %1 https://www.ncbi.nlm.nih.gov/pubmed/34478655?dopt=Abstract %R 10.1016/j.ajhg.2021.07.004 %0 Journal Article %J Am J Med Genet A %D 2021 %T Risk of sudden cardiac death in EXOSC5-related disease. %A Calame, Daniel G %A Herman, Isabella %A Fatih, Jawid M %A Du, Haowei %A Akay, Gulsen %A Jhangiani, Shalini N %A Coban-Akdemir, Zeynep %A Milewicz, Dianna M %A Richard A Gibbs %A Posey, Jennifer E %A Marafi, Dana %A Hunter, Jill V %A Fan, Yuxin %A James R Lupski %A Miyake, Christina Y %K Antigens, Neoplasm %K Atrioventricular Block %K Child %K Death, Sudden, Cardiac %K Echocardiography %K Electrocardiography %K Exosome Multienzyme Ribonuclease Complex %K Facies %K Female %K Genetic Association Studies %K Genetic Predisposition to Disease %K Humans %K Male %K Mutation %K Pedigree %K Phenotype %K RNA-Binding Proteins %K Sequence Analysis, DNA %K Young Adult %X

The RNA exosome is a multi-subunit complex involved in the processing, degradation, and regulated turnover of RNA. Several subunits are linked to Mendelian disorders, including pontocerebellar hypoplasia (EXOSC3, MIM #614678; EXOSC8, MIM #616081: and EXOSC9, MIM #618065) and short stature, hearing loss, retinitis pigmentosa, and distinctive facies (EXOSC2, MIM #617763). More recently, EXOSC5 (MIM *606492) was found to underlie an autosomal recessive neurodevelopmental disorder characterized by developmental delay, hypotonia, cerebellar abnormalities, and dysmorphic facies. An unusual feature of EXOSC5-related disease is the occurrence of complete heart block requiring a pacemaker in a subset of affected individuals. Here, we provide a detailed clinical and molecular characterization of two siblings with microcephaly, developmental delay, cerebellar volume loss, hypomyelination, with cardiac conduction and rhythm abnormalities including sinus node dysfunction, intraventricular conduction delay, atrioventricular block, and ventricular tachycardia (VT) due to compound heterozygous variants in EXOSC5: (1) NM_020158.4:c.341C > T (p.Thr114Ile; pathogenic, previously reported) and (2) NM_020158.4:c.302C > A (p.Thr101Lys; novel variant). A review of the literature revealed an additional family with biallelic EXOSC5 variants and cardiac conduction abnormalities. These clinical and molecular data provide compelling evidence that cardiac conduction abnormalities and arrhythmias are part of the EXOSC5-related disease spectrum and argue for proactive screening due to potential risk of sudden cardiac death.

%B Am J Med Genet A %V 185 %P 2532-2540 %8 2021 Aug %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/34089229?dopt=Abstract %R 10.1002/ajmg.a.62352 %0 Journal Article %J Am J Med Genet A %D 2021 %T Two novel bi-allelic KDELR2 missense variants cause osteogenesis imperfecta with neurodevelopmental features. %A Efthymiou, Stephanie %A Herman, Isabella %A Rahman, Fatima %A Anwar, Najwa %A Maroofian, Reza %A Yip, Janice %A Mitani, Tadahiro %A Calame, Daniel G %A Hunter, Jill V %A Sutton, V Reid %A Yilmaz Gulec, Elif %A Duan, Ruizhi %A Fatih, Jawid M %A Marafi, Dana %A Pehlivan, Davut %A Jhangiani, Shalini N %A Richard A Gibbs %A Posey, Jennifer E %A Maqbool, Shazia %A James R Lupski %A Houlden, Henry %K Alleles %K Child %K Child, Preschool %K Female %K Genetic Predisposition to Disease %K Humans %K Male %K Mutation, Missense %K Neurodevelopmental Disorders %K Osteogenesis Imperfecta %K Vesicular Transport Proteins %B Am J Med Genet A %V 185 %P 2241-2249 %8 2021 Jul %G eng %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/33964184?dopt=Abstract %R 10.1002/ajmg.a.62221 %0 Journal Article %J Adv Med Sci %D 2021 %T Variants in FLRT3 and SLC35E2B identified using exome sequencing in seven high myopia families from Central Europe. %A Swierkowska, Joanna %A Karolak, Justyna A %A Gambin, Tomasz %A Rydzanicz, Malgorzata %A Frajdenberg, Agata %A Mrugacz, Malgorzata %A Podfigurna-Musielak, Monika %A Stankiewicz, Pawel %A James R Lupski %A Gajecka, Marzena %K Adolescent %K Europe %K Exome %K Female %K Follow-Up Studies %K Genetic Predisposition to Disease %K Humans %K Male %K Membrane Glycoproteins %K Mutation %K Myopia %K Pedigree %K Prognosis %K Solute Carrier Proteins %X

PURPOSE: High myopia (HM) is an eye disorder with both environmental and genetic factors involved. Many genetic factors responsible for HM were recognized worldwide, but little is known about genetic variants underlying HM in Central Europe. Thus, the aim of this study was to identify rare sequence variants involved in HM in families from Central Europe to better understand the genetic basis of HM.

MATERIALS AND METHODS: We assessed 17 individuals from 7 unrelated Central European families with hereditary HM using exome sequencing (ES). Segregation of selected variants in other available family members was performed using Sanger sequencing.

RESULTS: Detected 73 rare variants were selected for verification. We observed 2 missense variants, c.938C>T in SLC35E2B - encoding solute carrier family 35 member E2B, and c.1642G>C in FLRT3 - encoding fibronectin leucine rich transmembrane protein, segregating with HM in one family.

CONCLUSIONS: FLRT3 ​and/or ​SLC35E2B ​could represent disease candidate genes and identified sequence variants might be responsible for HM in the studied family.

%B Adv Med Sci %V 66 %P 192-198 %8 2021 Mar %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/33711669?dopt=Abstract %R 10.1016/j.advms.2021.02.005 %0 Journal Article %J Nat Commun %D 2020 %T Author Correction: NEMF mutations that impair ribosome-associated quality control are associated with neuromuscular disease. %A Martin, Paige B %A Kigoshi-Tansho, Yu %A Sher, Roger B %A Ravenscroft, Gianina %A Stauffer, Jennifer E %A Kumar, Rajesh %A Yonashiro, Ryo %A Müller, Tina %A Griffith, Christopher %A Allen, William %A Pehlivan, Davut %A Harel, Tamar %A Zenker, Martin %A Howting, Denise %A Schanze, Denny %A Faqeih, Eissa A %A Almontashiri, Naif A M %A Maroofian, Reza %A Houlden, Henry %A Mazaheri, Neda %A Galehdari, Hamid %A Douglas, Ganka %A Posey, Jennifer E %A Ryan, Monique %A James R Lupski %A Laing, Nigel G %A Joazeiro, Claudio A P %A Cox, Gregory A %X

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

%B Nat Commun %V 11 %P 5022 %8 2020 Oct 01 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/33004807?dopt=Abstract %R 10.1038/s41467-020-18941-4 %0 Journal Article %J Ann Clin Transl Neurol %D 2020 %T Biallelic GRM7 variants cause epilepsy, microcephaly, and cerebral atrophy. %A Marafi, Dana %A Mitani, Tadahiro %A Isikay, Sedat %A Hertecant, Jozef %A Almannai, Mohammed %A Manickam, Kandamurugu %A Abou Jamra, Rami %A El-Hattab, Ayman W %A Rajah, Jaishen %A Fatih, Jawid M %A Du, Haowei %A Karaca, Ender %A Bayram, Yavuz %A Punetha, Jaya %A Rosenfeld, Jill A %A Jhangiani, Shalini N %A Eric Boerwinkle %A Akdemir, Zeynep C %A Erdin, Serkan %A Hunter, Jill V %A Richard A Gibbs %A Pehlivan, Davut %A Posey, Jennifer E %A James R Lupski %K Adolescent %K Alleles %K Atrophy %K Child %K Child, Preschool %K Cohort Studies %K Consanguinity %K Epilepsy %K Exome Sequencing %K Female %K Humans %K Infant %K Male %K Microcephaly %K Neurodevelopmental Disorders %K Pedigree %K Phenotype %K Receptors, Metabotropic Glutamate %X

OBJECTIVE: Defects in ion channels and neurotransmitter receptors are implicated in developmental and epileptic encephalopathy (DEE). Metabotropic glutamate receptor 7 (mGluR7), encoded by GRM7, is a presynaptic G-protein-coupled glutamate receptor critical for synaptic transmission. We previously proposed GRM7 as a candidate disease gene in two families with neurodevelopmental disorders (NDDs). One additional family has been published since. Here, we describe three additional families with GRM7 biallelic variants and deeply characterize the associated clinical neurological and electrophysiological phenotype and molecular data in 11 affected individuals from six unrelated families.

METHODS: Exome sequencing and family-based rare variant analyses on a cohort of 220 consanguineous families with NDDs revealed three families with GRM7 biallelic variants; three additional families were identified through literature search and collaboration with a clinical molecular laboratory.

RESULTS: We compared the observed clinical features and variants of 11 affected individuals from the six unrelated families. Identified novel deleterious variants included two homozygous missense variants (c.2671G>A:p.Glu891Lys and c.1973G>A:p.Arg685Gln) and one homozygous stop-gain variant (c.1975C>T:p.Arg659Ter). Developmental delay, neonatal- or infantile-onset epilepsy, and microcephaly were universal. Three individuals had hypothalamic-pituitary-axis dysfunction without pituitary structural abnormality. Neuroimaging showed cerebral atrophy and hypomyelination in a majority of cases. Two siblings demonstrated progressive loss of myelination by 2 years in both and an acquired microcephaly pattern in one. Five individuals died in early or late childhood.

CONCLUSION: Detailed clinical characterization of 11 individuals from six unrelated families demonstrates that rare biallelic GRM7 pathogenic variants can cause DEEs, microcephaly, hypomyelination, and cerebral atrophy.

%B Ann Clin Transl Neurol %V 7 %P 610-627 %8 2020 May %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/32286009?dopt=Abstract %R 10.1002/acn3.51003 %0 Journal Article %J Brain %D 2020 %T Biallelic in-frame deletion in TRAPPC4 in a family with developmental delay and cerebellar atrophy. %A Saad, Ahmed K %A Marafi, Dana %A Mitani, Tadahiro %A Jolly, Angad %A Du, Haowei %A Elbendary, Hasnaa M %A Jhangiani, Shalini N %A Akdemir, Zeynep C %A Richard A Gibbs %A Hunter, Jill V %A Carvalho, Claudia M B C %A Pehlivan, Davut %A Posey, Jennifer E %A Zaki, Maha S %A James R Lupski %K Atrophy %K Cerebellar Diseases %K Humans %K Intellectual Disability %K Sequence Deletion %B Brain %V 143 %P e83 %8 2020 Oct 01 %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/33011761?dopt=Abstract %R 10.1093/brain/awaa256 %0 Journal Article %J Expert Rev Mol Diagn %D 2020 %T Clinical genomics and contextualizing genome variation in the diagnostic laboratory. %A James R Lupski %A Liu, Pengfei %A Stankiewicz, Pawel %A Carvalho, Claudia M B %A Posey, Jennifer E %K Clinical Laboratory Techniques %K Computational Biology %K DNA Copy Number Variations %K Gene Dosage %K Genetic Association Studies %K Genetic Predisposition to Disease %K Genetic Testing %K Genetic Variation %K Genome, Human %K Genomics %K Humans %K Molecular Sequence Annotation %K Mutation %K Phenotype %K Rare Diseases %X

INTRODUCTION: The human genome contains the instructions for the development and biological homeostasis of the human organism and the genetic transmission of traits. Genome variation in human populations is the basis of evolution; individual or personal genomes vary tremendously, making each of us truly unique.

AREAS COVERED: Assaying this individual variation using genomic technologies has many applications in clinical medicine, from elucidating the biology of disease to designing strategies to ameliorate perturbations from homeostasis. Detecting pathogenic rare variation in a genome may provide a molecular diagnosis that can be informative for patient management and family healthcare.

EXPERT OPINION: Despite the increasing clinical use of unbiased genomic testing, including chromosome microarray analysis (CMA) with array comparative genomic hybridization (aCGH) or SNP arrays, clinical exome sequencing (cES), and whole-genome sequencing (WGS), to survey genome-wide for molecular aberrations, clinical acumen paired with an understanding of the limitations of each testing type will be needed to achieve molecular diagnoses. Potential opportunities for improving case solved rates, functionally annotating the majority of genes in the human genome, and further understanding genetic contributions to disease will empower clinical genomics and the precision medicine initiative.

%B Expert Rev Mol Diagn %V 20 %P 995-1002 %8 2020 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/32954863?dopt=Abstract %R 10.1080/14737159.2020.1826312 %0 Journal Article %J Genet Med %D 2020 %T CNVs cause autosomal recessive genetic diseases with or without involvement of SNV/indels. %A Bo Yuan %A Wang, Lei %A Liu, Pengfei %A Shaw, Chad %A Dai, Hongzheng %A Cooper, Lance %A Zhu, Wenmiao %A Anderson, Stephanie A %A Meng, Linyan %A Wang, Xia %A Wang, Yue %A Xia, Fan %A Xiao, Rui %A Braxton, Alicia %A Peacock, Sandra %A Schmitt, Eric %A Ward, Patricia A %A Vetrini, Francesco %A He, Weimin %A Chiang, Theodore %A Donna M Muzny %A Richard A Gibbs %A Beaudet, Arthur L %A Breman, Amy M %A Smith, Janice %A Cheung, Sau Wai %A Bacino, Carlos A %A Eng, Christine M %A Yang, Yaping %A James R Lupski %A Bi, Weimin %K Child %K DNA Copy Number Variations %K Exome Sequencing %K Exons %K Humans %K INDEL Mutation %K Retrospective Studies %X

PURPOSE: Improved resolution of molecular diagnostic technologies enabled detection of smaller sized exonic level copy-number variants (CNVs). The contribution of CNVs to autosomal recessive (AR) conditions may be better recognized using a large clinical cohort.

METHODS: We retrospectively investigated the CNVs' contribution to AR conditions in cases subjected to chromosomal microarray analysis (CMA, N = ~70,000) and/or clinical exome sequencing (ES, N = ~12,000) at Baylor Genetics; most had pediatric onset neurodevelopmental disorders.

RESULTS: CNVs contributed to biallelic variations in 87 cases, including 81 singletons and three affected sibling pairs. Seventy cases had CNVs affecting both alleles, and 17 had a CNV and a single-nucleotide variant (SNV)/indel in trans. In total, 94.3% of AR-CNVs affected one gene; among these 41.4% were single-exon and 35.0% were multiexon partial-gene events. Sixty-nine percent of homozygous AR-CNVs were embedded in homozygous genomic intervals. Five cases had large deletions unmasking an SNV/indel on the intact allele for a recessive condition, resulting in multiple molecular diagnoses.

CONCLUSIONS: AR-CNVs are often smaller in size, transmitted through generations, and underrecognized due to limitations in clinical CNV detection methods. Our findings from a large clinical cohort emphasized integrated CNV and SNV/indel analyses for precise clinical and molecular diagnosis especially in the context of genomic disorders.

%B Genet Med %V 22 %P 1633-1641 %8 2020 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/32576985?dopt=Abstract %R 10.1038/s41436-020-0864-8 %0 Journal Article %J Am J Med Genet A %D 2020 %T Congenital diaphragmatic hernia as a prominent feature of a SPECC1L-related syndrome. %A Wild, K Taylor %A Gordon, Tia %A Bhoj, Elizabeth J %A Du, Haowei %A Jhangiani, Shalini N %A Posey, Jennifer E %A James R Lupski %A Scott, Daryl A %A Zackai, Elaine H %K Abnormalities, Multiple %K Child, Preschool %K Female %K Gestational Age %K Hernias, Diaphragmatic, Congenital %K Humans %K Infant %K Infant, Newborn %K Male %K Mutation, Missense %K Phosphoproteins %K Syndrome %X

Congenital diaphragmatic hernias (CDH) confer substantial morbidity and mortality. Genetic defects, including chromosomal anomalies, copy number variants, and sequence variants are identified in ~30% of patients with CDH. A genetic etiology is not yet found in 70% of patients, however there is a growing number of genetic syndromes and single gene disorders associated with CDH. While there have been two reported individuals with X-linked Opitz G/BBB syndrome with MID1 mutations who have CDH as an associated feature, CDH appears to be a much more prominent feature of a SPECC1L-related autosomal dominant Opitz G/BBB syndrome. Features unique to autosomal dominant Opitz G/BBB syndrome include branchial fistulae, omphalocele, and a bicornuate uterus. Here we present one new individual and five previously reported individuals with CDH found to have SPECC1L mutations. These cases provide strong evidence that SPECC1L is a bona fide CDH gene. We conclude that a SPECC1L-related Opitz G/BBB syndrome should be considered in any patient with CDH who has additional features of hypertelorism, a prominent forehead, a broad nasal bridge, anteverted nares, cleft lip/palate, branchial fistulae, omphalocele, and/or bicornuate uterus.

%B Am J Med Genet A %V 182 %P 2919-2925 %8 2020 Dec %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/32954677?dopt=Abstract %R 10.1002/ajmg.a.61878 %0 Journal Article %J Hum Mutat %D 2020 %T Cytogenetically visible inversions are formed by multiple molecular mechanisms. %A Pettersson, Maria %A Grochowski, Christopher M %A Wincent, Josephine %A Eisfeldt, Jesper %A Breman, Amy M %A Cheung, Sau W %A Krepischi, Ana C V %A Rosenberg, Carla %A James R Lupski %A Ottosson, Jesper %A Lovmar, Lovisa %A Gacic, Jelena %A Lundberg, Elisabeth S %A Nilsson, Daniel %A Carvalho, Claudia M B %A Lindstrand, Anna %K Chromosome Inversion %K Comparative Genomic Hybridization %K DNA End-Joining Repair %K DNA Repair %K Female %K Gene Frequency %K Haplotypes %K Heterozygote %K Homologous Recombination %K Humans %K Karyotyping %K Male %K Pedigree %K Whole Genome Sequencing %X

Cytogenetically detected inversions are generally assumed to be copy number and phenotypically neutral events. While nonallelic homologous recombination is thought to play a major role, recent data suggest the involvement of other molecular mechanisms in inversion formation. Using a combination of short-read whole-genome sequencing (WGS), 10X Genomics Chromium WGS, droplet digital polymerase chain reaction and array comparative genomic hybridization we investigated the genomic structure of 18 large unique cytogenetically detected chromosomal inversions and achieved nucleotide resolution of at least one chromosomal inversion junction for 13/18 (72%). Surprisingly, we observed that seemingly copy number neutral inversions can be accompanied by a copy-number gain of up to 350 kb and local genomic complexities (3/18, 17%). In the resolved inversions, the mutational signatures are consistent with nonhomologous end-joining (8/13, 62%) or microhomology-mediated break-induced replication (5/13, 38%). Our study indicates that short-read 30x coverage WGS can detect a substantial fraction of chromosomal inversions. Moreover, replication-based mechanisms are responsible for approximately 38% of those events leading to a significant proportion of inversions that are actually accompanied by additional copy-number variation potentially contributing to the overall phenotypic presentation of those patients.

%B Hum Mutat %V 41 %P 1979-1998 %8 2020 Nov %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/32906200?dopt=Abstract %R 10.1002/humu.24106 %0 Journal Article %J Brain %D 2020 %T Deficiencies in vesicular transport mediated by TRAPPC4 are associated with severe syndromic intellectual disability. %A Van Bergen, Nicole J %A Guo, Yiran %A Al-Deri, Noraldin %A Lipatova, Zhanna %A Stanga, Daniela %A Zhao, Sarah %A Murtazina, Rakhilya %A Gyurkovska, Valeriya %A Pehlivan, Davut %A Mitani, Tadahiro %A Gezdirici, Alper %A Antony, Jayne %A Collins, Felicity %A Willis, Mary J H %A Coban Akdemir, Zeynep H %A Liu, Pengfei %A Punetha, Jaya %A Hunter, Jill V %A Jhangiani, Shalini N %A Fatih, Jawid M %A Rosenfeld, Jill A %A Posey, Jennifer E %A Richard A Gibbs %A Karaca, Ender %A Massey, Sean %A Ranasinghe, Thisara G %A Sleiman, Patrick %A Troedson, Chris %A James R Lupski %A Sacher, Michael %A Segev, Nava %A Hakonarson, Hakon %A Christodoulou, John %K Atrophy %K Autophagy %K Cerebellum %K Cerebral Cortex %K Child %K Child, Preschool %K Craniofacial Abnormalities %K Deafness %K Developmental Disabilities %K Epilepsy %K Female %K Fibroblasts %K Hearing Loss, Sensorineural %K Humans %K Infant %K Infant, Newborn %K Intellectual Disability %K Male %K Microcephaly %K Microscopy, Fluorescence %K Muscle Spasticity %K Nerve Tissue Proteins %K Neurodevelopmental Disorders %K Pedigree %K Quadriplegia %K RNA Splice Sites %K Syndrome %K Vesicular Transport Proteins %X

The conserved transport protein particle (TRAPP) complexes regulate key trafficking events and are required for autophagy. TRAPPC4, like its yeast Trs23 orthologue, is a core component of the TRAPP complexes and one of the essential subunits for guanine nucleotide exchange factor activity for Rab1 GTPase. Pathogenic variants in specific TRAPP subunits are associated with neurological disorders. We undertook exome sequencing in three unrelated families of Caucasian, Turkish and French-Canadian ethnicities with seven affected children that showed features of early-onset seizures, developmental delay, microcephaly, sensorineural deafness, spastic quadriparesis and progressive cortical and cerebellar atrophy in an effort to determine the genetic aetiology underlying neurodevelopmental disorders. All seven affected subjects shared the same identical rare, homozygous, potentially pathogenic variant in a non-canonical, well-conserved splice site within TRAPPC4 (hg19:chr11:g.118890966A>G; TRAPPC4: NM_016146.5; c.454+3A>G). Single nucleotide polymorphism array analysis revealed there was no haplotype shared between the tested Turkish and Caucasian families suggestive of a variant hotspot region rather than a founder effect. In silico analysis predicted the variant to cause aberrant splicing. Consistent with this, experimental evidence showed both a reduction in full-length transcript levels and an increase in levels of a shorter transcript missing exon 3, suggestive of an incompletely penetrant splice defect. TRAPPC4 protein levels were significantly reduced whilst levels of other TRAPP complex subunits remained unaffected. Native polyacrylamide gel electrophoresis and size exclusion chromatography demonstrated a defect in TRAPP complex assembly and/or stability. Intracellular trafficking through the Golgi using the marker protein VSVG-GFP-ts045 demonstrated significantly delayed entry into and exit from the Golgi in fibroblasts derived from one of the affected subjects. Lentiviral expression of wild-type TRAPPC4 in these fibroblasts restored trafficking, suggesting that the trafficking defect was due to reduced TRAPPC4 levels. Consistent with the recent association of the TRAPP complex with autophagy, we found that the fibroblasts had a basal autophagy defect and a delay in autophagic flux, possibly due to unsealed autophagosomes. These results were validated using a yeast trs23 temperature sensitive variant that exhibits constitutive and stress-induced autophagic defects at permissive temperature and a secretory defect at restrictive temperature. In summary we provide strong evidence for pathogenicity of this variant in a member of the core TRAPP subunit, TRAPPC4 that associates with vesicular trafficking and autophagy defects. This is the first report of a TRAPPC4 variant, and our findings add to the growing number of TRAPP-associated neurological disorders.

%B Brain %V 143 %P 112-130 %8 2020 Jan 01 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/31794024?dopt=Abstract %R 10.1093/brain/awz374 %0 Journal Article %J Hum Mutat %D 2020 %T A diagnostic ceiling for exome sequencing in cerebellar ataxia and related neurological disorders. %A Ngo, Kathie J %A Rexach, Jessica E %A Lee, Hane %A Petty, Lauren E %A Perlman, Susan %A Valera, Juliana M %A Deignan, Joshua L %A Mao, Yuanming %A Aker, Mamdouh %A Posey, Jennifer E %A Jhangiani, Shalini N %A Coban-Akdemir, Zeynep H %A Eric Boerwinkle %A Donna M Muzny %A Nelson, Alexandra B %A Hassin-Baer, Sharon %A Poke, Gemma %A Neas, Katherine %A Geschwind, Michael D %A Grody, Wayne W %A Richard A Gibbs %A Geschwind, Daniel H %A James R Lupski %A Below, Jennifer E %A Nelson, Stanley F %A Fogel, Brent L %K Cerebellar Ataxia %K DNA Copy Number Variations %K Exome %K Exome Sequencing %K Genetic Association Studies %K Genetic Linkage %K Genetic Predisposition to Disease %K Humans %K Microsatellite Repeats %K Nervous System Diseases %X

Genetic ataxias are associated with mutations in hundreds of genes with high phenotypic overlap complicating the clinical diagnosis. Whole-exome sequencing (WES) has increased the overall diagnostic rate considerably. However, the upper limit of this method remains ill-defined, hindering efforts to address the remaining diagnostic gap. To further assess the role of rare coding variation in ataxic disorders, we reanalyzed our previously published exome cohort of 76 predominantly adult and sporadic-onset patients, expanded the total number of cases to 260, and introduced analyses for copy number variation and repeat expansion in a representative subset. For new cases (n = 184), our resulting clinically relevant detection rate remained stable at 47% with 24% classified as pathogenic. Reanalysis of the previously sequenced 76 patients modestly improved the pathogenic rate by 7%. For the combined cohort (n = 260), the total observed clinical detection rate was 52% with 25% classified as pathogenic. Published studies of similar neurological phenotypes report comparable rates. This consistency across multiple cohorts suggests that, despite continued technical and analytical advancements, an approximately 50% diagnostic rate marks a relative ceiling for current WES-based methods and a more comprehensive genome-wide assessment is needed to identify the missing causative genetic etiologies for cerebellar ataxia and related neurodegenerative diseases.

%B Hum Mutat %V 41 %P 487-501 %8 2020 Feb %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/31692161?dopt=Abstract %R 10.1002/humu.23946 %0 Journal Article %J J Clin Invest %D 2020 %T Disease-associated CTNNBL1 mutation impairs somatic hypermutation by decreasing nuclear AID. %A Kuhny, Marcel %A Forbes, Lisa R %A Çakan, Elif %A Vega-Loza, Andrea %A Kostiuk, Valentyna %A Dinesh, Ravi K %A Glauzy, Salomé %A Stray-Pedersen, Asbjorg %A Pezzi, Ashley E %A Hanson, I Celine %A Vargas-Hernandez, Alexander %A Xu, Mina LuQuing %A Coban-Akdemir, Zeynep H %A Jhangiani, Shalini N %A Donna M Muzny %A Richard A Gibbs %A James R Lupski %A Chinn, Ivan K %A Schatz, David G %A Orange, Jordan S %A Meffre, Eric %K Amino Acid Substitution %K Apoptosis Regulatory Proteins %K B-Lymphocytes %K Cell Line %K Child, Preschool %K Common Variable Immunodeficiency %K Cytidine Deaminase %K Female %K Homozygote %K Humans %K Immunologic Memory %K Mutation, Missense %K Nuclear Proteins %K Somatic Hypermutation, Immunoglobulin %X

Patients with common variable immunodeficiency associated with autoimmune cytopenia (CVID+AIC) generate few isotype-switched B cells with severely decreased frequencies of somatic hypermutations (SHMs), but their underlying molecular defects remain poorly characterized. We identified a CVID+AIC patient who displays a rare homozygous missense M466V mutation in β-catenin-like protein 1 (CTNNBL1). Because CTNNBL1 binds activation-induced cytidine deaminase (AID) that catalyzes SHM, we tested AID interactions with the CTNNBL1 M466V variant. We found that the M466V mutation interfered with the association of CTNNBL1 with AID, resulting in decreased AID in the nuclei of patient EBV-transformed B cell lines and of CTNNBL1 466V/V Ramos B cells engineered to express only CTNNBL1 M466V using CRISPR/Cas9 technology. As a consequence, the scarce IgG+ memory B cells from the CTNNBL1 466V/V patient showed a low SHM frequency that averaged 6.7 mutations compared with about 18 mutations per clone in healthy-donor counterparts. In addition, CTNNBL1 466V/V Ramos B cells displayed a decreased incidence of SHM that was reduced by half compared with parental WT Ramos B cells, demonstrating that the CTNNBL1 M466V mutation is responsible for defective SHM induction. We conclude that CTNNBL1 plays an important role in regulating AID-dependent antibody diversification in humans.

%B J Clin Invest %V 130 %P 4411-4422 %8 2020 Aug 03 %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/32484799?dopt=Abstract %R 10.1172/JCI131297 %0 Journal Article %J J Neurointerv Surg %D 2020 %T Exome sequencing reveals a novel variant in causing intracranial aneurysm in a Chinese family. %A Ding, Xinghuan %A Zhao, Sen %A Zhang, Qianqian %A Yan, Zihui %A Wang, Yang %A Wu, Yong %A Li, Xiaoxin %A Liu, Jian %A Niu, Yuchen %A Zhang, Yisen %A Zhang, Mingqi %A Wang, Huizi %A Zhang, Ying %A Chen, Weisheng %A Yang, Xin-Zhuang %A Liu, Pengfei %A Posey, Jennifer E %A James R Lupski %A Wu, Zhihong %A Yang, Xinjian %A Wu, Nan %A Wang, Kun %K Adult %K Asian People %K Computational Biology %K Exome %K Female %K Genetic Variation %K Humans %K Intracranial Aneurysm %K Male %K Middle Aged %K Pedigree %K Phenotype %K Repressor Proteins %X

BACKGROUND: Genetic risk factors play an important role in the pathogenesis of familial intracranial aneurysms (FIAs); however, the molecular mechanisms remain largely unknown.

OBJECTIVE: To investigate potential FIA-causing genetic variants by rare variant interrogation and a family-based genomics approach in a large family with an extensive multigenerational pedigree with FIAs.

METHOD: Exome sequencing (ES) was performed in a dominant likely family with intracranial aneurysms (IAs). Variants were analyzed by an in-house developed pipeline and prioritized using various filtering strategies, including population frequency, variant type, and predicted variant pathogenicity. Sanger sequencing was also performed to evaluate the segregation of the variants with the phenotype.

RESULTS: Based on the ES data obtained from five individuals from a family with 7/21 living members affected with IAs, a total of 14 variants were prioritized as candidate variants. Familial segregation analysis revealed that c.2519T>C (p.Leu840Pro) segregated in accordance with Mendelian expectations with the phenotype within the family-that is, present in all IA-affected cases and absent from all unaffected members of the second generation. This missense variant is absent from public databases (1000genome, ExAC, gnomAD, ESP5400), and has damaging predictions by bioinformatics tools (Gerp ++ score = 5.88, CADD score = 16.43, MutationTaster score = 1, LRT score = 0). In addition, 840Leu in NFX1 is robustly conserved in mammals and maps in a region before the RING-type zinc finger domain.

CONCLUSION: c.2519T>C (p.Leu840Pro) may contribute to the pathogenetics of a subset of FIAs.

%B J Neurointerv Surg %V 12 %P 221-226 %8 2020 Feb %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/31401562?dopt=Abstract %R 10.1136/neurintsurg-2019-014900 %0 Journal Article %J Eur J Hum Genet %D 2020 %T Functional biology of the Steel syndrome founder allele and evidence for clan genomics derivation of COL27A1 pathogenic alleles worldwide. %A Gonzaga-Jauregui, Claudia %A Yesil, Gozde %A Nistala, Harikiran %A Gezdirici, Alper %A Bayram, Yavuz %A Nannuru, Kalyan C %A Pehlivan, Davut %A Bo Yuan %A Jimenez, Johanna %A Sahin, Yavuz %A Paine, Ingrid S %A Akdemir, Zeynep Coban %A Rajamani, Saathyaki %A Staples, Jeffrey %A Dronzek, John %A Howell, Kristen %A Fatih, Jawid M %A Smaldone, Silvia %A Schlesinger, Alan E %A Ramírez, Norman %A Cornier, Alberto S %A Kelly, Melissa A %A Haber, Robert %A Chim, Shek Man %A Nieman, Kristy %A Wu, Nan %A Walls, Johnathon %A Poueymirou, William %A Siao, Chia-Jen %A Sutton, V Reid %A Williams, Marc S %A Posey, Jennifer E %A Richard A Gibbs %A Carlo, Simon %A Tegay, David H %A Economides, Aris N %A James R Lupski %K Abnormalities, Multiple %K Adolescent %K Animals %K Bone Development %K Child %K Child, Preschool %K Consanguinity %K Extracellular Matrix %K Female %K Fibrillar Collagens %K Founder Effect %K Gene Frequency %K Hip Dislocation %K Homozygote %K Humans %K Male %K Mice %K Mice, Inbred C57BL %K Mutation %K Pedigree %K Scoliosis %K Syndrome %X

Previously we reported the identification of a homozygous COL27A1 (c.2089G>C; p.Gly697Arg) missense variant and proposed it as a founder allele in Puerto Rico segregating with Steel syndrome (STLS, MIM #615155); a rare osteochondrodysplasia characterized by short stature, congenital bilateral hip dysplasia, carpal coalitions, and scoliosis. We now report segregation of this variant in five probands from the initial clinical report defining the syndrome and an additional family of Puerto Rican descent with multiple affected adult individuals. We modeled the orthologous variant in murine Col27a1 and found it recapitulates some of the major Steel syndrome associated skeletal features including reduced body length, scoliosis, and a more rounded skull shape. Characterization of the in vivo murine model shows abnormal collagen deposition in the extracellular matrix and disorganization of the proliferative zone of the growth plate. We report additional COL27A1 pathogenic variant alleles identified in unrelated consanguineous Turkish kindreds suggesting Clan Genomics and identity-by-descent homozygosity contributing to disease in this population. The hypothesis that carrier states for this autosomal recessive osteochondrodysplasia may contribute to common complex traits is further explored in a large clinical population cohort. Our findings augment our understanding of COL27A1 biology and its role in skeletal development; and expand the functional allelic architecture in this gene underlying both rare and common disease phenotypes.

%B Eur J Hum Genet %V 28 %P 1243-1264 %8 2020 Sep %G eng %N 9 %1 https://www.ncbi.nlm.nih.gov/pubmed/32376988?dopt=Abstract %R 10.1038/s41431-020-0632-x %0 Journal Article %J Mol Genet Genomic Med %D 2020 %T Genetic and molecular mechanism for distinct clinical phenotypes conveyed by allelic truncating mutations implicated in FBN1. %A Lin, Mao %A Liu, Zhenlei %A Liu, Gang %A Zhao, Sen %A Li, Chao %A Chen, Weisheng %A Coban Akdemir, Zeynep %A Lin, Jiachen %A Song, Xiaofei %A Wang, Shengru %A Xu, Qiming %A Zhao, Yanxue %A Wang, Lianlei %A Zhang, Yuanqiang %A Yan, Zihui %A Liu, Sen %A Liu, Jiaqi %A Chen, Yixin %A Zuo, Yuzhi %A Yang, Xu %A Sun, Tianshu %A Yang, Xin-Zhuang %A Niu, Yuchen %A Li, Xiaoxin %A You, Wesley %A Qiu, Bintao %A Ding, Chen %A Liu, Pengfei %A Zhang, Shuyang %A Carvalho, Claudia M B %A Posey, Jennifer E %A Qiu, Guixing %A James R Lupski %A Wu, Zhihong %A Zhang, Jianguo %A Wu, Nan %K Adolescent %K Adult %K Child %K Female %K Fibrillin-1 %K HEK293 Cells %K Humans %K Lipodystrophy %K Marfan Syndrome %K Mutation %K Phenotype %K Progeria %K Protein Domains %K Smad2 Protein %X

BACKGROUND: The molecular and genetic mechanisms by which different single nucleotide variant alleles in specific genes, or at the same genetic locus, cause distinct disease phenotypes often remain unclear. Allelic truncating mutations of FBN1 could cause either classical Marfan syndrome (MFS) or a more complicated phenotype associated with Marfanoid-progeroid-lipodystrophy syndrome (MPLS).

METHODS: We investigated a small cohort, encompassing two classical MFS and one MPLS subjects from China, whose clinical presentation included scoliosis potentially requiring surgical intervention. Targeted next generation sequencing was performed on all the participants. We analyzed the molecular diagnosis, clinical features, and the potential molecular mechanism involved in the MPLS subject in our cohort.

RESULTS: We report a novel de novo FBN1 mutation for the first Chinese subject with MPLS, a more complicated fibrillinopathy, and two subjects with more classical MFS. We further predict that the MPLS truncating mutation, and others previously reported, is prone to escape the nonsense-mediated decay (NMD), while MFS mutations are predicted to be subjected to NMD. Also, the MPLS mutation occurs within the glucogenic hormone asprosin domain of FBN1. In vitro experiments showed that the single MPLS mutation p.Glu2759Cysfs*9 appears to perturb proper FBN1 protein aggregation as compared with the classical MFS mutation p.Tyr2596Thrfs*86. Both mutations appear to upregulate SMAD2 phosphorylation in vitro.

CONCLUSION: We provide direct evidence that a dominant-negative interaction of FBN1 potentially explains the complex MPLS phenotypes through genetic and functional analysis. Our study expands the mutation spectrum of FBN1 and highlights the potential molecular mechanism for MPLS.

%B Mol Genet Genomic Med %V 8 %P e1023 %8 2020 Jan %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/31774634?dopt=Abstract %R 10.1002/mgg3.1023 %0 Journal Article %J JBMR Plus %D 2020 %T Genetic Burden Contributing to Extremely Low or High Bone Mineral Density in a Senior Male Population From the Osteoporotic Fractures in Men Study (MrOS). %A Chen, Shan %A Jain, Mahim %A Jhangiani, Shalini %A Akdemir, Zeynep C %A Campeau, Philippe M %A Klein, Robert F %A Nielson, Carrie %A Dai, Hongzheng %A Donna M Muzny %A Eric Boerwinkle %A Richard A Gibbs %A Orwoll, Eric S %A James R Lupski %A Posey, Jennifer E %A Lee, Brendan %X

Worldwide, one in five men aged over 50 years will experience osteoporosis or a clinical bone fracture, with a greater fracture-related mortality rate than women. However, the genetic etiology of osteoporosis in men is still poorly understood. We aimed to identify the genetic variants and candidate genes associated with extremely low or high BMD for a better understanding of the biology underlying low bone density that may point to potential therapeutic targets for increasing bone mass. Subjects from the Osteoporotic Fractures in Men Study (MrOS) cohort were evaluated by age and BMI-adjusted total hip BMD. Those with BMD values 3 SDs away from the mean were selected and the remaining individuals whose adjusted BMD ranked at the highest or lowest 100 were included. Men with the lowest adjusted BMD ( = 98) and highest adjusted BMD ( = 110) were chosen for exome sequencing. Controls ( = 82) were men of Northern and Western European descent from the US Utah population of the 1000 Genomes Project. Fisher's exact test was performed to compare low- or high-BMD subjects with controls for single-gene associations. Additionally, sets of candidate genes causative of heritable disorders of connective tissue, including osteogenesis imperfecta (OI) and Ehlers-Danlos syndrome (EDS), were grouped for multigene and mutation burden analyses. No single-gene associations with rare variants were found for either the low BMD group (33 genes) or high BMD group (18 genes). In the group of OI genes, we detected a significant threefold increased accumulation of rare variants in low-BMD subjects compared with controls ( = 0.009). Additionally, genes associated with EDS had a twofold increased frequency in low-BMD subjects compared with controls ( = 0.03). These findings reveal a rare variant burden in OI and EDS disease genes at low BMD, which suggests a potential gene-panel approach to screen for multivariant associations in larger cohorts. © 2019 The Authors. published by Wiley Periodicals, Inc. on behalf of American Society for Bone and Mineral Research.

%B JBMR Plus %V 4 %P e10335 %8 2020 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/32161841?dopt=Abstract %R 10.1002/jbm4.10335 %0 Journal Article %J Genet Med %D 2020 %T Genotypic diversity and phenotypic spectrum of infantile liver failure syndrome type 1 due to variants in LARS1. %A Lenz, Dominic %A Smith, Desirée E C %A Crushell, Ellen %A Husain, Ralf A %A Salomons, Gajja S %A Alhaddad, Bader %A Bernstein, Jonathan A %A Bianzano, Alyssa %A Biskup, Saskia %A Brennenstuhl, Heiko %A Caldari, Dominique %A Dikow, Nicola %A Haack, Tobias B %A Hanson-Kahn, Andrea %A Harting, Inga %A Horn, Denise %A Hughes, Joanne %A Huijberts, Maya %A Isidor, Bertrand %A Kathemann, Simone %A Kopajtich, Robert %A Kotzaeridou, Urania %A Küry, Sébastien %A Lainka, Elke %A Laugwitz, Lucia %A James R Lupski %A Posey, Jennifer E %A Reynolds, Claire %A Rosenfeld, Jill A %A Schröter, Julian %A Vansenne, Fleur %A Wagner, Matias %A Weiß, Claudia %A Wolffenbuttel, Bruce H R %A Wortmann, Saskia B %A Kölker, Stefan %A Hoffmann, Georg F %A Prokisch, Holger %A Mendes, Marisa I %A Staufner, Christian %K Humans %K Liver Failure %K Muscle Hypotonia %K Mutation %K Seizures %X

PURPOSE: Biallelic variants in LARS1, coding for the cytosolic leucyl-tRNA synthetase, cause infantile liver failure syndrome 1 (ILFS1). Since its description in 2012, there has been no systematic analysis of the clinical spectrum and genetic findings.

METHODS: Individuals with biallelic variants in LARS1 were included through an international, multicenter collaboration including novel and previously published patients. Clinical variables were analyzed and functional studies were performed in patient-derived fibroblasts.

RESULTS: Twenty-five individuals from 15 families were ascertained including 12 novel patients with eight previously unreported variants. The most prominent clinical findings are recurrent elevation of liver transaminases up to liver failure and encephalopathic episodes, both triggered by febrile illness. Magnetic resonance image (MRI) changes during an encephalopathic episode can be consistent with metabolic stroke. Furthermore, growth retardation, microcytic anemia, neurodevelopmental delay, muscular hypotonia, and infection-related seizures are prevalent. Aminoacylation activity is significantly decreased in all patient cells studied upon temperature elevation in vitro.

CONCLUSION: ILFS1 is characterized by recurrent elevation of liver transaminases up to liver failure in conjunction with abnormalities of growth, blood, nervous system, and musculature. Encephalopathic episodes with seizures can occur independently from liver crises and may present with metabolic stroke.

%B Genet Med %V 22 %P 1863-1873 %8 2020 Nov %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/32699352?dopt=Abstract %R 10.1038/s41436-020-0904-4 %0 Journal Article %J Science %D 2020 %T HEM1 deficiency disrupts mTORC2 and F-actin control in inherited immunodysregulatory disease. %A Cook, Sarah A %A Comrie, William A %A Poli, M Cecilia %A Similuk, Morgan %A Oler, Andrew J %A Faruqi, Aiman J %A Kuhns, Douglas B %A Yang, Sheng %A Vargas-Hernandez, Alexander %A Carisey, Alexandre F %A Fournier, Benjamin %A Anderson, D Eric %A Price, Susan %A Smelkinson, Margery %A Abou Chahla, Wadih %A Forbes, Lisa R %A Mace, Emily M %A Cao, Tram N %A Coban-Akdemir, Zeynep H %A Jhangiani, Shalini N %A Donna M Muzny %A Richard A Gibbs %A James R Lupski %A Orange, Jordan S %A Cuvelier, Geoffrey D E %A Al Hassani, Moza %A Al Kaabi, Nawal %A Al Yafei, Zain %A Jyonouchi, Soma %A Raje, Nikita %A Caldwell, Jason W %A Huang, Yanping %A Burkhardt, Janis K %A Latour, Sylvain %A Chen, Baoyu %A ElGhazali, Gehad %A Rao, V Koneti %A Chinn, Ivan K %A Lenardo, Michael J %K Actins %K ADP-Ribosylation Factor 1 %K CD4-Positive T-Lymphocytes %K Cell Proliferation %K Cytokines %K Humans %K Immunologic Deficiency Syndromes %K Lymphoproliferative Disorders %K Mechanistic Target of Rapamycin Complex 2 %K Membrane Proteins %K Pedigree %K Phosphorylation %K Wiskott-Aldrich Syndrome Protein Family %X

Immunodeficiency often coincides with hyperactive immune disorders such as autoimmunity, lymphoproliferation, or atopy, but this coincidence is rarely understood on a molecular level. We describe five patients from four families with immunodeficiency coupled with atopy, lymphoproliferation, and cytokine overproduction harboring mutations in , which encodes the hematopoietic-specific HEM1 protein. These mutations cause the loss of the HEM1 protein and the WAVE regulatory complex (WRC) or disrupt binding to the WRC regulator, Arf1, thereby impairing actin polymerization, synapse formation, and immune cell migration. Diminished cortical actin networks caused by WRC loss led to uncontrolled cytokine release and immune hyperresponsiveness. HEM1 loss also blocked mechanistic target of rapamycin complex 2 (mTORC2)-dependent AKT phosphorylation, T cell proliferation, and selected effector functions, leading to immunodeficiency. Thus, the evolutionarily conserved HEM1 protein simultaneously regulates filamentous actin (F-actin) and mTORC2 signaling to achieve equipoise in immune responses.

%B Science %V 369 %P 202-207 %8 2020 Jul 10 %G eng %N 6500 %1 https://www.ncbi.nlm.nih.gov/pubmed/32647003?dopt=Abstract %R 10.1126/science.aay5663 %0 Journal Article %J J Clin Invest %D 2020 %T Human NK cell deficiency as a result of biallelic mutations in MCM10. %A Mace, Emily M %A Paust, Silke %A Conte, Matilde I %A Baxley, Ryan M %A Schmit, Megan M %A Patil, Sagar L %A Guilz, Nicole C %A Mukherjee, Malini %A Pezzi, Ashley E %A Chmielowiec, Jolanta %A Tatineni, Swetha %A Chinn, Ivan K %A Akdemir, Zeynep Coban %A Jhangiani, Shalini N %A Donna M Muzny %A Stray-Pedersen, Asbjørg %A Bradley, Rachel E %A Moody, Mo %A Connor, Philip P %A Heaps, Adrian G %A Steward, Colin %A Banerjee, Pinaki P %A Richard A Gibbs %A Borowiak, Malgorzata %A James R Lupski %A Jolles, Stephen %A Bielinsky, Anja K %A Orange, Jordan S %K Alleles %K Cell Cycle Checkpoints %K Cell Differentiation %K Cell Line %K Codon, Nonsense %K DNA Damage %K Fatal Outcome %K Female %K Gene Knockdown Techniques %K Heterozygote %K Humans %K Induced Pluripotent Stem Cells %K Infant %K Killer Cells, Natural %K Male %K Minichromosome Maintenance Proteins %K Models, Immunological %K Mutation %K Mutation, Missense %K Pedigree %K Primary Immunodeficiency Diseases %X

Human natural killer cell deficiency (NKD) arises from inborn errors of immunity that lead to impaired NK cell development, function, or both. Through the understanding of the biological perturbations in individuals with NKD, requirements for the generation of terminally mature functional innate effector cells can be elucidated. Here, we report a cause of NKD resulting from compound heterozygous mutations in minichromosomal maintenance complex member 10 (MCM10) that impaired NK cell maturation in a child with fatal susceptibility to CMV. MCM10 has not been previously associated with monogenic disease and plays a critical role in the activation and function of the eukaryotic DNA replisome. Through evaluation of patient primary fibroblasts, modeling patient mutations in fibroblast cell lines, and MCM10 knockdown in human NK cell lines, we have shown that loss of MCM10 function leads to impaired cell cycle progression and induction of DNA damage-response pathways. By modeling MCM10 deficiency in primary NK cell precursors, including patient-derived induced pluripotent stem cells, we further demonstrated that MCM10 is required for NK cell terminal maturation and acquisition of immunological system function. Together, these data define MCM10 as an NKD gene and provide biological insight into the requirement for the DNA replisome in human NK cell maturation and function.

%B J Clin Invest %V 130 %P 5272-5286 %8 2020 Oct 01 %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/32865517?dopt=Abstract %R 10.1172/JCI134966 %0 Journal Article %J Neurol Genet %D 2020 %T Integrated sequencing and array comparative genomic hybridization in familial Parkinson disease. %A Robak, Laurie A %A Du, Renqian %A Bo Yuan %A Gu, Shen %A Alfradique-Dunham, Isabel %A Kondapalli, Vismaya %A Hinojosa, Evelyn %A Stillwell, Amanda %A Young, Emily %A Zhang, Chaofan %A Song, Xiaofei %A Du, Haowei %A Gambin, Tomasz %A Jhangiani, Shalini N %A Coban Akdemir, Zeynep %A Donna M Muzny %A Tejomurtula, Anusha %A Ross, Owen A %A Shaw, Chad %A Jankovic, Joseph %A Bi, Weimin %A Posey, Jennifer E %A James R Lupski %A Shulman, Joshua M %X

OBJECTIVE: To determine how single nucleotide variants (SNVs) and copy number variants (CNVs) contribute to molecular diagnosis in familial Parkinson disease (PD), we integrated exome sequencing (ES) and genome-wide array-based comparative genomic hybridization (aCGH) and further probed CNV structure to reveal mutational mechanisms.

METHODS: We performed ES on 110 subjects with PD and a positive family history; 99 subjects were also evaluated using genome-wide aCGH. We interrogated ES and aCGH data for pathogenic SNVs and CNVs at Mendelian PD gene loci. We confirmed SNVs via Sanger sequencing and further characterized CNVs with custom-designed high-density aCGH, droplet digital PCR, and breakpoint sequencing.

RESULTS: Using ES, we discovered individuals with known pathogenic SNVs in (p.Glu365Lys, p.Thr408Met, p.Asn409Ser, and p.Leu483Pro) and (p.Arg1441Gly and p.Gly2019Ser). Two subjects were each double heterozygotes for variants in and . Based on aCGH, we additionally discovered cases with an duplication and heterozygous intragenic deletion. Five additional subjects harbored both SNVs (p.Asn52Metfs*29, p.Thr240Met, p.Pro437Leu, and p.Trp453*) and likely disrupting CNVs at the locus, consistent with compound heterozygosity. In nearly all cases, breakpoint sequencing revealed microhomology, a mutational signature consistent with CNV formation due to DNA replication errors.

CONCLUSIONS: Integrated ES and aCGH yielded a genetic diagnosis in 19.3% of our familial PD cohort. Our analyses highlight potential mechanisms for and CNV formation, uncover multilocus pathogenic variation, and identify novel SNVs and CNVs for further investigation as potential PD risk alleles.

%B Neurol Genet %V 6 %P e498 %8 2020 Oct %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/32802956?dopt=Abstract %R 10.1212/NXG.0000000000000498 %0 Journal Article %J Genet Med %D 2020 %T Low-level parental somatic mosaic SNVs in exomes from a large cohort of trios with diverse suspected Mendelian conditions. %A Gambin, Tomasz %A Liu, Qian %A Karolak, Justyna A %A Grochowski, Christopher M %A Xie, Nina G %A Wu, Lucia R %A Yan, Yan Helen %A Cao, Ye %A Coban Akdemir, Zeynep H %A Wilson, Theresa A %A Jhangiani, Shalini N %A Chen, Ed %A Eng, Christine M %A Donna M Muzny %A Posey, Jennifer E %A Yang, Yaping %A Zhang, David Y %A Shaw, Chad %A Liu, Pengfei %A James R Lupski %A Stankiewicz, Paweł %K Exome %K Exome Sequencing %K High-Throughput Nucleotide Sequencing %K Humans %K Mosaicism %K Parents %X

PURPOSE: The goal of this study was to assess the scale of low-level parental mosaicism in exome sequencing (ES) databases.

METHODS: We analyzed approximately 2000 family trio ES data sets from the Baylor-Hopkins Center for Mendelian Genomics (BHCMG) and Baylor Genetics (BG). Among apparent de novo single-nucleotide variants identified in the affected probands, we selected rare unique variants with variant allele fraction (VAF) between 30% and 70% in the probands and lower than 10% in one of the parents.

RESULTS: Of 102 candidate mosaic variants validated using amplicon-based next-generation sequencing, droplet digital polymerase chain reaction, or blocker displacement amplification, 27 (26.4%) were confirmed to be low- (VAF between 1% and 10%) or very low (VAF <1%) level mosaic. Detection precision in parental samples with two or more alternate reads was 63.6% (BHCMG) and 43.6% (BG). In nine investigated individuals, we observed variability of mosaic ratios among blood, saliva, fibroblast, buccal, hair, and urine samples.

CONCLUSION: Our computational pipeline enables robust discrimination between true and false positive candidate mosaic variants and efficient detection of low-level mosaicism in ES samples. We confirm that the presence of two or more alternate reads in the parental sample is a reliable predictor of low-level parental somatic mosaicism.

%B Genet Med %V 22 %P 1768-1776 %8 2020 Nov %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/32655138?dopt=Abstract %R 10.1038/s41436-020-0897-z %0 Journal Article %J Nat Commun %D 2020 %T NEMF mutations that impair ribosome-associated quality control are associated with neuromuscular disease. %A Martin, Paige B %A Kigoshi-Tansho, Yu %A Sher, Roger B %A Ravenscroft, Gianina %A Stauffer, Jennifer E %A Kumar, Rajesh %A Yonashiro, Ryo %A Müller, Tina %A Griffith, Christopher %A Allen, William %A Pehlivan, Davut %A Harel, Tamar %A Zenker, Martin %A Howting, Denise %A Schanze, Denny %A Faqeih, Eissa A %A Almontashiri, Naif A M %A Maroofian, Reza %A Houlden, Henry %A Mazaheri, Neda %A Galehdari, Hamid %A Douglas, Ganka %A Posey, Jennifer E %A Ryan, Monique %A James R Lupski %A Laing, Nigel G %A Joazeiro, Claudio A P %A Cox, Gregory A %K Amino Acid Sequence %K Animals %K Female %K Humans %K Male %K Mice %K Mice, Knockout %K Mutation %K Neuromuscular Diseases %K Proteolysis %K Ribosomes %K RNA-Binding Proteins %K Saccharomyces cerevisiae %K Saccharomyces cerevisiae Proteins %K Sequence Alignment %X

A hallmark of neurodegeneration is defective protein quality control. The E3 ligase Listerin (LTN1/Ltn1) acts in a specialized protein quality control pathway-Ribosome-associated Quality Control (RQC)-by mediating proteolytic targeting of incomplete polypeptides produced by ribosome stalling, and Ltn1 mutation leads to neurodegeneration in mice. Whether neurodegeneration results from defective RQC and whether defective RQC contributes to human disease have remained unknown. Here we show that three independently-generated mouse models with mutations in a different component of the RQC complex, NEMF/Rqc2, develop progressive motor neuron degeneration. Equivalent mutations in yeast Rqc2 selectively interfere with its ability to modify aberrant translation products with C-terminal tails which assist with RQC-mediated protein degradation, suggesting a pathomechanism. Finally, we identify NEMF mutations expected to interfere with function in patients from seven families presenting juvenile neuromuscular disease. These uncover NEMF's role in translational homeostasis in the nervous system and implicate RQC dysfunction in causing neurodegeneration.

%B Nat Commun %V 11 %P 4625 %8 2020 Sep 15 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/32934225?dopt=Abstract %R 10.1038/s41467-020-18327-6 %0 Journal Article %J Genomics %D 2020 %T Parental somatic mosaicism for CNV deletions - A need for more sensitive and precise detection methods in clinical diagnostics settings. %A Liu, Qian %A Karolak, Justyna A %A Grochowski, Christopher M %A Wilson, Theresa A %A Rosenfeld, Jill A %A Bacino, Carlos A %A Lalani, Seema R %A Patel, Ankita %A Breman, Amy %A Smith, Janice L %A Cheung, Sau Wai %A James R Lupski %A Bi, Weimin %A Stankiewicz, Pawel %K Clinical Laboratory Techniques %K DNA Copy Number Variations %K Female %K High-Throughput Nucleotide Sequencing %K Humans %K Inheritance Patterns %K Male %K Mosaicism %K Polymerase Chain Reaction %K Sequence Analysis, DNA %X

To further assess the scale and level of parental somatic mosaicism, we queried the CMA database at Baylor Genetics. We selected 50 unrelated families where clinically relevant apparent de novo CNV-deletions were found in the affected probands. Parental blood samples screening using deletion junction-specific PCR revealed four parents with somatic mosaicism. Droplet digital PCR (ddPCR), qPCR, and amplicon-based next-generation sequencing (NGS) were applied to validate these findings. Using ddPCR levels of mosaicism ranged from undetectable to 18.5%. Amplicon-based NGS and qPCR for the father with undetectable mosaicism was able to detect mosaicism at 0.39%. In one mother, ddPCR analysis revealed 15.6%, 10.6%, 8.2%, and undetectable levels of mosaicism in her blood, buccal cells, saliva, and urine samples, respectively. Our data suggest that more sensitive and precise methods, e.g. CNV junction-specific LR-PCR, ddPCR, or qPCR may allow for a more refined assessment of the potential disease recurrence risk for an identified variant.

%B Genomics %V 112 %P 2937-2941 %8 2020 Sep %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/32387503?dopt=Abstract %R 10.1016/j.ygeno.2020.05.003 %0 Journal Article %J Hum Mutat %D 2020 %T Phenotypic expansion in KIF1A-related dominant disorders: A description of novel variants and review of published cases. %A Montenegro-Garreaud, Ximena %A Hansen, Adam W %A Khayat, Michael M %A Chander, Varuna %A Grochowski, Christopher M %A Jiang, Yunyun %A Li, He %A Mitani, Tadahiro %A Kessler, Elena %A Jayaseelan, Joy %A Shen, Hua %A Gezdirici, Alper %A Pehlivan, Davut %A Meng, Qingchang %A Rosenfeld, Jill A %A Jhangiani, Shalini N %A Madan-Khetarpal, Suneeta %A Scott, Daryl A %A Abarca-Barriga, Hugo %A Trubnykova, Milana %A Marie-Claude Gingras %A Donna M Muzny %A Posey, Jennifer E %A Liu, Pengfei %A James R Lupski %A Richard A Gibbs %K Child %K Child, Preschool %K Family %K Female %K Genes, Dominant %K Genetic Predisposition to Disease %K Humans %K Kinesins %K Male %K Mutation %K Pedigree %K Peru %K Phenotype %X

KIF1A is a molecular motor for membrane-bound cargo important to the development and survival of sensory neurons. KIF1A dysfunction has been associated with several Mendelian disorders with a spectrum of overlapping phenotypes, ranging from spastic paraplegia to intellectual disability. We present a novel pathogenic in-frame deletion in the KIF1A molecular motor domain inherited by two affected siblings from an unaffected mother with apparent germline mosaicism. We identified eight additional cases with heterozygous, pathogenic KIF1A variants ascertained from a local data lake. Our data provide evidence for the expansion of KIF1A-associated phenotypes to include hip subluxation and dystonia as well as phenotypes observed in only a single case: gelastic cataplexy, coxa valga, and double collecting system. We review the literature and suggest that KIF1A dysfunction is better understood as a single neuromuscular disorder with variable involvement of other organ systems than a set of discrete disorders converging at a single locus.

%B Hum Mutat %V 41 %P 2094-2104 %8 2020 Dec %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/32935419?dopt=Abstract %R 10.1002/humu.24118 %0 Journal Article %J Am J Med Genet A %D 2020 %T Phenotypic expansion of POGZ-related intellectual disability syndrome (White-Sutton syndrome). %A Assia Batzir, Nurit %A Posey, Jennifer E %A Song, Xiaofei %A Akdemir, Zeynep Coban %A Rosenfeld, Jill A %A Brown, Chester W %A Chen, Emily %A Holtrop, Shannon G %A Mizerik, Elizabeth %A Nieto Moreno, Margarita %A Payne, Katelyn %A Raas-Rothschild, Annick %A Scott, Richard %A Vernon, Hilary J %A Zadeh, Neda %A James R Lupski %A Sutton, V Reid %K Adolescent %K Adult %K Autistic Disorder %K Child %K Child, Preschool %K Exome %K Exome Sequencing %K Female %K Heterozygote %K Humans %K Infant %K Intellectual Disability %K Language Development Disorders %K Male %K Microcephaly %K Middle Aged %K Mutation %K Phenotype %K Transposases %K Young Adult %X

White-Sutton syndrome (WHSUS) is a recently-identified genetic disorder resulting from de novo heterozygous pathogenic variants in POGZ. Thus far, over 50 individuals have been reported worldwide, however phenotypic characterization and data regarding the natural history are still incomplete. Here we report the clinical features of 22 individuals with 21 unique loss of function POGZ variants. We observed a broad spectrum of intellectual disability and/or developmental delay with or without autism, and speech delay in all individuals. Other common problems included ocular abnormalities, hearing loss and gait abnormalities. A validated sleep disordered breathing questionnaire identified symptoms of obstructive sleep apnea in 4/12 (33%) individuals. A higher-than-expected proportion of cases also had gastrointestinal phenotypes, both functional and anatomical, as well as genitourinary anomalies. In line with previous publications, we observed an increased body mass index (BMI) z-score compared to the general population (mean 0.59, median 0.9; p 0.0253). Common facial features included microcephaly, broad forehead, midface hypoplasia, triangular mouth, broad nasal root and flat nasal bridge. Analysis of the Baylor Genetics clinical laboratory database revealed that POGZ variants were implicated in approximately 0.14% of cases who underwent clinical exome sequencing for neurological indications with or without involvement of other body systems. This study describes a greater allelic series and expands the phenotypic spectrum of this new syndromic form of intellectual disability and autism.

%B Am J Med Genet A %V 182 %P 38-52 %8 2020 Jan %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/31782611?dopt=Abstract %R 10.1002/ajmg.a.61380 %0 Journal Article %J Curr Protoc Hum Genet %D 2020 %T Quantitative Assessment of Parental Somatic Mosaicism for Copy-Number Variant (CNV) Deletions. %A Liu, Qian %A Grochowski, Christopher M %A Bi, Weimin %A James R Lupski %A Stankiewicz, Paweł %K DNA Copy Number Variations %K Genetic Diseases, Inborn %K High-Throughput Nucleotide Sequencing %K Humans %K Mosaicism %K Parents %K Polymorphism, Single Nucleotide %K Real-Time Polymerase Chain Reaction %X

As genome sequencing methodologies have become more sensitive in detecting low-frequency rare-variant events, the link between post-zygotic mutagenesis and somatic mosaicism in the etiology of several human genetic conditions other than cancers has become more clear. Given that current clinical-genomics diagnostic methods have limited detection sensitivity for mosaic events, a copy-number variant (CNV) deletion inherited from a parent with low-level (<10%) mosaicism can be erroneously interpreted in the proband to represent a de novo germline event. Here, we describe three sensitive, precise, and cost-efficient methods that can quantitatively assess the potential degree of parental somatic mosaicism levels for CNV deletions: droplet digital PCR (ddPCR), PCR amplicon-based next-generation sequencing (NGS), and quantitative PCR. ddPCR using the EvaGreen fluorescent dye protocol can specifically quantify the deleted or non-deleted alleles by analyzing the number of droplets positive for a fluorescent signal for each event. PCR amplicon-based NGS assesses the allele frequencies of a heterozygous single-nucleotide polymorphism within a deletion region. The difference in number of reads between the two genotypes indicates the level of somatic mosaicism for the CNV deletion. Quantitative PCR can be applied where the relative quantity of the deletion junction-specific product represents the level of mosaicism. Clinical implementation of these quantitative variant-detection methods enables potentially more accurate assessment of disease recurrence risk in family-based genetic counseling, allowing couples to engage in more informed family planning. © 2020 by John Wiley & Sons, Inc. Basic Protocol: Droplet digital PCR (ddPCR) Alternate Protocol 1: PCR amplicon-based next-generation sequencing Alternate Protocol 2: Quantitative real-time PCR (qPCR).

%B Curr Protoc Hum Genet %V 106 %P e99 %8 2020 Jun %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/32176465?dopt=Abstract %R 10.1002/cphg.99 %0 Journal Article %J Hum Mutat %D 2020 %T Recurrent arginine substitutions in the ACTG2 gene are the primary driver of disease burden and severity in visceral myopathy. %A Assia Batzir, Nurit %A Kishor Bhagwat, Pranjali %A Larson, Austin %A Coban Akdemir, Zeynep %A Bagłaj, Maciej %A Bofferding, Leon %A Bosanko, Katherine B %A Bouassida, Skander %A Callewaert, Bert %A Cannon, Ashley %A Enchautegui Colon, Yazmin %A Garnica, Adolfo D %A Harr, Margaret H %A Heck, Sandra %A Hurst, Anna C E %A Jhangiani, Shalini N %A Isidor, Bertrand %A Littlejohn, Rebecca O %A Liu, Pengfei %A Magoulas, Pilar %A Mar Fan, Helen %A Marom, Ronit %A McLean, Scott %A Nezarati, Marjan M %A Nugent, Kimberly M %A Petersen, Michael B %A Rocha, Maria L %A Roeder, Elizabeth %A Smigiel, Robert %A Tully, Ian %A Weisfeld-Adams, James %A Wells, Katerina O %A Posey, Jennifer E %A James R Lupski %A Beaudet, Arthur L %A Wangler, Michael F %K Abnormalities, Multiple %K Actins %K Adult %K Amino Acid Substitution %K Arginine %K Colon %K DNA Mutational Analysis %K Exome Sequencing %K Female %K Genetic Association Studies %K Genetic Predisposition to Disease %K Genotype %K Humans %K Intestinal Pseudo-Obstruction %K Male %K Molecular Diagnostic Techniques %K Mutation %K Phenotype %K Urinary Bladder %K Young Adult %X

Visceral myopathy with abnormal intestinal and bladder peristalsis includes a clinical spectrum with megacystis-microcolon intestinal hypoperistalsis syndrome and chronic intestinal pseudo-obstruction. The vast majority of cases are caused by dominant variants in ACTG2; however, the overall genetic architecture of visceral myopathy has not been well-characterized. We ascertained 53 families, with visceral myopathy based on megacystis, functional bladder/gastrointestinal obstruction, or microcolon. A combination of targeted ACTG2 sequencing and exome sequencing was used. We report a molecular diagnostic rate of 64% (34/53), of which 97% (33/34) is attributed to ACTG2. Strikingly, missense mutations in five conserved arginine residues involving CpG dinucleotides accounted for 49% (26/53) of disease in the cohort. As a group, the ACTG2-negative cases had a more favorable clinical outcome and more restricted disease. Within the ACTG2-positive group, poor outcomes (characterized by total parenteral nutrition dependence, death, or transplantation) were invariably due to one of the arginine missense alleles. Analysis of specific residues suggests a severity spectrum of p.Arg178>p.Arg257>p.Arg40 along with other less-frequently reported sites p.Arg63 and p.Arg211. These results provide genotype-phenotype correlation for ACTG2-related disease and demonstrate the importance of arginine missense changes in visceral myopathy.

%B Hum Mutat %V 41 %P 641-654 %8 2020 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/31769566?dopt=Abstract %R 10.1002/humu.23960 %0 Journal Article %J Am J Hum Genet %D 2020 %T Recurrent De Novo NAHR Reciprocal Duplications in the ATAD3 Gene Cluster Cause a Neurogenetic Trait with Perturbed Cholesterol and Mitochondrial Metabolism. %A Gunning, Adam C %A Strucinska, Klaudia %A Muñoz Oreja, Mikel %A Parrish, Andrew %A Caswell, Richard %A Stals, Karen L %A Durigon, Romina %A Durlacher-Betzer, Karina %A Cunningham, Mitchell H %A Grochowski, Christopher M %A Baptista, Julia %A Tysoe, Carolyn %A Baple, Emma %A Lahiri, Nayana %A Homfray, Tessa %A Scurr, Ingrid %A Armstrong, Catherine %A Dean, John %A Fernandez Pelayo, Uxoa %A Jones, Aleck W E %A Taylor, Robert W %A Misra, Vinod K %A Yoon, Wan Hee %A Wright, Caroline F %A James R Lupski %A Spinazzola, Antonella %A Harel, Tamar %A Holt, Ian J %A Ellard, Sian %K Amino Acid Sequence %K ATPases Associated with Diverse Cellular Activities %K Brain Diseases %K Cardiomyopathies %K Cholesterol %K Corneal Opacity %K DNA Copy Number Variations %K Female %K Gene Duplication %K Gene Rearrangement %K Homologous Recombination %K Humans %K Infant %K Infant, Newborn %K Male %K Membrane Proteins %K Mitochondria %K Mitochondrial Diseases %K Mitochondrial Proteins %K Muscle Hypotonia %K Mutation %K Protein Conformation %K Seizures %K Sequence Homology %X

Recent studies have identified both recessive and dominant forms of mitochondrial disease that result from ATAD3A variants. The recessive form includes subjects with biallelic deletions mediated by non-allelic homologous recombination. We report five unrelated neonates with a lethal metabolic disorder characterized by cardiomyopathy, corneal opacities, encephalopathy, hypotonia, and seizures in whom a monoallelic reciprocal duplication at the ATAD3 locus was identified. Analysis of the breakpoint junction fragment indicated that these 67 kb heterozygous duplications were likely mediated by non-allelic homologous recombination at regions of high sequence identity in ATAD3A exon 11 and ATAD3C exon 7. At the recombinant junction, the duplication allele produces a fusion gene derived from ATAD3A and ATAD3C, the protein product of which lacks key functional residues. Analysis of fibroblasts derived from two affected individuals shows that the fusion gene product is expressed and stable. These cells display perturbed cholesterol and mitochondrial DNA organization similar to that observed for individuals with severe ATAD3A deficiency. We hypothesize that the fusion protein acts through a dominant-negative mechanism to cause this fatal mitochondrial disorder. Our data delineate a molecular diagnosis for this disorder, extend the clinical spectrum associated with structural variation at the ATAD3 locus, and identify a third mutational mechanism for ATAD3 gene cluster variants. These results further affirm structural variant mutagenesis mechanisms in sporadic disease traits, emphasize the importance of copy number analysis in molecular genomic diagnosis, and highlight some of the challenges of detecting and interpreting clinically relevant rare gene rearrangements from next-generation sequencing data.

%B Am J Hum Genet %V 106 %P 272-279 %8 2020 Feb 06 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/32004445?dopt=Abstract %R 10.1016/j.ajhg.2020.01.007 %0 Journal Article %J Hum Mutat %D 2020 %T TBX6 missense variants expand the mutational spectrum in a non-Mendelian inheritance disease. %A Chen, Weisheng %A Lin, Jiachen %A Wang, Lianlei %A Li, Xiaoxin %A Zhao, Sen %A Liu, Jiaqi %A Akdemir, Zeynep C %A Zhao, Yanxue %A Du, Renqian %A Ye, Yongyu %A Song, Xiaofei %A Zhang, Yuanqiang %A Yan, Zihui %A Yang, Xinzhuang %A Lin, Mao %A Shen, Jianxiong %A Wang, Shengru %A Gao, Na %A Yang, Ying %A Liu, Ying %A Li, Wenli %A Liu, Jia %A Zhang, Na %A Yang, Xu %A Xu, Yuan %A Zhang, Jianguo %A Delgado, Mauricio R %A Posey, Jennifer E %A Qiu, Guixing %A Rios, Jonathan J %A Liu, Pengfei %A Wise, Carol A %A Zhang, Feng %A Wu, Zhihong %A James R Lupski %A Wu, Nan %K Alleles %K Cell Line %K Exome Sequencing %K Female %K Gene Expression %K Genes, Reporter %K Genetic Association Studies %K Genetic Predisposition to Disease %K Genotype %K Haplotypes %K Humans %K Inheritance Patterns %K Male %K Models, Molecular %K Molecular Diagnostic Techniques %K Mutation, Missense %K Phenotype %K Protein Conformation %K Radiography %K Sequence Analysis, DNA %K Spine %K Structure-Activity Relationship %K T-Box Domain Proteins %X

Congenital scoliosis (CS) is a birth defect with variable clinical and anatomical manifestations due to spinal malformation. The genetic etiology underlying about 10% of CS cases in the Chinese population is compound inheritance by which the gene dosage is reduced below that of haploinsufficiency. In this genetic model, the trait manifests as a result of the combined effect of a rare variant and common pathogenic variant allele at a locus. From exome sequencing (ES) data of 523 patients in Asia and two patients in Texas, we identified six TBX6 gene-disruptive variants from 11 unrelated CS patients via ES and in vitro functional testing. The in trans mild hypomorphic allele was identified in 10 of the 11 subjects; as anticipated these 10 shared a similar spinal deformity of hemivertebrae. The remaining case has a homozygous variant in TBX6 (c.418C>T) and presents a more severe spinal deformity phenotype. We found decreased transcriptional activity and abnormal cellular localization as the molecular mechanisms for TBX6 missense loss-of-function alleles. Expanding the mutational spectrum of TBX6 pathogenic alleles enabled an increased molecular diagnostic detection rate, provided further evidence for the gene dosage-dependent genetic model underlying CS, and refined clinical classification.

%B Hum Mutat %V 41 %P 182-195 %8 2020 Jan %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/31471994?dopt=Abstract %R 10.1002/humu.23907 %0 Journal Article %J Am J Med Genet A %D 2020 %T Whole-genome sequencing reveals complex chromosome rearrangement disrupting NIPBL in infant with Cornelia de Lange syndrome. %A Plesser Duvdevani, Morasha %A Pettersson, Maria %A Eisfeldt, Jesper %A Avraham, Ortal %A Dagan, Judith %A Frumkin, Ayala %A James R Lupski %A Lindstrand, Anna %A Harel, Tamar %K Cell Cycle Proteins %K Chromosome Aberrations %K Chromosomes %K De Lange Syndrome %K Genetic Predisposition to Disease %K Humans %K Infant %K Male %K Translocation, Genetic %K Whole Genome Sequencing %X

Clinical laboratory diagnostic evaluation of the genomes of children with suspected genetic disorders, including chromosomal microarray and exome sequencing, cannot detect copy number neutral genomic rearrangements such as inversions, balanced translocations, and complex chromosomal rearrangements (CCRs). We describe an infant with a clinical diagnosis of Cornelia de Lange syndrome (CdLS) in whom chromosome analysis revealed a de novo complex balanced translocation, 46,XY,t(5;7;6)(q11.2;q32;q13)dn. Subsequent molecular characterization by whole-genome sequencing (WGS) identified 23 breakpoints, delineating segments derived from four chromosomes (5;6;7;21) in ancestral or inverted orientation. One of the breakpoints disrupted a known CdLS gene, NIPBL. Further investigation revealed paternal origin of the CCR allele, clustering of the breakpoint junctions, and molecular repair signatures suggestive of a single catastrophic event. Notably, very short DNA segments (25 and 41 bp) were included in the reassembled chromosomes, lending additional support that the DNA repair machinery can detect and repair such segments. Interestingly, there was an independent paternally derived miniscule complex rearrangement, possibly predisposing to subsequent genomic instability. In conclusion, we report a CCR causing a monogenic Mendelian disorder, urging WGS analysis of similar unsolved cases with suspected Mendelian disorders. Breakpoint analysis allowed for identification of the underlying molecular diagnosis and implicated chromoanagenesis in CCR formation.

%B Am J Med Genet A %V 182 %P 1143-1151 %8 2020 May %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/32125084?dopt=Abstract %R 10.1002/ajmg.a.61539 %0 Journal Article %J Am J Med Genet A %D 2020 %T Wolff-Parkinson-White syndrome: De novo variants and evidence for mutational burden in genes associated with atrial fibrillation. %A Coban-Akdemir, Zeynep H %A Charng, Wu-Lin %A Azamian, Mahshid %A Paine, Ingrid S %A Punetha, Jaya %A Grochowski, Christopher M %A Gambin, Tomasz %A Valdes, Santiago O %A Cannon, Bryan %A Zapata, Gladys %A Hernandez, Patricia P %A Jhangiani, Shalini %A Harshavardhan Doddapaneni %A Jianhong Hu %A Boricha, Fatima %A Donna M Muzny %A Eric Boerwinkle %A Yang, Yaping %A Richard A Gibbs %A Posey, Jennifer E %A Wehrens, Xander H T %A Belmont, John W %A Kim, Jeffrey J %A Miyake, Christina Y %A James R Lupski %A Lalani, Seema R %K Adolescent %K Adult %K AMP-Activated Protein Kinases %K Ankyrins %K Atrial Fibrillation %K Carrier Proteins %K Child %K Cohort Studies %K Cytoskeletal Proteins %K DNA-Binding Proteins %K Exome Sequencing %K Female %K Genetic Association Studies %K Genetic Predisposition to Disease %K Heart Atria %K Homeodomain Proteins %K Humans %K LIM Domain Proteins %K Male %K Mutation %K Transcription Factors %K Wolff-Parkinson-White Syndrome %K Young Adult %X

BACKGROUND: Wolff-Parkinson-White (WPW) syndrome is a relatively common arrhythmia affecting ~1-3/1,000 individuals. Mutations in PRKAG2 have been described in rare patients in association with cardiomyopathy. However, the genetic basis of WPW in individuals with a structurally normal heart remains poorly understood. Sudden death due to atrial fibrillation (AF) can also occur in these individuals. Several studies have indicated that despite ablation of an accessory pathway, the risk of AF remains high in patients compared to general population.

METHODS: We applied exome sequencing in 305 subjects, including 65 trios, 80 singletons, and 6 multiple affected families. We used de novo analysis, candidate gene approach, and burden testing to explore the genetic contributions to WPW.

RESULTS: A heterozygous deleterious variant in PRKAG2 was identified in one subject, accounting for 0.6% (1/151) of the genetic basis of WPW in this study. Another individual with WPW and left ventricular hypertrophy carried a known pathogenic variant in MYH7. We found rare de novo variants in genes associated with arrhythmia and cardiomyopathy (ANK2, NEBL, PITX2, and PRDM16) in this cohort. There was an increased burden of rare deleterious variants (MAF ≤ 0.005) with CADD score ≥ 25 in genes linked to AF in cases compared to controls (P = .0023).

CONCLUSIONS: Our findings show an increased burden of rare deleterious variants in genes linked to AF in WPW syndrome, suggesting that genetic factors that determine the development of accessory pathways may be linked to an increased susceptibility of atrial muscle to AF in a subset of patients.

%B Am J Med Genet A %V 182 %P 1387-1399 %8 2020 Jun %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/32233023?dopt=Abstract %R 10.1002/ajmg.a.61571 %0 Journal Article %J Hum Mutat %D 2020 %T Xq22 deletions and correlation with distinct neurological disease traits in females: Further evidence for a contiguous gene syndrome. %A Hijazi, Hadia %A Coelho, Fernanda S %A Gonzaga-Jauregui, Claudia %A Bernardini, Laura %A Mar, Soe S %A Manning, Melanie A %A Hanson-Kahn, Andrea %A Naidu, Sakkubai %A Srivastava, Siddharth %A Lee, Jennifer A %A Jones, Julie R %A Friez, Michael J %A Alberico, Thomas %A Torres, Barbara %A Fang, Ping %A Cheung, Sau Wai %A Song, Xiaofei %A Davis-Williams, Angelique %A Jornlin, Carly %A Wight, Patricia A %A Patyal, Pankaj %A Taube, Jennifer %A Poretti, Andrea %A Inoue, Ken %A Zhang, Feng %A Pehlivan, Davut %A Carvalho, Claudia M B %A Hobson, Grace M %A James R Lupski %K Child %K Child, Preschool %K Chromosome Breakpoints %K Chromosome Deletion %K Chromosome Mapping %K Chromosomes, Human, X %K Comparative Genomic Hybridization %K Female %K Genetic Association Studies %K Genetic Predisposition to Disease %K Humans %K Male %K Nervous System Diseases %K Pedigree %K Phenotype %K Quantitative Trait, Heritable %K Repetitive Sequences, Nucleic Acid %K Sex Factors %K Syndrome %K X Chromosome Inactivation %X

Xq22 deletions that encompass PLP1 (Xq22-PLP1-DEL) are notable for variable expressivity of neurological disease traits in females ranging from a mild late-onset form of spastic paraplegia type 2 (MIM# 312920), sometimes associated with skewed X-inactivation, to an early-onset neurological disease trait (EONDT) of severe developmental delay, intellectual disability, and behavioral abnormalities. Size and gene content of Xq22-PLP1-DEL vary and were proposed as potential molecular etiologies underlying variable expressivity in carrier females where two smallest regions of overlap (SROs) were suggested to influence disease. We ascertained a cohort of eight unrelated patients harboring Xq22-PLP1-DEL and performed high-density array comparative genomic hybridization and breakpoint-junction sequencing. Molecular characterization of Xq22-PLP1-DEL from 17 cases (eight herein and nine published) revealed an overrepresentation of breakpoints that reside within repeats (11/17, ~65%) and the clustering of ~47% of proximal breakpoints in a genomic instability hotspot with characteristic non-B DNA density. These findings implicate a potential role for genomic architecture in stimulating the formation of Xq22-PLP1-DEL. The correlation of Xq22-PLP1-DEL gene content with neurological disease trait in female cases enabled refinement of the associated SROs to a single genomic interval containing six genes. Our data support the hypothesis that genes contiguous to PLP1 contribute to EONDT.

%B Hum Mutat %V 41 %P 150-168 %8 2020 Jan %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/31448840?dopt=Abstract %R 10.1002/humu.23902 %0 Journal Article %J Am J Med Genet A %D 2019 %T Biallelic and De Novo Variants in DONSON Reveal a Clinical Spectrum of Cell Cycle-opathies with Microcephaly, Dwarfism and Skeletal Abnormalities. %A Karaca, Ender %A Posey, Jennifer E %A Bostwick, Bret %A Liu, Pengfei %A Gezdirici, Alper %A Yesil, Gozde %A Coban Akdemir, Zeynep %A Bayram, Yavuz %A Harms, Frederike L %A Meinecke, Peter %A Alawi, Malik %A Bacino, Carlos A %A Sutton, V Reid %A Kortüm, Fanny %A James R Lupski %K Alleles %K Bone and Bones %K Cell Cycle %K Cell Cycle Proteins %K Child %K Child, Preschool %K Dwarfism %K Family %K Female %K Humans %K Infant %K Infant, Newborn %K Male %K Microcephaly %K Nuclear Proteins %K Pedigree %K Phenotype %X

Co-occurrence of primordial dwarfism and microcephaly together with particular skeletal findings are seen in a wide range of Mendelian syndromes including microcephaly micromelia syndrome (MMS, OMIM 251230), microcephaly, short stature, and limb abnormalities (MISSLA, OMIM 617604), and microcephalic primordial dwarfisms (MPDs). Genes associated with these syndromes encode proteins that have crucial roles in DNA replication or in other critical steps of the cell cycle that link DNA replication to cell division. We identified four unrelated families with five affected individuals having biallelic or de novo variants in DONSON presenting with a core phenotype of severe short stature (z score < -3 SD), additional skeletal abnormalities, and microcephaly. Two apparently unrelated families with identical homozygous c.631C > T p.(Arg211Cys) variant had clinical features typical of Meier-Gorlin syndrome (MGS), while two siblings with compound heterozygous c.346delG p.(Asp116Ile*62) and c.1349A > G p.(Lys450Arg) variants presented with Seckel-like phenotype. We also identified a de novo c.683G > T p.(Trp228Leu) variant in DONSON in a patient with prominent micrognathia, short stature and hypoplastic femur and tibia, clinically diagnosed with Femoral-Facial syndrome (FFS, OMIM 134780). Biallelic variants in DONSON have been recently described in individuals with microcephalic dwarfism. These studies also demonstrated that DONSON has an essential conserved role in the cell cycle. Here we describe novel biallelic and de novo variants that are associated with MGS, Seckel-like phenotype and FFS, the last of which has not been associated with any disease gene to date.

%B Am J Med Genet A %V 179 %P 2056-2066 %8 2019 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/31407851?dopt=Abstract %R 10.1002/ajmg.a.61315 %0 Journal Article %J Ann Clin Transl Neurol %D 2019 %T Biallelic CACNA2D2 variants in epileptic encephalopathy and cerebellar atrophy. %A Punetha, Jaya %A Karaca, Ender %A Gezdirici, Alper %A Lamont, Ryan E %A Pehlivan, Davut %A Marafi, Dana %A Appendino, Juan P %A Hunter, Jill V %A Akdemir, Zeynep C %A Fatih, Jawid M %A Jhangiani, Shalini N %A Richard A Gibbs %A Innes, A Micheil %A Posey, Jennifer E %A James R Lupski %K Adult %K Atrophy %K Calcium Channels %K Cerebellar Ataxia %K Cerebellar Diseases %K Epilepsy %K Female %K Humans %K Male %K Mutation, Missense %K Pedigree %K Seizures %K Siblings %K Spasms, Infantile %X

OBJECTIVE: To characterize the molecular and clinical phenotypic basis of developmental and epileptic encephalopathies caused by rare biallelic variants in CACNA2D2.

METHODS: Two affected individuals from a family with clinical features of early onset epileptic encephalopathy were recruited for exome sequencing at the Centers for Mendelian Genomics to identify their molecular diagnosis. GeneMatcher facilitated identification of a second family with a shared candidate disease gene identified through clinical gene panel-based testing.

RESULTS: Rare biallelic CACNA2D2 variants have been previously reported in three families with developmental and epileptic encephalopathy, and one family with congenital ataxia. We identified three individuals in two unrelated families with novel homozygous rare variants in CACNA2D2 with clinical features of developmental and epileptic encephalopathy and cerebellar atrophy. Family 1 includes two affected siblings with a likely damaging homozygous rare missense variant c.1778G>C; p.(Arg593Pro) in CACNA2D2. Family 2 includes a proband with a homozygous rare nonsense variant c.485_486del; p.(Tyr162Ter) in CACNA2D2. We compared clinical and molecular findings from all nine individuals reported to date and note that cerebellar atrophy is shared among all.

INTERPRETATION: Our study supports the candidacy of CACNA2D2 as a disease gene associated with a phenotypic spectrum of neurological disease that include features of developmental and epileptic encephalopathy, ataxia, and cerebellar atrophy. Age at presentation may affect apparent penetrance of neurogenetic trait manifestations and of a particular clinical neurological endophenotype, for example, seizures or ataxia.

%B Ann Clin Transl Neurol %V 6 %P 1395-1406 %8 2019 Aug %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/31402629?dopt=Abstract %R 10.1002/acn3.50824 %0 Journal Article %J Am J Hum Genet %D 2019 %T Bi-allelic Pathogenic Variants in TUBGCP2 Cause Microcephaly and Lissencephaly Spectrum Disorders. %A Mitani, Tadahiro %A Punetha, Jaya %A Akalin, Ibrahim %A Pehlivan, Davut %A Dawidziuk, Mateusz %A Coban Akdemir, Zeynep %A Yilmaz, Sarenur %A Aslan, Ezgi %A Hunter, Jill V %A Hijazi, Hadia %A Grochowski, Christopher M %A Jhangiani, Shalini N %A Karaca, Ender %A Fatih, Jawid M %A Iwanowski, Piotr %A Gambin, Tomasz %A Wlasienko, Pawel %A Goszczanska-Ciuchta, Alicja %A Bekiesinska-Figatowska, Monika %A Hosseini, Masoumeh %A Arzhangi, Sanaz %A Najmabadi, Hossein %A Rosenfeld, Jill A %A Du, Haowei %A Marafi, Dana %A Blaser, Susan %A Teitelbaum, Ronni %A Silver, Rachel %A Posey, Jennifer E %A Ropers, Hans-Hilger %A Richard A Gibbs %A Wiszniewski, Wojciech %A James R Lupski %A Chitayat, David %A Kahrizi, Kimia %A Gawlinski, Pawel %K Alleles %K Brain %K Cell Movement %K Child %K Exome %K Female %K Genetic Variation %K Homozygote %K Humans %K Lissencephaly %K Male %K Microcephaly %K Microtubule-Associated Proteins %K Microtubules %K Nervous System Malformations %K Neurons %K Phenotype %K Tubulin %X

Lissencephaly comprises a spectrum of malformations of cortical development. This spectrum includes agyria, pachygyria, and subcortical band heterotopia; each represents anatomical malformations of brain cortical development caused by neuronal migration defects. The molecular etiologies of neuronal migration anomalies are highly enriched for genes encoding microtubules and microtubule-associated proteins, and this enrichment highlights the critical role for these genes in cortical growth and gyrification. Using exome sequencing and family based rare variant analyses, we identified a homozygous variant (c.997C>T [p.Arg333Cys]) in TUBGCP2, encoding gamma-tubulin complex protein 2 (GCP2), in two individuals from a consanguineous family; both individuals presented with microcephaly and developmental delay. GCP2 forms the multiprotein γ-tubulin ring complex (γ-TuRC) together with γ-tubulin and other GCPs to regulate the assembly of microtubules. By querying clinical exome sequencing cases and through GeneMatcher-facilitated collaborations, we found three additional families with bi-allelic variation and similarly affected phenotypes including a homozygous variant (c.1843G>C [p.Ala615Pro]) in two families and compound heterozygous variants consisting of one missense variant (c.889C>T [p.Arg297Cys]) and one splice variant (c.2025-2A>G) in another family. Brain imaging from all five affected individuals revealed varying degrees of cortical malformations including pachygyria and subcortical band heterotopia, presumably caused by disruption of neuronal migration. Our data demonstrate that pathogenic variants in TUBGCP2 cause an autosomal recessive neurodevelopmental trait consisting of a neuronal migration disorder, and our data implicate GCP2 as a core component of γ-TuRC in neuronal migrating cells.

%B Am J Hum Genet %V 105 %P 1005-1015 %8 2019 Nov 07 %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/31630790?dopt=Abstract %R 10.1016/j.ajhg.2019.09.017 %0 Journal Article %J Nat Commun %D 2019 %T Biallelic VARS variants cause developmental encephalopathy with microcephaly that is recapitulated in vars knockout zebrafish. %A Siekierska, Aleksandra %A Stamberger, Hannah %A Deconinck, Tine %A Oprescu, Stephanie N %A Partoens, Michèle %A Zhang, Yifan %A Sourbron, Jo %A Adriaenssens, Elias %A Mullen, Patrick %A Wiencek, Patrick %A Hardies, Katia %A Lee, Jeong-Soo %A Giong, Hoi-Khoanh %A Distelmaier, Felix %A Elpeleg, Orly %A Helbig, Katherine L %A Hersh, Joseph %A Isikay, Sedat %A Jordan, Elizabeth %A Karaca, Ender %A Kecskes, Angela %A James R Lupski %A Kovacs-Nagy, Reka %A May, Patrick %A Narayanan, Vinodh %A Pendziwiat, Manuela %A Ramsey, Keri %A Rangasamy, Sampathkumar %A Shinde, Deepali N %A Spiegel, Ronen %A Timmerman, Vincent %A von Spiczak, Sarah %A Helbig, Ingo %A Weckhuysen, Sarah %A Francklyn, Christopher %A Antonellis, Anthony %A de Witte, Peter %A De Jonghe, Peter %K Alleles %K Animals %K Brain Diseases %K Cell Line %K Disease Models, Animal %K Epilepsy %K Female %K Fibroblasts %K Gene Knockout Techniques %K Genetic Predisposition to Disease %K Humans %K Loss of Function Mutation %K Male %K Microcephaly %K Models, Molecular %K Neurodevelopmental Disorders %K Pedigree %K Prosencephalon %K Valine-tRNA Ligase %K Zebrafish %X

Aminoacyl tRNA synthetases (ARSs) link specific amino acids with their cognate transfer RNAs in a critical early step of protein translation. Mutations in ARSs have emerged as a cause of recessive, often complex neurological disease traits. Here we report an allelic series consisting of seven novel and two previously reported biallelic variants in valyl-tRNA synthetase (VARS) in ten patients with a developmental encephalopathy with microcephaly, often associated with early-onset epilepsy. In silico, in vitro, and yeast complementation assays demonstrate that the underlying pathomechanism of these mutations is most likely a loss of protein function. Zebrafish modeling accurately recapitulated some of the key neurological disease traits. These results provide both genetic and biological insights into neurodevelopmental disease and pave the way for further in-depth research on ARS related recessive disorders and precision therapies.

%B Nat Commun %V 10 %P 708 %8 2019 Feb 12 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/30755616?dopt=Abstract %R 10.1038/s41467-018-07953-w %0 Journal Article %J Genet Med %D 2019 %T Clinical exome sequencing reveals locus heterogeneity and phenotypic variability of cohesinopathies. %A Bo Yuan %A Neira, Juanita %A Pehlivan, Davut %A Santiago-Sim, Teresa %A Song, Xiaofei %A Rosenfeld, Jill %A Posey, Jennifer E %A Patel, Vipulkumar %A Jin, Weihong %A Adam, Margaret P %A Baple, Emma L %A Dean, John %A Fong, Chin-To %A Hickey, Scott E %A Hudgins, Louanne %A Leon, Eyby %A Madan-Khetarpal, Suneeta %A Rawlins, Lettie %A Rustad, Cecilie F %A Stray-Pedersen, Asbjørg %A Tveten, Kristian %A Wenger, Olivia %A Diaz, Jullianne %A Jenkins, Laura %A Martin, Laura %A McGuire, Marianne %A Pietryga, Marguerite %A Ramsdell, Linda %A Slattery, Leah %A Abid, Farida %A Bertuch, Alison A %A Grange, Dorothy %A Immken, Ladonna %A Schaaf, Christian P %A Van Esch, Hilde %A Bi, Weimin %A Cheung, Sau Wai %A Breman, Amy M %A Smith, Janice L %A Shaw, Chad %A Crosby, Andrew H %A Christine M Eng %A Yang, Yaping %A James R Lupski %A Xiao, Rui %A Liu, Pengfei %K Adolescent %K Alleles %K Antigens, Nuclear %K Biological Variation, Population %K Carrier Proteins %K Cell Cycle Proteins %K Child %K Child, Preschool %K Chromosomal Proteins, Non-Histone %K Cohort Studies %K De Lange Syndrome %K Exome %K Female %K Gene Frequency %K Genetic Heterogeneity %K Humans %K INDEL Mutation %K Male %K Mutation %K Nuclear Proteins %K Phenotype %K Polymorphism, Single Nucleotide %K Proto-Oncogene Proteins %K Retrospective Studies %K Whole Exome Sequencing %X

PURPOSE: Defects in the cohesin pathway are associated with cohesinopathies, notably Cornelia de Lange syndrome (CdLS). We aimed to delineate pathogenic variants in known and candidate cohesinopathy genes from a clinical exome perspective.

METHODS: We retrospectively studied patients referred for clinical exome sequencing (CES, N = 10,698). Patients with causative variants in novel or recently described cohesinopathy genes were enrolled for phenotypic characterization.

RESULTS: Pathogenic or likely pathogenic single-nucleotide and insertion/deletion variants (SNVs/indels) were identified in established disease genes including NIPBL (N = 5), SMC1A (N = 14), SMC3 (N = 4), RAD21 (N = 2), and HDAC8 (N = 8). The phenotypes in this genetically defined cohort skew towards the mild end of CdLS spectrum as compared with phenotype-driven cohorts. Candidate or recently reported cohesinopathy genes were supported by de novo SNVs/indels in STAG1 (N = 3), STAG2 (N = 5), PDS5A (N = 1), and WAPL (N = 1), and one inherited SNV in PDS5A. We also identified copy-number deletions affecting STAG1 (two de novo, one of unknown inheritance) and STAG2 (one of unknown inheritance). Patients with STAG1 and STAG2 variants presented with overlapping features yet without characteristic facial features of CdLS.

CONCLUSION: CES effectively identified disease-causing alleles at the mild end of the cohensinopathy spectrum and enabled characterization of candidate disease genes.

%B Genet Med %V 21 %P 663-675 %8 2019 03 %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/30158690?dopt=Abstract %R 10.1038/s41436-018-0085-6 %0 Journal Article %J Am J Hum Genet %D 2019 %T Complex Compound Inheritance of Lethal Lung Developmental Disorders Due to Disruption of the TBX-FGF Pathway. %A Karolak, Justyna A %A Vincent, Marie %A Deutsch, Gail %A Gambin, Tomasz %A Cogné, Benjamin %A Pichon, Olivier %A Vetrini, Francesco %A Mefford, Heather C %A Dines, Jennifer N %A Golden-Grant, Katie %A Dipple, Katrina %A Freed, Amanda S %A Leppig, Kathleen A %A Dishop, Megan %A Mowat, David %A Bennetts, Bruce %A Gifford, Andrew J %A Weber, Martin A %A Lee, Anna F %A Boerkoel, Cornelius F %A Bartell, Tina M %A Ward-Melver, Catherine %A Besnard, Thomas %A Petit, Florence %A Bache, Iben %A Tümer, Zeynep %A Denis-Musquer, Marie %A Joubert, Madeleine %A Martinovic, Jelena %A Bénéteau, Claire %A Molin, Arnaud %A Carles, Dominique %A André, Gwenaelle %A Bieth, Eric %A Chassaing, Nicolas %A Devisme, Louise %A Chalabreysse, Lara %A Pasquier, Laurent %A Secq, Véronique %A Don, Massimiliano %A Orsaria, Maria %A Missirian, Chantal %A Mortreux, Jérémie %A Sanlaville, Damien %A Pons, Linda %A Küry, Sébastien %A Bézieau, Stéphane %A Liet, Jean-Michel %A Joram, Nicolas %A Bihouée, Tiphaine %A Scott, Daryl A %A Brown, Chester W %A Scaglia, Fernando %A Tsai, Anne Chun-Hui %A Grange, Dorothy K %A Phillips, John A %A Pfotenhauer, Jean P %A Jhangiani, Shalini N %A Gonzaga-Jauregui, Claudia G %A Chung, Wendy K %A Schauer, Galen M %A Lipson, Mark H %A Mercer, Catherine L %A van Haeringen, Arie %A Liu, Qian %A Popek, Edwina %A Coban Akdemir, Zeynep H %A James R Lupski %A Szafranski, Przemyslaw %A Isidor, Bertrand %A Le Caignec, Cedric %A Stankiewicz, Paweł %K DNA Copy Number Variations %K Female %K Fibroblast Growth Factor 10 %K Gene Expression Regulation %K Gestational Age %K Humans %K Infant, Newborn %K Infant, Newborn, Diseases %K Lung %K Lung Diseases %K Male %K Maternal Inheritance %K Organogenesis %K Paternal Inheritance %K Pedigree %K Polymorphism, Single Nucleotide %K Receptor, Fibroblast Growth Factor, Type 2 %K Signal Transduction %K T-Box Domain Proteins %X

Primary defects in lung branching morphogenesis, resulting in neonatal lethal pulmonary hypoplasias, are incompletely understood. To elucidate the pathogenetics of human lung development, we studied a unique collection of samples obtained from deceased individuals with clinically and histopathologically diagnosed interstitial neonatal lung disorders: acinar dysplasia (n = 14), congenital alveolar dysplasia (n = 2), and other lethal lung hypoplasias (n = 10). We identified rare heterozygous copy-number variant deletions or single-nucleotide variants (SNVs) involving TBX4 (n = 8 and n = 2, respectively) or FGF10 (n = 2 and n = 2, respectively) in 16/26 (61%) individuals. In addition to TBX4, the overlapping ∼2 Mb recurrent and nonrecurrent deletions at 17q23.1q23.2 identified in seven individuals with lung hypoplasia also remove a lung-specific enhancer region. Individuals with coding variants involving either TBX4 or FGF10 also harbored at least one non-coding SNV in the predicted lung-specific enhancer region, which was absent in 13 control individuals with the overlapping deletions but without any structural lung anomalies. The occurrence of rare coding variants involving TBX4 or FGF10 with the putative hypomorphic non-coding SNVs implies a complex compound inheritance of these pulmonary hypoplasias. Moreover, they support the importance of TBX4-FGF10-FGFR2 epithelial-mesenchymal signaling in human lung organogenesis and help to explain the histopathological continuum observed in these rare lethal developmental disorders of the lung.

%B Am J Hum Genet %V 104 %P 213-228 %8 2019 Feb 07 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/30639323?dopt=Abstract %R 10.1016/j.ajhg.2018.12.010 %0 Journal Article %J Genome Med %D 2019 %T Copy number variant and runs of homozygosity detection by microarrays enabled more precise molecular diagnoses in 11,020 clinical exome cases. %A Dharmadhikari, Avinash V %A Ghosh, Rajarshi %A Bo Yuan %A Liu, Pengfei %A Dai, Hongzheng %A Al Masri, Sami %A Scull, Jennifer %A Posey, Jennifer E %A Jiang, Allen H %A He, Weimin %A Vetrini, Francesco %A Braxton, Alicia A %A Ward, Patricia %A Chiang, Theodore %A Qu, Chunjing %A Gu, Shen %A Shaw, Chad A %A Smith, Janice L %A Lalani, Seema %A Stankiewicz, Pawel %A Cheung, Sau-Wai %A Bacino, Carlos A %A Patel, Ankita %A Breman, Amy M %A Wang, Xia %A Meng, Linyan %A Xiao, Rui %A Xia, Fan %A Donna M Muzny %A Richard A Gibbs %A Beaudet, Arthur L %A Eng, Christine M %A James R Lupski %A Yang, Yaping %A Bi, Weimin %K Chromosome Aberrations %K DNA Copy Number Variations %K Exome Sequencing %K Female %K Genetic Testing %K Homozygote %K Humans %K Limit of Detection %K Male %K Microarray Analysis %X

BACKGROUND: Exome sequencing (ES) has been successfully applied in clinical detection of single nucleotide variants (SNVs) and small indels. However, identification of copy number variants (CNVs) using ES data remains challenging. The purpose of this study is to understand the contribution of CNVs and copy neutral runs of homozygosity (ROH) in molecular diagnosis of patients referred for ES.

METHODS: In a cohort of 11,020 consecutive ES patients, an Illumina SNP array analysis interrogating mostly coding SNPs was performed as a quality control (QC) measurement and for CNV/ROH detection. Among these patients, clinical chromosomal microarray analysis (CMA) was performed at Baylor Genetics (BG) on 3229 patients, either before, concurrently, or after ES. We retrospectively analyzed the findings from CMA and the QC array.

RESULTS: The QC array can detect ~ 70% of pathogenic/likely pathogenic CNVs (PCNVs) detectable by CMA. Out of the 11,020 ES cases, the QC array identified PCNVs in 327 patients and uniparental disomy (UPD) disorder-related ROH in 10 patients. The overall PCNV/UPD detection rate was 5.9% in the 3229 ES patients who also had CMA at BG; PCNV/UPD detection rate was higher in concurrent ES and CMA than in ES with prior CMA (7.2% vs 4.6%). The PCNVs/UPD contributed to the molecular diagnoses in 17.4% (189/1089) of molecularly diagnosed ES cases with CMA and were estimated to contribute in 10.6% of all molecularly diagnosed ES cases. Dual diagnoses with both PCNVs and SNVs were detected in 38 patients. PCNVs affecting single recessive disorder genes in a compound heterozygous state with SNVs were detected in 4 patients, and homozygous deletions (mostly exonic deletions) were detected in 17 patients. A higher PCNV detection rate was observed for patients with syndromic phenotypes and/or cardiovascular abnormalities.

CONCLUSIONS: Our clinical genomics study demonstrates that detection of PCNV/UPD through the QC array or CMA increases ES diagnostic rate, provides more precise molecular diagnosis for dominant as well as recessive traits, and enables more complete genetic diagnoses in patients with dual or multiple molecular diagnoses. Concurrent ES and CMA using an array with exonic coverage for disease genes enables most effective detection of both CNVs and SNVs and therefore is recommended especially in time-sensitive clinical situations.

%B Genome Med %V 11 %P 30 %8 2019 May 17 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/31101064?dopt=Abstract %R 10.1186/s13073-019-0639-5 %0 Journal Article %J Genome Med %D 2019 %T Correction to: De novo and inherited TCF20 pathogenic variants are associated with intellectual disability, dysmorphic features, hypotonia, and neurological impairments with similarities to Smith-Magenis syndrome. %A Vetrini, Francesco %A McKee, Shane %A Rosenfeld, Jill A %A Suri, Mohnish %A Lewis, Andrea M %A Nugent, Kimberly Margaret %A Roeder, Elizabeth %A Littlejohn, Rebecca O %A Holder, Sue %A Zhu, Wenmiao %A Alaimo, Joseph T %A Graham, Brett %A Harris, Jill M %A Gibson, James B %A Pastore, Matthew %A McBride, Kim L %A Komara, Makanko %A Al-Gazali, Lihadh %A Al Shamsi, Aisha %A Fanning, Elizabeth A %A Wierenga, Klaas J %A Scott, Daryl A %A Ben-Neriah, Ziva %A Meiner, Vardiella %A Cassuto, Hanoch %A Elpeleg, Orly %A Lloyd Holder, J %A Burrage, Lindsay C %A Seaver, Laurie H %A Van Maldergem, Lionel %A Mahida, Sonal %A Soul, Janet S %A Marlatt, Margaret %A Matyakhina, Ludmila %A Vogt, Julie %A Gold, June-Anne %A Park, Soo-Mi %A Varghese, Vinod %A Lampe, Anne K %A Kumar, Ajith %A Lees, Melissa %A Holder-Espinasse, Muriel %A McConnell, Vivienne %A Bernhard, Birgitta %A Blair, Ed %A Harrison, Victoria %A Donna M Muzny %A Richard A Gibbs %A Sarah H Elsea %A Posey, Jennifer E %A Bi, Weimin %A Lalani, Seema %A Xia, Fan %A Yang, Yaping %A Eng, Christine M %A James R Lupski %A Liu, Pengfei %X

It was highlighted that the original article [1] contained a typographical error in the Results section. Subject 17 was incorrectly cited as Subject 1. This Correction article shows the revised statement. The original article has been updated.

%B Genome Med %V 11 %P 16 %8 2019 Mar 25 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/30909959?dopt=Abstract %R 10.1186/s13073-019-0630-1 %0 Journal Article %J Genome Med %D 2019 %T De novo and inherited TCF20 pathogenic variants are associated with intellectual disability, dysmorphic features, hypotonia, and neurological impairments with similarities to Smith-Magenis syndrome. %A Vetrini, Francesco %A McKee, Shane %A Rosenfeld, Jill A %A Suri, Mohnish %A Lewis, Andrea M %A Nugent, Kimberly Margaret %A Roeder, Elizabeth %A Littlejohn, Rebecca O %A Holder, Sue %A Zhu, Wenmiao %A Alaimo, Joseph T %A Graham, Brett %A Harris, Jill M %A Gibson, James B %A Pastore, Matthew %A McBride, Kim L %A Komara, Makanko %A Al-Gazali, Lihadh %A Al Shamsi, Aisha %A Fanning, Elizabeth A %A Wierenga, Klaas J %A Scott, Daryl A %A Ben-Neriah, Ziva %A Meiner, Vardiella %A Cassuto, Hanoch %A Elpeleg, Orly %A Holder, J Lloyd %A Burrage, Lindsay C %A Seaver, Laurie H %A Van Maldergem, Lionel %A Mahida, Sonal %A Soul, Janet S %A Marlatt, Margaret %A Matyakhina, Ludmila %A Vogt, Julie %A Gold, June-Anne %A Park, Soo-Mi %A Varghese, Vinod %A Lampe, Anne K %A Kumar, Ajith %A Lees, Melissa %A Holder-Espinasse, Muriel %A McConnell, Vivienne %A Bernhard, Birgitta %A Blair, Ed %A Harrison, Victoria %A Donna M Muzny %A Richard A Gibbs %A Sarah H Elsea %A Posey, Jennifer E %A Bi, Weimin %A Lalani, Seema %A Xia, Fan %A Yang, Yaping %A Eng, Christine M %A James R Lupski %A Liu, Pengfei %K Adolescent %K Child %K Child, Preschool %K Craniofacial Abnormalities %K Developmental Disabilities %K Female %K Humans %K INDEL Mutation %K Infant %K Intellectual Disability %K Male %K Muscle Hypotonia %K Smith-Magenis Syndrome %K Transcription Factors %K Young Adult %X

BACKGROUND: Neurodevelopmental disorders are genetically and phenotypically heterogeneous encompassing developmental delay (DD), intellectual disability (ID), autism spectrum disorders (ASDs), structural brain abnormalities, and neurological manifestations with variants in a large number of genes (hundreds) associated. To date, a few de novo mutations potentially disrupting TCF20 function in patients with ID, ASD, and hypotonia have been reported. TCF20 encodes a transcriptional co-regulator structurally related to RAI1, the dosage-sensitive gene responsible for Smith-Magenis syndrome (deletion/haploinsufficiency) and Potocki-Lupski syndrome (duplication/triplosensitivity).

METHODS: Genome-wide analyses by exome sequencing (ES) and chromosomal microarray analysis (CMA) identified individuals with heterozygous, likely damaging, loss-of-function alleles in TCF20. We implemented further molecular and clinical analyses to determine the inheritance of the pathogenic variant alleles and studied the spectrum of phenotypes.

RESULTS: We report 25 unique inactivating single nucleotide variants/indels (1 missense, 1 canonical splice-site variant, 18 frameshift, and 5 nonsense) and 4 deletions of TCF20. The pathogenic variants were detected in 32 patients and 4 affected parents from 31 unrelated families. Among cases with available parental samples, the variants were de novo in 20 instances and inherited from 4 symptomatic parents in 5, including in one set of monozygotic twins. Two pathogenic loss-of-function variants were recurrent in unrelated families. Patients presented with a phenotype characterized by developmental delay, intellectual disability, hypotonia, variable dysmorphic features, movement disorders, and sleep disturbances.

CONCLUSIONS: TCF20 pathogenic variants are associated with a novel syndrome manifesting clinical characteristics similar to those observed in Smith-Magenis syndrome. Together with previously described cases, the clinical entity of TCF20-associated neurodevelopmental disorders (TAND) emerges from a genotype-driven perspective.

%B Genome Med %V 11 %P 12 %8 2019 Feb 28 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/30819258?dopt=Abstract %R 10.1186/s13073-019-0623-0 %0 Journal Article %J Genome Med %D 2019 %T Distinct patterns of complex rearrangements and a mutational signature of microhomeology are frequently observed in PLP1 copy number gain structural variants. %A Bahrambeigi, Vahid %A Song, Xiaofei %A Sperle, Karen %A Beck, Christine R %A Hijazi, Hadia %A Grochowski, Christopher M %A Gu, Shen %A Seeman, Pavel %A Woodward, Karen J %A Carvalho, Claudia M B %A Hobson, Grace M %A James R Lupski %K Chromosome Breakpoints %K Comparative Genomic Hybridization %K DNA Copy Number Variations %K Gene Duplication %K Gene Rearrangement %K Genetic Association Studies %K Genetic Predisposition to Disease %K Genome, Human %K Genomic Instability %K Genomics %K Humans %K Mutation %K Myelin Proteolipid Protein %K Polymorphism, Single Nucleotide %X

BACKGROUND: We investigated the features of the genomic rearrangements in a cohort of 50 male individuals with proteolipid protein 1 (PLP1) copy number gain events who were ascertained with Pelizaeus-Merzbacher disease (PMD; MIM: 312080). We then compared our new data to previous structural variant mutagenesis studies involving the Xq22 region of the human genome. The aggregate data from 159 sequenced join-points (discontinuous sequences in the reference genome that are joined during the rearrangement process) were studied. Analysis of these data from 150 individuals enabled the spectrum and relative distribution of the underlying genomic mutational signatures to be delineated.

METHODS: Genomic rearrangements in PMD individuals with PLP1 copy number gain events were investigated by high-density customized array or clinical chromosomal microarray analysis and breakpoint junction sequence analysis.

RESULTS: High-density customized array showed that the majority of cases (33/50; ~ 66%) present with single duplications, although complex genomic rearrangements (CGRs) are also frequent (17/50; ~ 34%). Breakpoint mapping to nucleotide resolution revealed further previously unknown structural and sequence complexities, even in single duplications. Meta-analysis of all studied rearrangements that occur at the PLP1 locus showed that single duplications were found in ~ 54% of individuals and that, among all CGR cases, triplication flanked by duplications is the most frequent CGR array CGH pattern observed. Importantly, in ~ 32% of join-points, there is evidence for a mutational signature of microhomeology (highly similar yet imperfect sequence matches).

CONCLUSIONS: These data reveal a high frequency of CGRs at the PLP1 locus and support the assertion that replication-based mechanisms are prominent contributors to the formation of CGRs at Xq22. We propose that microhomeology can facilitate template switching, by stabilizing strand annealing of the primer using W-C base complementarity, and is a mutational signature for replicative repair.

%B Genome Med %V 11 %P 80 %8 2019 Dec 09 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/31818324?dopt=Abstract %R 10.1186/s13073-019-0676-0 %0 Journal Article %J J Clin Endocrinol Metab %D 2019 %T Exome Sequencing of a Primary Ovarian Insufficiency Cohort Reveals Common Molecular Etiologies for a Spectrum of Disease. %A Jolly, Angad %A Bayram, Yavuz %A Turan, Serap %A Aycan, Zehra %A Tos, Tulay %A Abali, Zehra Yavas %A Hacihamdioglu, Bulent %A Coban Akdemir, Zeynep Hande %A Hijazi, Hadia %A Bas, Serpil %A Atay, Zeynep %A Guran, Tulay %A Abali, Saygin %A Bas, Firdevs %A Darendeliler, Feyza %A Colombo, Roberto %A Barakat, Tahsin Stefan %A Rinne, Tuula %A White, Janson J %A Yesil, Gozde %A Gezdirici, Alper %A Gulec, Elif Yilmaz %A Karaca, Ender %A Pehlivan, Davut %A Jhangiani, Shalini N %A Donna M Muzny %A Poyrazoglu, Sukran %A Bereket, Abdullah %A Richard A Gibbs %A Posey, Jennifer E %A James R Lupski %K Cell Cycle Proteins %K Cohort Studies %K DNA Helicases %K DNA-Binding Proteins %K Exome Sequencing %K Female %K Gene Frequency %K Humans %K Hypogonadism %K Immunoglobulins %K Minichromosome Maintenance Proteins %K Primary Ovarian Insufficiency %X

CONTEXT: Primary ovarian insufficiency (POI) encompasses a spectrum of premature menopause, including both primary and secondary amenorrhea. For 75% to 90% of individuals with hypergonadotropic hypogonadism presenting as POI, the molecular etiology is unknown. Common etiologies include chromosomal abnormalities, environmental factors, and congenital disorders affecting ovarian development and function, as well as syndromic and nonsyndromic single gene disorders suggesting POI represents a complex trait.

OBJECTIVE: To characterize the contribution of known disease genes to POI and identify molecular etiologies and biological underpinnings of POI.

DESIGN, SETTING, AND PARTICIPANTS: We applied exome sequencing (ES) and family-based genomics to 42 affected female individuals from 36 unrelated Turkish families, including 31 with reported parental consanguinity.

RESULTS: This analysis identified likely damaging, potentially contributing variants and molecular diagnoses in 16 families (44%), including 11 families with likely damaging variants in known genes and five families with predicted deleterious variants in disease genes (IGSF10, MND1, MRPS22, and SOHLH1) not previously associated with POI. Of the 16 families, 2 (13%) had evidence for potentially pathogenic variants at more than one locus. Absence of heterozygosity consistent with identity-by-descent mediated recessive disease burden contributes to molecular diagnosis in 15 of 16 (94%) families. GeneMatcher allowed identification of additional families from diverse genetic backgrounds.

CONCLUSIONS: ES analysis of a POI cohort further characterized locus heterogeneity, reaffirmed the association of genes integral to meiotic recombination, demonstrated the likely contribution of genes involved in hypothalamic development, and documented multilocus pathogenic variation suggesting the potential for oligogenic inheritance contributing to the development of POI.

%B J Clin Endocrinol Metab %V 104 %P 3049-3067 %8 2019 Aug 01 %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/31042289?dopt=Abstract %R 10.1210/jc.2019-00248 %0 Journal Article %J Eur J Hum Genet %D 2019 %T Genetic architecture of laterality defects revealed by whole exome sequencing. %A Li, Alexander H %A Hanchard, Neil A %A Azamian, Mahshid %A D'Alessandro, Lisa C A %A Coban-Akdemir, Zeynep %A Lopez, Keila N %A Hall, Nancy J %A Dickerson, Heather %A Nicosia, Annarita %A Fernbach, Susan %A Boone, Philip M %A Gambin, Tomaz %A Karaca, Ender %A Gu, Shen %A Bo Yuan %A Jhangiani, Shalini N %A Harshavardhan Doddapaneni %A Jianhong Hu %A Dinh, Huyen %A Jayaseelan, Joy %A Donna M Muzny %A Lalani, Seema %A Towbin, Jeffrey %A Penny, Daniel %A Fraser, Charles %A Martin, James %A James R Lupski %A Richard A Gibbs %A Eric Boerwinkle %A Ware, Stephanie M %A Belmont, John W %K Animals %K Body Patterning %K Embryonic Development %K Exome Sequencing %K Female %K Genetic Association Studies %K Genome, Human %K Genomics %K GTP Phosphohydrolases %K Heart Defects, Congenital %K Heterotaxy Syndrome %K Humans %K Male %K Peroxidases %K Zebrafish %K Zebrafish Proteins %X

Aberrant left-right patterning in the developing human embryo can lead to a broad spectrum of congenital malformations. The causes of most laterality defects are not known, with variants in established genes accounting for <20% of cases. We sought to characterize the genetic spectrum of these conditions by performing whole-exome sequencing of 323 unrelated laterality cases. We investigated the role of rare, predicted-damaging variation in 1726 putative laterality candidate genes derived from model organisms, pathway analyses, and human phenotypes. We also evaluated the contribution of homo/hemizygous exon deletions and gene-based burden of rare variation. A total of 28 candidate variants (26 rare predicted-damaging variants and 2 hemizygous deletions) were identified, including variants in genes known to cause heterotaxy and primary ciliary dyskinesia (ACVR2B, NODAL, ZIC3, DNAI1, DNAH5, HYDIN, MMP21), and genes without a human phenotype association, but with prior evidence for a role in embryonic laterality or cardiac development. Sanger validation of the latter variants in probands and their parents revealed no de novo variants, but apparent transmitted heterozygous (ROCK2, ISL1, SMAD2), and hemizygous (RAI2, RIPPLY1) variant patterns. Collectively, these variants account for 7.1% of our study subjects. We also observe evidence for an excess burden of rare, predicted loss-of-function variation in PXDNL and BMS1- two genes relevant to the broader laterality phenotype. These findings highlight potential new genes in the development of laterality defects, and suggest extensive locus heterogeneity and complex genetic models in this class of birth defects.

%B Eur J Hum Genet %V 27 %P 563-573 %8 2019 Apr %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/30622330?dopt=Abstract %R 10.1038/s41431-018-0307-z %0 Journal Article %J Am J Hum Genet %D 2019 %T A Genocentric Approach to Discovery of Mendelian Disorders. %A Hansen, Adam W %A Mullai Murugan %A Li, He %A Khayat, Michael M %A Wang, Liwen %A Rosenfeld, Jill %A B. Kim Andrews %A Jhangiani, Shalini N %A Coban Akdemir, Zeynep H %A Fritz J Sedlazeck %A Ashley-Koch, Allison E %A Liu, Pengfei %A Donna M Muzny %A Davis, Erica E %A Katsanis, Nicholas %A Aniko Sabo %A Posey, Jennifer E %A Yang, Yaping %A Wangler, Michael F %A Eng, Christine M %A Sutton, V Reid %A James R Lupski %A Eric Boerwinkle %A Richard A Gibbs %K Databases, Genetic %K Exome %K Exome Sequencing %K Genetic Diseases, Inborn %K Genetic Predisposition to Disease %K Genetic Variation %K Genomics %K Humans %K Pedigree %K Phenotype %X

The advent of inexpensive, clinical exome sequencing (ES) has led to the accumulation of genetic data from thousands of samples from individuals affected with a wide range of diseases, but for whom the underlying genetic and molecular etiology of their clinical phenotype remains unknown. In many cases, detailed phenotypes are unavailable or poorly recorded and there is little family history to guide study. To accelerate discovery, we integrated ES data from 18,696 individuals referred for suspected Mendelian disease, together with relatives, in an Apache Hadoop data lake (Hadoop Architecture Lake of Exomes [HARLEE]) and implemented a genocentric analysis that rapidly identified 154 genes harboring variants suspected to cause Mendelian disorders. The approach did not rely on case-specific phenotypic classifications but was driven by optimization of gene- and variant-level filter parameters utilizing historical Mendelian disease-gene association discovery data. Variants in 19 of the 154 candidate genes were subsequently reported as causative of a Mendelian trait and additional data support the association of all other candidate genes with disease endpoints.

%B Am J Hum Genet %V 105 %P 974-986 %8 2019 Nov 07 %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/31668702?dopt=Abstract %R 10.1016/j.ajhg.2019.09.027 %0 Journal Article %J Am J Hum Genet %D 2019 %T The Genomics of Arthrogryposis, a Complex Trait: Candidate Genes and Further Evidence for Oligogenic Inheritance. %A Pehlivan, Davut %A Bayram, Yavuz %A Gunes, Nilay %A Coban Akdemir, Zeynep %A Shukla, Anju %A Bierhals, Tatjana %A Tabakci, Burcu %A Sahin, Yavuz %A Gezdirici, Alper %A Fatih, Jawid M %A Gulec, Elif Yilmaz %A Yesil, Gozde %A Punetha, Jaya %A Ocak, Zeynep %A Grochowski, Christopher M %A Karaca, Ender %A Albayrak, Hatice Mutlu %A Radhakrishnan, Periyasamy %A Erdem, Haktan Bagis %A Sahin, Ibrahim %A Yildirim, Timur %A Bayhan, Ilhan A %A Bursali, Aysegul %A Elmas, Muhsin %A Yuksel, Zafer %A Ozdemir, Ozturk %A Silan, Fatma %A Yildiz, Onur %A Yesilbas, Osman %A Isikay, Sedat %A Balta, Burhan %A Gu, Shen %A Jhangiani, Shalini N %A Harshavardhan Doddapaneni %A Jianhong Hu %A Donna M Muzny %A Eric Boerwinkle %A Richard A Gibbs %A Tsiakas, Konstantinos %A Hempel, Maja %A Girisha, Katta Mohan %A Gul, Davut %A Posey, Jennifer E %A Elcioglu, Nursel H %A Tuysuz, Beyhan %A James R Lupski %K Adolescent %K Adult %K Arthrogryposis %K Child %K Child, Preschool %K Cohort Studies %K Connectin %K DNA Copy Number Variations %K Exome Sequencing %K Female %K Genetic Markers %K Genomics %K Gestational Age %K Humans %K Infant %K Infant, Newborn %K Male %K Mosaicism %K Multifactorial Inheritance %K Mutation %K Pedigree %K Ryanodine Receptor Calcium Release Channel %K Vesicular Transport Proteins %K Young Adult %X

Arthrogryposis is a clinical finding that is present either as a feature of a neuromuscular condition or as part of a systemic disease in over 400 Mendelian conditions. The underlying molecular etiology remains largely unknown because of genetic and phenotypic heterogeneity. We applied exome sequencing (ES) in a cohort of 89 families with the clinical sign of arthrogryposis. Additional molecular techniques including array comparative genomic hybridization (aCGH) and Droplet Digital PCR (ddPCR) were performed on individuals who were found to have pathogenic copy number variants (CNVs) and mosaicism, respectively. A molecular diagnosis was established in 65.2% (58/89) of families. Eleven out of 58 families (19.0%) showed evidence for potential involvement of pathogenic variation at more than one locus, probably driven by absence of heterozygosity (AOH) burden due to identity-by-descent (IBD). RYR3, MYOM2, ERGIC1, SPTBN4, and ABCA7 represent genes, identified in two or more families, for which mutations are probably causative for arthrogryposis. We also provide evidence for the involvement of CNVs in the etiology of arthrogryposis and for the idea that both mono-allelic and bi-allelic variants in the same gene cause either similar or distinct syndromes. We were able to identify the molecular etiology in nine out of 20 families who underwent reanalysis. In summary, our data from family-based ES further delineate the molecular etiology of arthrogryposis, yielded several candidate disease-associated genes, and provide evidence for mutational burden in a biological pathway or network. Our study also highlights the importance of reanalysis of individuals with unsolved diagnoses in conjunction with sequencing extended family members.

%B Am J Hum Genet %V 105 %P 132-150 %8 2019 Jul 03 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/31230720?dopt=Abstract %R 10.1016/j.ajhg.2019.05.015 %0 Journal Article %J Clin Genet %D 2019 %T Heterozygous CTNNB1 and TBX4 variants in a patient with abnormal lung growth, pulmonary hypertension, microcephaly, and spasticity. %A Karolak, Justyna A %A Szafranski, Przemyslaw %A Kilner, David %A Patel, Chirag %A Scurry, Bonnie %A Kinning, Esther %A Chandler, Kate %A Jhangiani, Shalini N %A Coban Akdemir, Zeynep H %A James R Lupski %A Popek, Edwina %A Stankiewicz, Paweł %K Alleles %K beta Catenin %K DNA Mutational Analysis %K Exome Sequencing %K Genetic Association Studies %K Genetic Predisposition to Disease %K Genetic Variation %K Heterozygote %K Humans %K Hypertension, Pulmonary %K Immunohistochemistry %K Microcephaly %K Muscle Spasticity %K Mutation %K Phenotype %K T-Box Domain Proteins %X

The canonical wingless (Wnt) and fibroblast growth factor (FGF) signaling pathways involving CTNNB1 and TBX4, respectively, are crucial for the regulation of human development. Perturbations of these pathways and disruptions from biological homeostasis have been associated with abnormal morphogenesis of multiple organs, including the lung. The aim of this study was to identify the underlying genetic cause of abnormal lung growth, pulmonary hypertension (PAH), severe microcephaly, and muscle spasticity in a full-term newborn, who died at 4 months of age due to progressively worsening PAH and respiratory failure. Family trio exome sequencing showed a de novo heterozygous nonsense c.1603C>T (p.Arg535*) variant in CTNNB1 and a paternally inherited heterozygous missense c.1198G>A (p.Glu400Lys) variant in TBX4, both predicted to be likely deleterious. We expand the phenotypic spectrum associated with CTNNB1 and TBX4 variants and indicate that they could act synergistically to produce a distinct more severe phenotype. Our findings further support a recently proposed complex compound inheritance model in lethal lung developmental diseases and the contention that dual molecular diagnoses can parsimoniously explain blended phenotypes.

%B Clin Genet %V 96 %P 366-370 %8 2019 Oct %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/31309540?dopt=Abstract %R 10.1111/cge.13605 %0 Journal Article %J Am J Hum Genet %D 2019 %T Homozygous Missense Variants in NTNG2, Encoding a Presynaptic Netrin-G2 Adhesion Protein, Lead to a Distinct Neurodevelopmental Disorder. %A Dias, Caroline M %A Punetha, Jaya %A Zheng, Céline %A Mazaheri, Neda %A Rad, Abolfazl %A Efthymiou, Stephanie %A Petersen, Andrea %A Dehghani, Mohammadreza %A Pehlivan, Davut %A Partlow, Jennifer N %A Posey, Jennifer E %A Salpietro, Vincenzo %A Gezdirici, Alper %A Malamiri, Reza Azizi %A Al Menabawy, Nihal M %A Selim, Laila A %A Vahidi Mehrjardi, Mohammad Yahya %A Banu, Selina %A Polla, Daniel L %A Yang, Edward %A Rezazadeh Varaghchi, Jamileh %A Mitani, Tadahiro %A van Beusekom, Ellen %A Najafi, Maryam %A Sedaghat, Alireza %A Keller-Ramey, Jennifer %A Durham, Leslie %A Coban-Akdemir, Zeynep %A Karaca, Ender %A Orlova, Valeria %A Schaeken, Lieke L M %A Sherafat, Amir %A Jhangiani, Shalini N %A Stanley, Valentina %A Shariati, Gholamreza %A Galehdari, Hamid %A Gleeson, Joseph G %A Walsh, Christopher A %A James R Lupski %A Seiradake, Elena %A Houlden, Henry %A van Bokhoven, Hans %A Maroofian, Reza %K Adolescent %K Adult %K Child %K Child, Preschool %K Exome %K Exome Sequencing %K Female %K GPI-Linked Proteins %K Homozygote %K Humans %K Intellectual Disability %K Male %K Mutation, Missense %K Netrins %K Neurodevelopmental Disorders %K Pedigree %K Young Adult %X

NTNG2 encodes netrin-G2, a membrane-anchored protein implicated in the molecular organization of neuronal circuitry and synaptic organization and diversification in vertebrates. In this study, through a combination of exome sequencing and autozygosity mapping, we have identified 16 individuals (from seven unrelated families) with ultra-rare homozygous missense variants in NTNG2; these individuals present with shared features of a neurodevelopmental disorder consisting of global developmental delay, severe to profound intellectual disability, muscle weakness and abnormal tone, autistic features, behavioral abnormalities, and variable dysmorphisms. The variants disrupt highly conserved residues across the protein. Functional experiments, including in silico analysis of the protein structure, in vitro assessment of cell surface expression, and in vitro knockdown, revealed potential mechanisms of pathogenicity of the variants, including loss of protein function and decreased neurite outgrowth. Our data indicate that appropriate expression of NTNG2 plays an important role in neurotypical development.

%B Am J Hum Genet %V 105 %P 1048-1056 %8 2019 Nov 07 %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/31668703?dopt=Abstract %R 10.1016/j.ajhg.2019.09.025 %0 Journal Article %J Genet Med %D 2019 %T Insights into genetics, human biology and disease gleaned from family based genomic studies. %A Posey, Jennifer E %A O'Donnell-Luria, Anne H %A Chong, Jessica X %A Harel, Tamar %A Jhangiani, Shalini N %A Coban Akdemir, Zeynep H %A Buyske, Steven %A Pehlivan, Davut %A Carvalho, Claudia M B %A Baxter, Samantha %A Sobreira, Nara %A Liu, Pengfei %A Wu, Nan %A Rosenfeld, Jill A %A Kumar, Sushant %A Avramopoulos, Dimitri %A White, Janson J %A Doheny, Kimberly F %A Witmer, P Dane %A Boehm, Corinne %A Sutton, V Reid %A Donna M Muzny %A Eric Boerwinkle %A Gunel, Murat %A Nickerson, Deborah A %A Mane, Shrikant %A MacArthur, Daniel G %A Richard A Gibbs %A Hamosh, Ada %A Lifton, Richard P %A Matise, Tara C %A Rehm, Heidi L %A Gerstein, Mark %A Bamshad, Michael J %A Valle, David %A Lupski, James R %K Databases, Genetic %K Exome Sequencing %K Genetic Diseases, Inborn %K Genetic Heterogeneity %K Genetic Predisposition to Disease %K Genome, Human %K Genomics %K Humans %K National Institutes of Health (U.S.) %K Pedigree %K United States %X

Identifying genes and variants contributing to rare disease phenotypes and Mendelian conditions informs biology and medicine, yet potential phenotypic consequences for variation of >75% of the ~20,000 annotated genes in the human genome are lacking. Technical advances to assess rare variation genome-wide, particularly exome sequencing (ES), enabled establishment in the United States of the National Institutes of Health (NIH)-supported Centers for Mendelian Genomics (CMGs) and have facilitated collaborative studies resulting in novel "disease gene" discoveries. Pedigree-based genomic studies and rare variant analyses in families with suspected Mendelian conditions have led to the elucidation of hundreds of novel disease genes and highlighted the impact of de novo mutational events, somatic variation underlying nononcologic traits, incompletely penetrant alleles, phenotypes with high locus heterogeneity, and multilocus pathogenic variation. Herein, we highlight CMG collaborative discoveries that have contributed to understanding both rare and common diseases and discuss opportunities for future discovery in single-locus Mendelian disorder genomics. Phenotypic annotation of all human genes; development of bioinformatic tools and analytic methods; exploration of non-Mendelian modes of inheritance including reduced penetrance, multilocus variation, and oligogenic inheritance; construction of allelic series at a locus; enhanced data sharing worldwide; and integration with clinical genomics are explored. Realizing the full contribution of rare disease research to functional annotation of the human genome, and further illuminating human biology and health, will lay the foundation for the Precision Medicine Initiative.

%B Genet Med %V 21 %P 798-812 %8 2019 Apr %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/30655598?dopt=Abstract %R 10.1038/s41436-018-0408-7 %0 Journal Article %J Genome Med %D 2019 %T Interchromosomal template-switching as a novel molecular mechanism for imprinting perturbations associated with Temple syndrome. %A Carvalho, Claudia M B %A Coban-Akdemir, Zeynep %A Hijazi, Hadia %A Bo Yuan %A Pendleton, Matthew %A Harrington, Eoghan %A Beaulaurier, John %A Juul, Sissel %A Turner, Daniel J %A Kanchi, Rupa S %A Jhangiani, Shalini N %A Donna M Muzny %A Richard A Gibbs %A Stankiewicz, Pawel %A Belmont, John W %A Shaw, Chad A %A Cheung, Sau Wai %A Hanchard, Neil A %A Sutton, V Reid %A Bader, Patricia I %A James R Lupski %K Chromosome Aberrations %K Chromosome Disorders %K Chromosomes, Human, Pair 14 %K DNA Methylation %K DNA Replication %K Genomic Imprinting %K Humans %K Male %K Pedigree %K Phenotype %K Polymorphism, Single Nucleotide %K Young Adult %X

BACKGROUND: Intrachromosomal triplications (TRP) can contribute to disease etiology via gene dosage effects, gene disruption, position effects, or fusion gene formation. Recently, post-zygotic de novo triplications adjacent to copy-number neutral genomic intervals with runs of homozygosity (ROH) have been shown to result in uniparental isodisomy (UPD). The genomic structure of these complex genomic rearrangements (CGRs) shows a consistent pattern of an inverted triplication flanked by duplications (DUP-TRP/INV-DUP) formed by an iterative DNA replisome template-switching mechanism during replicative repair of a single-ended, double-stranded DNA (seDNA), the ROH results from an interhomolog or nonsister chromatid template switch. It has been postulated that these CGRs may lead to genetic abnormalities in carriers due to dosage-sensitive genes mapping within the copy-number variant regions, homozygosity for alleles at a locus causing an autosomal recessive (AR) disease trait within the ROH region, or imprinting-associated diseases.

METHODS: Here, we report a family wherein the affected subject carries a de novo 2.2-Mb TRP followed by 42.2 Mb of ROH and manifests clinical features overlapping with those observed in association with chromosome 14 maternal UPD (UPD(14)mat). UPD(14)mat can cause clinical phenotypic features enabling a diagnosis of Temple syndrome. This CGR was then molecularly characterized by high-density custom aCGH, genome-wide single-nucleotide polymorphism (SNP) and methylation arrays, exome sequencing (ES), and the Oxford Nanopore long-read sequencing technology.

RESULTS: We confirmed the postulated DUP-TRP/INV-DUP structure by multiple orthogonal genomic technologies in the proband. The methylation status of known differentially methylated regions (DMRs) on chromosome 14 revealed that the subject shows the typical methylation pattern of UPD(14)mat. Consistent with these molecular findings, the clinical features overlap with those observed in Temple syndrome, including speech delay.

CONCLUSIONS: These data provide experimental evidence that, in humans, triplication can lead to segmental UPD and imprinting disease. Importantly, genotype/phenotype analyses further reveal how a post-zygotically generated complex structural variant, resulting from a replication-based mutational mechanism, contributes to expanding the clinical phenotype of known genetic syndromes. Mechanistically, such events can distort transmission genetics resulting in homozygosity at a locus for which only one parent is a carrier as well as cause imprinting diseases.

%B Genome Med %V 11 %P 25 %8 2019 Apr 23 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/31014393?dopt=Abstract %R 10.1186/s13073-019-0633-y %0 Journal Article %J Cell %D 2019 %T Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2. %A Beck, Christine R %A Carvalho, Claudia M B %A Akdemir, Zeynep C %A Fritz J Sedlazeck %A Song, Xiaofei %A Meng, Qingchang %A Hu, Jianhong %A Harshavardhan Doddapaneni %A Chong, Zechen %A Chen, Edward S %A Thornton, Philip C %A Liu, Pengfei %A Bo Yuan %A Withers, Marjorie %A Jhangiani, Shalini N %A Kalra, Divya %A Kimberly Walker %A English, Adam C %A Yi Han %A Chen, Ken %A Donna M Muzny %A Ira, Grzegorz %A Shaw, Chad A %A Richard A Gibbs %A Hastings, P J %A Lupski, James R %K Abnormalities, Multiple %K Chromosome Breakpoints %K Chromosome Disorders %K Chromosome Duplication %K Chromosomes, Human, Pair 17 %K DNA Copy Number Variations %K DNA Repair %K DNA Replication %K Gene Rearrangement %K Genome, Human %K Genomic Structural Variation %K Humans %K INDEL Mutation %K Models, Genetic %K Mutation %K Polymorphism, Single Nucleotide %K Recombination, Genetic %K Sequence Analysis, DNA %K Smith-Magenis Syndrome %X

DNA rearrangements resulting in human genome structural variants (SVs) are caused by diverse mutational mechanisms. We used long- and short-read sequencing technologies to investigate end products of de novo chromosome 17p11.2 rearrangements and query the molecular mechanisms underlying both recurrent and non-recurrent events. Evidence for an increased rate of clustered single-nucleotide variant (SNV) mutation in cis with non-recurrent rearrangements was found. Indel and SNV formation are associated with both copy-number gains and losses of 17p11.2, occur up to ∼1 Mb away from the breakpoint junctions, and favor C > G transversion substitutions; results suggest that single-stranded DNA is formed during the genesis of the SV and provide compelling support for a microhomology-mediated break-induced replication (MMBIR) mechanism for SV formation. Our data show an additional mutational burden of MMBIR consisting of hypermutation confined to the locus and manifesting as SNVs and indels predominantly within genes.

%B Cell %V 176 %P 1310-1324.e10 %8 2019 Mar 07 %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/30827684?dopt=Abstract %R 10.1016/j.cell.2019.01.045 %0 Journal Article %J Hum Mutat %D 2019 %T Missense variants in TAF1 and developmental phenotypes: challenges of determining pathogenicity. %A Cheng, Hanyin %A Capponi, Simona %A Wakeling, Emma %A Marchi, Elaine %A Li, Quan %A Zhao, Mengge %A Weng, Chunhua %A Stefan, Piatek G %A Ahlfors, Helena %A Kleyner, Robert %A Rope, Alan %A Lumaka, Aimé %A Lukusa, Prosper %A Devriendt, Koenraad %A Vermeesch, Joris %A Posey, Jennifer E %A Palmer, Elizabeth E %A Murray, Lucinda %A Leon, Eyby %A Diaz, Jullianne %A Worgan, Lisa %A Mallawaarachchi, Amalia %A Vogt, Julie %A de Munnik, Sonja A %A Dreyer, Lauren %A Baynam, Gareth %A Ewans, Lisa %A Stark, Zornitza %A Lunke, Sebastian %A Gonçalves, Ana R %A Soares, Gabriela %A Oliveira, Jorge %A Fassi, Emily %A Willing, Marcia %A Waugh, Jeff L %A Faivre, Laurence %A Riviere, Jean-Baptiste %A Moutton, Sebastien %A Mohammed, Shehla %A Payne, Katelyn %A Walsh, Laurence %A Begtrup, Amber %A Guillen Sacoto, Maria J %A Douglas, Ganka %A Alexander, Nora %A Buckley, Michael F %A Mark, Paul R %A Adès, Lesley C %A Sandaradura, Sarah A %A James R Lupski %A Roscioli, Tony %A Agrawal, Pankaj B %A Kline, Antonie D %A Wang, Kai %A Timmers, H T Marc %A Lyon, Gholson J %X

We recently described a new neurodevelopmental syndrome (TAF1/MRXS33 intellectual disability syndrome) (MIM# 300966) caused by pathogenic variants involving the X-linked gene TAF1, which participates in RNA polymerase II transcription. The initial study reported eleven families, and the syndrome was defined as presenting early in life with hypotonia, facial dysmorphia, and developmental delay that evolved into intellectual disability (ID) and/or autism spectrum disorder (ASD). We have now identified an additional 27 families through a genotype-first approach. Familial segregation analysis, clinical phenotyping, and bioinformatics were capitalized on to assess potential variant pathogenicity, and molecular modelling was performed for those variants falling within structurally characterized domains of TAF1. A novel phenotypic clustering approach was also applied, in which the phenotypes of affected individuals were classified using 51 standardized Human Phenotype Ontology (HPO) terms. Phenotypes associated with TAF1 variants show considerable pleiotropy and clinical variability, but prominent among previously unreported effects were brain morphological abnormalities, seizures, hearing loss, and heart malformations. Our allelic series broadens the phenotypic spectrum of TAF1/MRXS33 intellectual disability syndrome and the range of TAF1 molecular defects in humans. It also illustrates the challenges for determining the pathogenicity of inherited missense variants, particularly for genes mapping to chromosome X. This article is protected by copyright. All rights reserved.

%B Hum Mutat %8 2019 Oct 23 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/31646703?dopt=Abstract %R 10.1002/humu.23936 %0 Journal Article %J Am J Hum Genet %D 2019 %T Missense Variants in the Histone Acetyltransferase Complex Component Gene TRRAP Cause Autism and Syndromic Intellectual Disability. %A Cogné, Benjamin %A Ehresmann, Sophie %A Beauregard-Lacroix, Eliane %A Rousseau, Justine %A Besnard, Thomas %A Garcia, Thomas %A Petrovski, Slavé %A Avni, Shiri %A McWalter, Kirsty %A Blackburn, Patrick R %A Sanders, Stephan J %A Uguen, Kévin %A Harris, Jacqueline %A Cohen, Julie S %A Blyth, Moira %A Lehman, Anna %A Berg, Jonathan %A Li, Mindy H %A Kini, Usha %A Joss, Shelagh %A von der Lippe, Charlotte %A Gordon, Christopher T %A Humberson, Jennifer B %A Robak, Laurie %A Scott, Daryl A %A Sutton, Vernon R %A Skraban, Cara M %A Johnston, Jennifer J %A Poduri, Annapurna %A Nordenskjöld, Magnus %A Shashi, Vandana %A Gerkes, Erica H %A Bongers, Ernie M H F %A Gilissen, Christian %A Zarate, Yuri A %A Kvarnung, Malin %A Lally, Kevin P %A Kulch, Peggy A %A Daniels, Brina %A Hernandez-Garcia, Andres %A Stong, Nicholas %A McGaughran, Julie %A Retterer, Kyle %A Tveten, Kristian %A Sullivan, Jennifer %A Geisheker, Madeleine R %A Stray-Pedersen, Asbjorg %A Tarpinian, Jennifer M %A Klee, Eric W %A Sapp, Julie C %A Zyskind, Jacob %A Holla, Øystein L %A Bedoukian, Emma %A Filippini, Francesca %A Guimier, Anne %A Picard, Arnaud %A Busk, Øyvind L %A Punetha, Jaya %A Pfundt, Rolph %A Lindstrand, Anna %A Nordgren, Ann %A Kalb, Fayth %A Desai, Megha %A Ebanks, Ashley Harmon %A Jhangiani, Shalini N %A Dewan, Tammie %A Coban Akdemir, Zeynep H %A Telegrafi, Aida %A Zackai, Elaine H %A Begtrup, Amber %A Song, Xiaofei %A Toutain, Annick %A Wentzensen, Ingrid M %A Odent, Sylvie %A Bonneau, Dominique %A Latypova, Xénia %A Deb, Wallid %A Redon, Sylvia %A Bilan, Frédéric %A Legendre, Marine %A Troyer, Caitlin %A Whitlock, Kerri %A Caluseriu, Oana %A Murphree, Marine I %A Pichurin, Pavel N %A Agre, Katherine %A Gavrilova, Ralitza %A Rinne, Tuula %A Park, Meredith %A Shain, Catherine %A Heinzen, Erin L %A Xiao, Rui %A Amiel, Jeanne %A Lyonnet, Stanislas %A Isidor, Bertrand %A Biesecker, Leslie G %A Lowenstein, Dan %A Posey, Jennifer E %A Denommé-Pichon, Anne-Sophie %A Férec, Claude %A Yang, Xiang-Jiao %A Rosenfeld, Jill A %A Gilbert-Dussardier, Brigitte %A Audebert-Bellanger, Séverine %A Redon, Richard %A Stessman, Holly A F %A Nellaker, Christoffer %A Yang, Yaping %A James R Lupski %A Goldstein, David B %A Eichler, Evan E %A Bolduc, Francois %A Bézieau, Stéphane %A Küry, Sébastien %A Campeau, Philippe M %K Adaptor Proteins, Signal Transducing %K Adolescent %K Adult %K Amino Acid Sequence %K Autistic Disorder %K Child %K Child, Preschool %K Female %K Genetic Association Studies %K Humans %K Infant %K Intellectual Disability %K Male %K Mutation, Missense %K Nuclear Proteins %K Prognosis %K Sequence Homology %K Syndrome %K Young Adult %X

Acetylation of the lysine residues in histones and other DNA-binding proteins plays a major role in regulation of eukaryotic gene expression. This process is controlled by histone acetyltransferases (HATs/KATs) found in multiprotein complexes that are recruited to chromatin by the scaffolding subunit transformation/transcription domain-associated protein (TRRAP). TRRAP is evolutionarily conserved and is among the top five genes intolerant to missense variation. Through an international collaboration, 17 distinct de novo or apparently de novo variants were identified in TRRAP in 24 individuals. A strong genotype-phenotype correlation was observed with two distinct clinical spectra. The first is a complex, multi-systemic syndrome associated with various malformations of the brain, heart, kidneys, and genitourinary system and characterized by a wide range of intellectual functioning; a number of affected individuals have intellectual disability (ID) and markedly impaired basic life functions. Individuals with this phenotype had missense variants clustering around the c.3127G>A p.(Ala1043Thr) variant identified in five individuals. The second spectrum manifested with autism spectrum disorder (ASD) and/or ID and epilepsy. Facial dysmorphism was seen in both groups and included upslanted palpebral fissures, epicanthus, telecanthus, a wide nasal bridge and ridge, a broad and smooth philtrum, and a thin upper lip. RNA sequencing analysis of skin fibroblasts derived from affected individuals skin fibroblasts showed significant changes in the expression of several genes implicated in neuronal function and ion transport. Thus, we describe here the clinical spectrum associated with TRRAP pathogenic missense variants, and we suggest a genotype-phenotype correlation useful for clinical evaluation of the pathogenicity of the variants.

%B Am J Hum Genet %V 104 %P 530-541 %8 2019 Mar 07 %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/30827496?dopt=Abstract %R 10.1016/j.ajhg.2019.01.010 %0 Journal Article %J Dev Cell %D 2019 %T Mutations in ANKLE2, a ZIKA Virus Target, Disrupt an Asymmetric Cell Division Pathway in Drosophila Neuroblasts to Cause Microcephaly. %A Link, Nichole %A Chung, Hyunglok %A Jolly, Angad %A Withers, Marjorie %A Tepe, Burak %A Arenkiel, Benjamin R %A Shah, Priya S %A Krogan, Nevan J %A Aydin, Hatip %A Geckinli, Bilgen B %A Tos, Tulay %A Isikay, Sedat %A Tuysuz, Beyhan %A Mochida, Ganesh H %A Thomas, Ajay X %A Clark, Robin D %A Mirzaa, Ghayda M %A James R Lupski %A Bellen, Hugo J %K Animals %K Asymmetric Cell Division %K Cell Division %K Cell Polarity %K Drosophila melanogaster %K Humans %K Membrane Proteins %K Microcephaly %K Mutation %K Neural Stem Cells %K Neurons %K Nuclear Proteins %K Zika Virus %X

The apical Par complex, which contains atypical protein kinase C (aPKC), Bazooka (Par-3), and Par-6, is required for establishing polarity during asymmetric division of neuroblasts in Drosophila, and its activity depends on L(2)gl. We show that loss of Ankle2, a protein associated with microcephaly in humans and known to interact with Zika protein NS4A, reduces brain volume in flies and impacts the function of the Par complex. Reducing Ankle2 levels disrupts endoplasmic reticulum (ER) and nuclear envelope morphology, releasing the kinase Ballchen-VRK1 into the cytosol. These defects are associated with reduced phosphorylation of aPKC, disruption of Par-complex localization, and spindle alignment defects. Importantly, removal of one copy of ballchen or l(2)gl suppresses Ankle2 mutant phenotypes and restores viability and brain size. Human mutational studies implicate the above-mentioned genes in microcephaly and motor neuron disease. We suggest that NS4A, ANKLE2, VRK1, and LLGL1 define a pathway impinging on asymmetric determinants of neural stem cell division.

%B Dev Cell %V 51 %P 713-729.e6 %8 2019 Dec 16 %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/31735666?dopt=Abstract %R 10.1016/j.devcel.2019.10.009 %0 Journal Article %J J Exp Med %D 2019 %T A novel disorder involving dyshematopoiesis, inflammation, and HLH due to aberrant CDC42 function. %A Lam, Michael T %A Coppola, Simona %A Krumbach, Oliver H F %A Prencipe, Giusi %A Insalaco, Antonella %A Cifaldi, Cristina %A Brigida, Immacolata %A Zara, Erika %A Scala, Serena %A Di Cesare, Silvia %A Martinelli, Simone %A Di Rocco, Martina %A Pascarella, Antonia %A Niceta, Marcello %A Pantaleoni, Francesca %A Ciolfi, Andrea %A Netter, Petra %A Carisey, Alexandre F %A Diehl, Michael %A Akbarzadeh, Mohammad %A Conti, Francesca %A Merli, Pietro %A Pastore, Anna %A Levi Mortera, Stefano %A Camerini, Serena %A Farina, Luciapia %A Buchholzer, Marcel %A Pannone, Luca %A Cao, Tram N %A Coban-Akdemir, Zeynep H %A Jhangiani, Shalini N %A Donna M Muzny %A Richard A Gibbs %A Basso-Ricci, Luca %A Chiriaco, Maria %A Dvorsky, Radovan %A Putignani, Lorenza %A Carsetti, Rita %A Janning, Petra %A Stray-Pedersen, Asbjorg %A Erichsen, Hans Christian %A Horne, AnnaCarin %A Bryceson, Yenan T %A Torralba-Raga, Lamberto %A Ramme, Kim %A Rosti, Vittorio %A Bracaglia, Claudia %A Messia, Virginia %A Palma, Paolo %A Finocchi, Andrea %A Locatelli, Franco %A Chinn, Ivan K %A James R Lupski %A Mace, Emily M %A Cancrini, Caterina %A Aiuti, Alessandro %A Ahmadian, Mohammad R %A Orange, Jordan S %A De Benedetti, Fabrizio %A Tartaglia, Marco %K Alleles %K Amino Acid Substitution %K Animals %K Binding Sites %K cdc42 GTP-Binding Protein %K Cell Line, Tumor %K Child %K Disease Susceptibility %K Female %K Genetic Association Studies %K Genotype %K Humans %K Infant %K Lymphohistiocytosis, Hemophagocytic %K Male %K Mice %K Models, Molecular %K Molecular Conformation %K Mutation %K Phenotype %K Protein Binding %X

Hemophagocytic lymphohistiocytosis (HLH) is characterized by immune dysregulation due to inadequate restraint of overactivated immune cells and is associated with a variable clinical spectrum having overlap with more common pathophysiologies. HLH is difficult to diagnose and can be part of inflammatory syndromes. Here, we identify a novel hematological/autoinflammatory condition (NOCARH syndrome) in four unrelated patients with superimposable features, including neonatal-onset cytopenia with dyshematopoiesis, autoinflammation, rash, and HLH. Patients shared the same de novo mutation (Chr1:22417990C>T, p.R186C) and altered hematopoietic compartment, immune dysregulation, and inflammation. mutations had been associated with syndromic neurodevelopmental disorders. In vitro and in vivo assays documented unique effects of p.R186C on CDC42 localization and function, correlating with the distinctiveness of the trait. Emapalumab was critical to the survival of one patient, who underwent successful bone marrow transplantation. Early recognition of the disorder and establishment of treatment followed by bone marrow transplant are important to survival.

%B J Exp Med %V 216 %P 2778-2799 %8 2019 Dec 02 %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/31601675?dopt=Abstract %R 10.1084/jem.20190147 %0 Journal Article %J Front Pediatr %D 2019 %T Novel Heterozygous Mutation in Is Associated With Early Onset CVID and a Functional Defect in NK Cells Complicated by Disseminated CMV Infection and Severe Nephrotic Syndrome. %A Aird, Alejandra %A Lagos, Macarena %A Vargas-Hernandez, Alexander %A Posey, Jennifer E %A Coban-Akdemir, Zeynep %A Jhangiani, Shalini %A Mace, Emily M %A Reyes, Anaid %A King, Alejandra %A Cavagnaro, Felipe %A Forbes, Lisa R %A Chinn, Ivan K %A James R Lupski %A Orange, Jordan S %A Poli, Maria Cecilia %X

Nuclear factor kappa-B subunit 2 (NF-κB2/p100/p52), encoded by (MIM: 164012) belongs to the NF-κB family of transcription factors that play a critical role in inflammation, immunity, cell proliferation, differentiation and survival. Heterozygous C-terminal mutations in have been associated with early-onset common variable immunodeficiency (CVID), central adrenal insufficiency and ectodermal dysplasia. Only two previously reported cases have documented decreased natural killer (NK) cell cytotoxicity, and little is known about the role of NF-κB2 in NK cell maturation and function. Here we report a 13-year-old female that presented at 6 years of age with a history of early onset recurrent sinopulmonary infections, progressive hair loss, and hypogamaglobulinemia consistent with a clinical diagnosis of CVID. At 9 years of age she had cytomegalovirus (CMV) pneumonia that responded to ganciclovir treatment. Functional NK cell testing demonstrated decreased NK cell cytotoxicity despite normal NK cell numbers, consistent with a greater susceptibility to systemic CMV infection. Research exome sequencing (ES) was performed and revealed a novel heterozygous nonsense mutation in (c.2611C>T, p.Gln871) that was not carried by either of her parents. The variant was Sanger sequenced and confirmed to be in the patient. At age 12, she presented with a reactivation of the systemic CMV infection that was associated with severe and progressive nephrotic syndrome with histologic evidence of pedicellar effacement and negative immunofluorescence. To our knowledge, this is the third NF-κB2 deficient patient in which an abnormal NK cell function has been observed, suggesting a role for non-canonical NF-κB2 signaling in NK cell cytotoxicity. NK cell function should be assessed in patients with mutations in the non-canonical NF-κB pathway to explore the risk for systemic viral infections that may lead to severe complications and impact patient survival. Similarly NF-κB2 should be considered in patients with combined immunodeficiency who have aberrant NK cell function. Further studies are needed to characterize the role of NF-κB2 in NK cell cytotoxic function.

%B Front Pediatr %V 7 %P 303 %8 2019 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/31417880?dopt=Abstract %R 10.3389/fped.2019.00303 %0 Journal Article %J Am J Med Genet A %D 2019 %T Objective measures of sleep disturbances in children with Potocki-Lupski syndrome. %A Kaplan, Kevin %A McCool, Caroline %A James R Lupski %A Glaze, Daniel %A Potocki, Lorraine %K Abnormalities, Multiple %K Adolescent %K Child %K Chromosome Disorders %K Chromosome Duplication %K Female %K Humans %K Male %K Sleep Wake Disorders %K Surveys and Questionnaires %X

Potocki-Lupski syndrome (PTLS; MIM 610883) is a neurodevelopmental disorder caused by a microduplication, a 3.7 Mb copy number variant, mapping within chromosome 17p11.2, encompassing the dosage-sensitive RAI1 gene. Whereas RAI1 triplosensitivity causes PTLS, haploinsufficiency of RAI1 due to 17p11.2 microdeletion causes the clinically distinct Smith-Magenis syndrome (SMS; MIM 182290). Most individuals with SMS have an inversion of the melatonin cycle. Subjects with PTLS have mild sleep disturbances such as sleep apnea with no melatonin abnormalities described. Sleep patterns and potential disturbances in subjects with PTLS have not been objectively characterized. We delineated sleep characteristics in 23 subjects with PTLS who underwent a polysomnogram at Texas Children's Hospital. Eleven of these subjects (58%) completed the Child's Sleep Habits Questionnaire (CSHQ). Urinary melatonin was measured in one patient and published previously. While the circadian rhythm of melatonin in PTLS appears not to be disrupted, we identified significant differences in sleep efficiency, percentage of rapid eye movement sleep, oxygen nadir, obstructive apnea hypopnea index, and periodic limb movements between prepubertal subjects with PTLS and previously published normative data. Data from the CSHQ indicate that 64% (7/11) of parents do not identify a sleep disturbance in their children. Our data indicate that younger individuals, <10 years, with PTLS have statistically significant abnormalities in five components of sleep despite lack of recognition of substantial sleep disturbances by parents. Our data support the contention that patients with PTLS should undergo clinical evaluations for sleep disordered breathing and periodic limb movement disorder, both of which are treatable conditions.

%B Am J Med Genet A %V 179 %P 1982-1986 %8 2019 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/31342617?dopt=Abstract %R 10.1002/ajmg.a.61307 %0 Journal Article %J Am J Hum Genet %D 2019 %T Paralog Studies Augment Gene Discovery: DDX and DHX Genes. %A Paine, Ingrid %A Posey, Jennifer E %A Grochowski, Christopher M %A Jhangiani, Shalini N %A Rosenheck, Sarah %A Kleyner, Robert %A Marmorale, Taylor %A Yoon, Margaret %A Wang, Kai %A Robison, Reid %A Cappuccio, Gerarda %A Pinelli, Michele %A Magli, Adriano %A Coban Akdemir, Zeynep %A Hui, Joannie %A Yeung, Wai Lan %A Wong, Bibiana K Y %A Ortega, Lucia %A Bekheirnia, Mir Reza %A Bierhals, Tatjana %A Hempel, Maja %A Johannsen, Jessika %A Santer, René %A Aktas, Dilek %A Alikaşifoğlu, Mehmet %A Bozdogan, Sevcan %A Aydin, Hatip %A Karaca, Ender %A Bayram, Yavuz %A Ityel, Hadas %A Dorschner, Michael %A White, Janson J %A Wilichowski, Ekkehard %A Wortmann, Saskia B %A Casella, Erasmo B %A Kitajima, Joao Paulo %A Kok, Fernando %A Monteiro, Fabiola %A Donna M Muzny %A Bamshad, Michael %A Richard A Gibbs %A Sutton, V Reid %A Van Esch, Hilde %A Brunetti-Pierri, Nicola %A Hildebrandt, Friedhelm %A Brautbar, Ariel %A Van den Veyver, Ignatia B %A Glass, Ian %A Lessel, Davor %A Lyon, Gholson J %A James R Lupski %K DEAD-box RNA Helicases %K Exome Sequencing %K Female %K Genetic Association Studies %K Humans %K Infant %K Infant, Newborn %K Male %K Mutation, Missense %K Neoplasm Proteins %K Neurodevelopmental Disorders %K Pedigree %K RNA Helicases %X

Members of a paralogous gene family in which variation in one gene is known to cause disease are eight times more likely to also be associated with human disease. Recent studies have elucidated DHX30 and DDX3X as genes for which pathogenic variant alleles are involved in neurodevelopmental disorders. We hypothesized that variants in paralogous genes encoding members of the DExD/H-box RNA helicase superfamily might also underlie developmental delay and/or intellectual disability (DD and/or ID) disease phenotypes. Here we describe 15 unrelated individuals who have DD and/or ID, central nervous system (CNS) dysfunction, vertebral anomalies, and dysmorphic features and were found to have probably damaging variants in DExD/H-box RNA helicase genes. In addition, these individuals exhibit a variety of other tissue and organ system involvement including ocular, outer ear, hearing, cardiac, and kidney tissues. Five individuals with homozygous (one), compound-heterozygous (two), or de novo (two) missense variants in DHX37 were identified by exome sequencing. We identified ten total individuals with missense variants in three other DDX/DHX paralogs: DHX16 (four individuals), DDX54 (three individuals), and DHX34 (three individuals). Most identified variants are rare, predicted to be damaging, and occur at conserved amino acid residues. Taken together, these 15 individuals implicate the DExD/H-box helicases in both dominantly and recessively inherited neurodevelopmental phenotypes and highlight the potential for more than one disease mechanism underlying these disorders.

%B Am J Hum Genet %V 105 %P 302-316 %8 2019 Aug 01 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/31256877?dopt=Abstract %R 10.1016/j.ajhg.2019.06.001 %0 Journal Article %J N Engl J Med %D 2019 %T Reanalysis of Clinical Exome Sequencing Data. %A Liu, Pengfei %A Meng, Linyan %A Normand, Elizabeth A %A Xia, Fan %A Song, Xiaofei %A Ghazi, Andrew %A Rosenfeld, Jill %A Magoulas, Pilar L %A Braxton, Alicia %A Ward, Patricia %A Dai, Hongzheng %A Bo Yuan %A Bi, Weimin %A Xiao, Rui %A Wang, Xia %A Chiang, Theodore %A Vetrini, Francesco %A He, Weimin %A Cheng, Hanyin %A Dong, Jie %A Gijavanekar, Charul %A Benke, Paul J %A Bernstein, Jonathan A %A Eble, Tanya %A Eroglu, Yasemen %A Erwin, Deanna %A Escobar, Luis %A Gibson, James B %A Gripp, Karen %A Kleppe, Soledad %A Koenig, Mary K %A Lewis, Andrea M %A Natowicz, Marvin %A Mancias, Pedro %A Minor, LaKeesha %A Scaglia, Fernando %A Schaaf, Christian P %A Streff, Haley %A Vernon, Hilary %A Uhles, Crescenda L %A Zackai, Elaine H %A Wu, Nan %A Sutton, V Reid %A Beaudet, Arthur L %A Donna M Muzny %A Richard A Gibbs %A Posey, Jennifer E %A Lalani, Seema %A Shaw, Chad %A Christine M Eng %A James R Lupski %A Yang, Yaping %K Exome %K Genetic Diseases, Inborn %K Genetic Testing %K Humans %K Mutation %K Phenotype %K Sequence Analysis, DNA %K Whole Exome Sequencing %B N Engl J Med %V 380 %P 2478-2480 %8 2019 06 20 %G eng %N 25 %1 https://www.ncbi.nlm.nih.gov/pubmed/31216405?dopt=Abstract %R 10.1056/NEJMc1812033 %0 Journal Article %J Genet Med %D 2019 %T TBX6-associated congenital scoliosis (TACS) as a clinically distinguishable subtype of congenital scoliosis: further evidence supporting the compound inheritance and TBX6 gene dosage model. %A Liu, Jiaqi %A Wu, Nan %A Yang, Nan %A Takeda, Kazuki %A Chen, Weisheng %A Li, Weiyu %A Du, Renqian %A Liu, Sen %A Zhou, Yangzhong %A Zhang, Ling %A Liu, Zhenlei %A Zuo, Yuzhi %A Zhao, Sen %A Blank, Robert %A Pehlivan, Davut %A Dong, Shuangshuang %A Zhang, Jianguo %A Shen, Jianxiong %A Si, Nuo %A Wang, Yipeng %A Liu, Gang %A Li, Shugang %A Zhao, Yanxue %A Zhao, Hong %A Chen, Yixin %A Zhao, Yu %A Song, Xiaofei %A Hu, Jianhua %A Lin, Mao %A Tian, Ye %A Bo Yuan %A Yu, Keyi %A Niu, Yuchen %A Yu, Bin %A Li, Xiaoxin %A Chen, Jia %A Yan, Zihui %A Zhu, Qiankun %A Meng, Xiaolu %A Chen, Xiaoli %A Su, Jianzhong %A Zhao, Xiuli %A Wang, Xiaoyue %A Ming, Yue %A Li, Xiao %A Raggio, Cathleen L %A Zhang, Baozhong %A Weng, Xisheng %A Zhang, Shuyang %A Zhang, Xue %A Watanabe, Kota %A Matsumoto, Morio %A Jin, Li %A Shen, Yiping %A Sobreira, Nara L %A Posey, Jennifer E %A Giampietro, Philip F %A Valle, David %A Liu, Pengfei %A Wu, Zhihong %A Ikegawa, Shiro %A James R Lupski %A Zhang, Feng %A Qiu, Guixing %K Animals %K Cohort Studies %K Disease Models, Animal %K Gene Dosage %K Humans %K Inheritance Patterns %K Mice %K Models, Genetic %K Scoliosis %K Spine %K T-Box Domain Proteins %X

PURPOSE: To characterize clinically measurable endophenotypes, implicating the TBX6 compound inheritance model.

METHODS: Patients with congenital scoliosis (CS) from China(N = 345, cohort 1), Japan (N = 142, cohort 2), and the United States (N = 10, cohort 3) were studied. Clinically measurable endophenotypes were compared according to the TBX6 genotypes. A mouse model for Tbx6 compound inheritance (N = 52) was investigated by micro computed tomography (micro-CT). A clinical diagnostic algorithm (TACScore) was developed to assist in clinical recognition of TBX6-associated CS (TACS).

RESULTS: In cohort 1, TACS patients (N = 33) were significantly younger at onset than the remaining CS patients (P = 0.02), presented with one or more hemivertebrae/butterfly vertebrae (P = 4.9 × 10), and exhibited vertebral malformations involving the lower part of the spine (T8-S5, P = 4.4 × 10); observations were confirmed in two replication cohorts. Simple rib anomalies were prevalent in TACS patients (P = 3.1 × 10), while intraspinal anomalies were uncommon (P = 7.0 × 10). A clinically usable TACScore was developed with an area under the curve (AUC) of 0.9 (P = 1.6 × 10). A Tbx6 mouse model supported that a gene dosage effect underlies the TACS phenotype.

CONCLUSION: TACS is a clinically distinguishable entity with consistent clinically measurable endophenotypes. The type and distribution of vertebral column abnormalities in TBX6/Tbx6 compound inheritance implicate subtle perturbations in gene dosage as a cause of spine developmental birth defects responsible for about 10% of CS.

%B Genet Med %V 21 %P 1548-1558 %8 2019 07 %G eng %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/30636772?dopt=Abstract %R 10.1038/s41436-018-0377-x %0 Journal Article %J Am J Med Genet A %D 2018 %T A biallelic ANTXR1 variant expands the anthrax toxin receptor associated phenotype to tooth agenesis. %A Dinckan, Nuriye %A Du, Renqian %A Akdemir, Zeynep C %A Bayram, Yavuz %A Jhangiani, Shalini N %A Doddapaneni, Harsha %A Hu, Jianhong %A Muzny, Donna M %A Guven, Yeliz %A Aktoren, Oya %A Kayserili, Hulya %A Boerwinkle, Eric %A Gibbs, Richard A %A Posey, Jennifer E %A Lupski, James R %A Uyguner, Zehra O %A Letra, Ariadne %K Alleles %K Amino Acid Substitution %K Animals %K Anodontia %K Child %K Consanguinity %K Exome Sequencing %K Facies %K Genetic Association Studies %K Genotype %K Humans %K Male %K Mice %K Microfilament Proteins %K Mutation %K Neoplasm Proteins %K Pedigree %K Phenotype %K Radiography %K Receptors, Cell Surface %X

Tooth development is regulated by multiple genetic pathways, which ultimately drive the complex interactions between the oral epithelium and mesenchyme. Disruptions at any time point during this process may lead to failure of tooth development, also known as tooth agenesis (TA). TA is a common craniofacial abnormality in humans and represents the failure to develop one or more permanent teeth. Many genes and potentially subtle variants in these genes contribute to the TA phenotype. We report the clinical and genetic impact of a rare homozygous ANTXR1 variant (c.1312C>T), identified by whole exome sequencing (WES), in a consanguineous Turkish family with TA. Mutations in ANTXR1 have been associated with GAPO (growth retardation, alopecia, pseudoanodontia, and optic atrophy) syndrome and infantile hemangioma, however no clinical characteristics associated with these conditions were observed in our study family. We detected the expression of Antxr1 in oral and dental tissues of developing mouse embryos, further supporting a role for this gene in tooth development. Our findings implicate ANTXR1 as a candidate gene for isolated TA, suggest the involvement of specific hypomorphic alleles, and expand the previously known ANTXR1-associated phenotypes.

%B Am J Med Genet A %V 176 %P 1015-1022 %8 2018 Apr %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/29436111?dopt=Abstract %R 10.1002/ajmg.a.38625 %0 Journal Article %J Am J Hum Genet %D 2018 %T Bi-allelic CCDC47 Variants Cause a Disorder Characterized by Woolly Hair, Liver Dysfunction, Dysmorphic Features, and Global Developmental Delay. %A Morimoto, Marie %A Waller-Evans, Helen %A Ammous, Zineb %A Song, Xiaofei %A Strauss, Kevin A %A Pehlivan, Davut %A Gonzaga-Jauregui, Claudia %A Puffenberger, Erik G %A Holst, Charles R %A Karaca, Ender %A Brigatti, Karlla W %A Maguire, Emily %A Coban-Akdemir, Zeynep H %A Amagata, Akiko %A Lau, C Christopher %A Chepa-Lotrea, Xenia %A Macnamara, Ellen %A Tos, Tulay %A Isikay, Sedat %A Nehrebecky, Michele %A Overton, John D %A Klein, Matthew %A Markello, Thomas C %A Posey, Jennifer E %A Adams, David R %A Lloyd-Evans, Emyr %A Lupski, James R %A Gahl, William A %A Malicdan, May Christine V %X

Ca signaling is vital for various cellular processes including synaptic vesicle exocytosis, muscle contraction, regulation of secretion, gene transcription, and cellular proliferation. The endoplasmic reticulum (ER) is the largest intracellular Ca store, and dysregulation of ER Ca signaling and homeostasis contributes to the pathogenesis of various complex disorders and Mendelian disease traits. We describe four unrelated individuals with a complex multisystem disorder characterized by woolly hair, liver dysfunction, pruritus, dysmorphic features, hypotonia, and global developmental delay. Through whole-exome sequencing and family-based genomics, we identified bi-allelic variants in CCDC47 that encodes the Ca-binding ER transmembrane protein CCDC47. CCDC47, also known as calumin, has been shown to bind Ca with low affinity and high capacity. In mice, loss of Ccdc47 leads to embryonic lethality, suggesting that Ccdc47 is essential for early development. Characterization of cells from individuals with predicted likely damaging alleles showed decreased CCDC47 mRNA expression and protein levels. In vitro cellular experiments showed decreased total ER Ca storage, impaired Ca signaling mediated by the IPR Ca release channel, and reduced ER Ca refilling via store-operated Ca entry. These results, together with the previously described role of CCDC47 in Ca signaling and development, suggest that bi-allelic loss-of-function variants in CCDC47 underlie the pathogenesis of this multisystem disorder.

%B Am J Hum Genet %V 103 %P 794-807 %8 2018 Nov 01 %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/30401460?dopt=Abstract %R 10.1016/j.ajhg.2018.09.014 %0 Journal Article %J Eur J Hum Genet %D 2018 %T Biallelic variants in KIF14 cause intellectual disability with microcephaly. %A Makrythanasis, Periklis %A Maroofian, Reza %A Stray-Pedersen, Asbjørg %A Musaev, Damir %A Zaki, Maha S %A Mahmoud, Iman G %A Selim, Laila %A Elbadawy, Amera %A Jhangiani, Shalini N %A Coban Akdemir, Zeynep H %A Gambin, Tomasz %A Sorte, Hanne S %A Heiberg, Arvid %A McEvoy-Venneri, Jennifer %A James, Kiely N %A Stanley, Valentina %A Belandres, Denice %A Guipponi, Michel %A Santoni, Federico A %A Ahangari, Najmeh %A Tara, Fatemeh %A Doosti, Mohammad %A Iwaszkiewicz, Justyna %A Zoete, Vincent %A Backe, Paul Hoff %A Hamamy, Hanan %A Gleeson, Joseph G %A Lupski, James R %A Karimiani, Ehsan Ghayoor %A Antonarakis, Stylianos E %K Child %K Child, Preschool %K Female %K Humans %K Intellectual Disability %K Kinesins %K Loss of Function Mutation %K Microcephaly %K Mutation, Missense %K Oncogene Proteins %K Pedigree %K Phenotype %K Protein Domains %K Syndrome %X

Kinesin proteins are critical for various cellular functions such as intracellular transport and cell division, and many members of the family have been linked to monogenic disorders and cancer. We report eight individuals with intellectual disability and microcephaly from four unrelated families with parental consanguinity. In the affected individuals of each family, homozygosity for likely pathogenic variants in KIF14 were detected; two loss-of-function (p.Asn83Ilefs*3 and p.Ser1478fs), and two missense substitutions (p.Ser841Phe and p.Gly459Arg). KIF14 is a mitotic motor protein that is required for spindle localization of the mitotic citron rho-interacting kinase, CIT, also mutated in microcephaly. Our results demonstrate the involvement of KIF14 in development and reveal a wide phenotypic variability ranging from fetal lethality to moderate developmental delay and microcephaly.

%B Eur J Hum Genet %V 26 %P 330-339 %8 2018 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/29343805?dopt=Abstract %R 10.1038/s41431-017-0088-9 %0 Journal Article %J Hum Genet %D 2018 %T The coexistence of copy number variations (CNVs) and single nucleotide polymorphisms (SNPs) at a locus can result in distorted calculations of the significance in associating SNPs to disease. %A Liu, Jiaqi %A Zhou, Yangzhong %A Liu, Sen %A Song, Xiaofei %A Yang, Xin-Zhuang %A Fan, Yanhui %A Chen, Weisheng %A Akdemir, Zeynep Coban %A Yan, Zihui %A Zuo, Yuzhi %A Du, Renqian %A Liu, Zhenlei %A Bo Yuan %A Zhao, Sen %A Liu, Gang %A Chen, Yixin %A Zhao, Yanxue %A Lin, Mao %A Zhu, Qiankun %A Niu, Yuchen %A Liu, Pengfei %A Ikegawa, Shiro %A Song, You-Qiang %A Posey, Jennifer E %A Qiu, Guixing %A Zhang, Feng %A Wu, Zhihong %A James R Lupski %A Wu, Nan %K Adolescent %K Congenital Abnormalities %K DNA Copy Number Variations %K Female %K Genetic Predisposition to Disease %K Genome, Human %K Genome-Wide Association Study %K Genomics %K Genotype %K Haplotypes %K Humans %K Phenotype %K Polymorphism, Single Nucleotide %K Scoliosis %X

With the recent advance in genome-wide association studies (GWAS), disease-associated single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) have been extensively reported. Accordingly, the issue of incorrect identification of recombination events that can induce the distortion of multi-allelic or hemizygous variants has received more attention. However, the potential distorted calculation bias or significance of a detected association in a GWAS due to the coexistence of CNVs and SNPs in the same genomic region may remain under-recognized. Here we performed the association study within a congenital scoliosis (CS) cohort whose genetic etiology was recently elucidated as a compound inheritance model, including mostly one rare variant deletion CNV null allele and one common variant non-coding hypomorphic haplotype of the TBX6 gene. We demonstrated that the existence of a deletion in TBX6 led to an overestimation of the contribution of the SNPs on the hypomorphic allele. Furthermore, we generalized a model to explain the calculation bias, or distorted significance calculation for an association study, that can be 'induced' by CNVs at a locus. Meanwhile, overlapping between the disease-associated SNPs from published GWAS and common CNVs (overlap 10%) and pathogenic/likely pathogenic CNVs (overlap 99.69%) was significantly higher than the random distribution (p < 1 × 10 and p = 0.034, respectively), indicating that such co-existence of CNV and SNV alleles might generally influence data interpretation and potential outcomes of a GWAS. We also verified and assessed the influence of colocalizing CNVs to the detection sensitivity of disease-associated SNP variant alleles in another adolescent idiopathic scoliosis (AIS) genome-wide association study. We proposed that detecting co-existent CNVs when evaluating the association signals between SNPs and disease traits could improve genetic model analyses and better integrate GWAS with robust Mendelian principles.

%B Hum Genet %V 137 %P 553-567 %8 2018 Jul %G eng %N 6-7 %1 https://www.ncbi.nlm.nih.gov/pubmed/30019117?dopt=Abstract %R 10.1007/s00439-018-1910-3 %0 Journal Article %J Am J Med Genet A %D 2018 %T A comprehensive clinical and genetic study in 127 patients with ID in Kinshasa, DR Congo. %A Lumaka, Aimé %A Race, Valerie %A Peeters, Hilde %A Corveleyn, Anniek %A Coban-Akdemir, Zeynep %A Jhangiani, Shalini N %A Song, Xiaofei %A Mubungu, Gerrye %A Posey, Jennifer %A Lupski, James R %A Vermeesch, Joris R %A Lukusa, Prosper %A Devriendt, Koenraad %K Adolescent %K Adult %K Algorithms %K Child %K Child, Preschool %K Comparative Genomic Hybridization %K Democratic Republic of the Congo %K Developmental Disabilities %K Disease Management %K Exome Sequencing %K Facies %K Female %K Genetic Association Studies %K Genetic Markers %K Genetic Predisposition to Disease %K Genetic Testing %K Homeodomain Proteins %K Humans %K Infant %K Intellectual Disability %K Male %K Phenotype %K Syndrome %K Transcription Factors %K Trinucleotide Repeat Expansion %K Trinucleotide Repeats %K Workflow %K X Chromosome Inactivation %K Young Adult %X

Pathogenic variants account for 4 to 41% of patients with intellectual disability (ID) or developmental delay (DD). In Sub-Saharan Africa, the prevalence of ID is thought to be higher, but data in Central Africa are limited to some case reports. In addition, clinical descriptions of some syndromes are not available for this population. This study aimed at providing an estimate for the fraction of ID/DD for which an underlying etiological genetic cause may be elucidated and provide insights into their clinical presentation in special institutions in a Central African country. A total of 127 patients (33 females and 94 males, mean age 10.03 ± 4.68 years), were recruited from six institutions across Kinshasa. A clinical diagnosis was achieved in 44 but molecular confirmation was achieved in 21 of the 22 patients with expected genetic defect (95% clinical sensitivity). Identified diseases included Down syndrome (15%), submicroscopic copy number variants (9%), aminoacylase deficiency (0.8%), Partington syndrome in one patient (0.8%) and his similarly affected brother, X-linked syndromic Mental Retardation type 33 (0.8%), and two conditions without clear underlying molecular genetic etiologies (Oculo-Auriculo-Vertebral and Amniotic Bands Sequence). We have shown that genetic etiologies, similar to those reported in Caucasian subjects, are a common etiologic cause of ID in African patients from Africa. We have confirmed the diagnostic utility of clinical characterization prior to genetic testing. Finally, our clinical descriptions provide insights into the presentation of these genetic diseases in African patients.

%B Am J Med Genet A %V 176 %P 1897-1909 %8 2018 Sep %G eng %N 9 %1 https://www.ncbi.nlm.nih.gov/pubmed/30088852?dopt=Abstract %R 10.1002/ajmg.a.40382 %0 Journal Article %J Eur J Hum Genet %D 2018 %T Comprehensive genomic analysis of patients with disorders of cerebral cortical development. %A Wiszniewski, Wojciech %A Gawlinski, Pawel %A Gambin, Tomasz %A Bekiesinska-Figatowska, Monika %A Obersztyn, Ewa %A Antczak-Marach, Dorota %A Akdemir, Zeynep Hande Coban %A Harel, Tamar %A Karaca, Ender %A Jurek, Marta %A Sobecka, Katarzyna %A Nowakowska, Beata %A Kruk, Malgorzata %A Terczynska, Iwona %A Goszczanska-Ciuchta, Alicja %A Rudzka-Dybala, Mariola %A Jamroz, Ewa %A Pyrkosz, Antoni %A Jakubiuk-Tomaszuk, Anna %A Iwanowski, Piotr %A Gieruszczak-Bialek, Dorota %A Piotrowicz, Malgorzata %A Sasiadek, Maria %A Kochanowska, Iwona %A Gurda, Barbara %A Steinborn, Barbara %A Dawidziuk, Mateusz %A Castaneda, Jennifer %A Wlasienko, Pawel %A Bezniakow, Natalia %A Jhangiani, Shalini N %A Hoffman-Zacharska, Dorota %A Bal, Jerzy %A Szczepanik, Elzbieta %A Boerwinkle, Eric %A Gibbs, Richard A %A Lupski, James R %K Cadherins %K DNA Copy Number Variations %K Exome %K Female %K Genetic Heterogeneity %K Humans %K Male %K Malformations of Cortical Development %K Nerve Tissue Proteins %K Polymorphism, Single Nucleotide %K Receptors, Cell Surface %X

Malformations of cortical development (MCDs) manifest with structural brain anomalies that lead to neurologic sequelae, including epilepsy, cerebral palsy, developmental delay, and intellectual disability. To investigate the underlying genetic architecture of patients with disorders of cerebral cortical development, a cohort of 54 patients demonstrating neuroradiologic signs of MCDs was investigated. Individual genomes were interrogated for single-nucleotide variants (SNV) and copy number variants (CNV) with whole-exome sequencing and chromosomal microarray studies. Variation affecting known MCDs-associated genes was found in 16/54 cases, including 11 patients with SNV, 2 patients with CNV, and 3 patients with both CNV and SNV, at distinct loci. Diagnostic pathogenic SNV and potentially damaging variants of unknown significance (VUS) were identified in two groups of seven individuals each. We demonstrated that de novo variants are important among patients with MCDs as they were identified in 10/16 individuals with a molecular diagnosis. Three patients showed changes in known MCDs genes  and a clinical phenotype beyond the usual characteristics observed, i.e., phenotypic expansion, for a particular known disease gene clinical entity. We also discovered 2 likely candidate genes, CDH4, and ASTN1, with human and animal studies supporting their roles in brain development, and 5 potential candidate genes. Our findings emphasize genetic heterogeneity of MCDs disorders and postulate potential novel candidate genes involved in cerebral cortical development.

%B Eur J Hum Genet %V 26 %P 1121-1131 %8 2018 Aug %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/29706646?dopt=Abstract %R 10.1038/s41431-018-0137-z %0 Journal Article %J Blood %D 2018 %T Genetic and mechanistic diversity in pediatric hemophagocytic lymphohistiocytosis. %A Chinn, Ivan K %A Eckstein, Olive S %A Peckham-Gregory, Erin C %A Goldberg, Baruch R %A Forbes, Lisa R %A Nicholas, Sarah K %A Mace, Emily M %A Vogel, Tiphanie P %A Abhyankar, Harshal A %A Diaz, Maria I %A Heslop, Helen E %A Krance, Robert A %A Martinez, Caridad A %A Nguyen, Trung C %A Bashir, Dalia A %A Goldman, Jordana R %A Stray-Pedersen, Asbjørg %A Pedroza, Luis A %A Poli, M Cecilia %A Aldave-Becerra, Juan C %A McGhee, Sean A %A Al-Herz, Waleed %A Chamdin, Aghiad %A Coban-Akdemir, Zeynep H %A Jhangiani, Shalini N %A Muzny, Donna M %A Cao, Tram N %A Hong, Diana N %A Gibbs, Richard A %A Lupski, James R %A Orange, Jordan S %A McClain, Kenneth L %A Allen, Carl E %K Adolescent %K Child %K Child, Preschool %K Cohort Studies %K Female %K Genetic Testing %K Genome, Human %K Genome-Wide Association Study %K High-Throughput Nucleotide Sequencing %K Humans %K Infant %K Infant, Newborn %K Lymphohistiocytosis, Hemophagocytic %K Male %K Multifactorial Inheritance %X

The HLH-2004 criteria are used to diagnose hemophagocytic lymphohistiocytosis (HLH), yet concern exists for their misapplication, resulting in suboptimal treatment of some patients. We sought to define the genomic spectrum and associated outcomes of a diverse cohort of children who met the HLH-2004 criteria. Genetic testing was performed clinically or through research-based whole-exome sequencing. Clinical metrics were analyzed with respect to genomic results. Of 122 subjects enrolled over the course of 17 years, 101 subjects received genetic testing. Biallelic familial HLH (fHLH) gene defects were identified in only 19 (19%) and correlated with presentation at younger than 1 year of age ( < .0001). Digenic fHLH variants were observed but lacked statistical support for disease association. In 28 (58%) of 48 subjects, research whole-exome sequencing analyses successfully identified likely molecular explanations, including underlying primary immunodeficiency diseases, dysregulated immune activation and proliferation disorders, and potentially novel genetic conditions. Two-thirds of patients identified by the HLH-2004 criteria had underlying etiologies for HLH, including genetic defects, autoimmunity, and malignancy. Overall survival was 45%, and increased mortality correlated with HLH triggered by infection or malignancy ( < .05). Differences in survival did not correlate with genetic profile or extent of therapy. HLH should be conceptualized as a phenotype of critical illness characterized by toxic activation of immune cells from different underlying mechanisms. In most patients with HLH, targeted sequencing of fHLH genes remains insufficient for identifying pathogenic mechanisms. Whole-exome sequencing, however, may identify specific therapeutic opportunities and affect hematopoietic stem cell transplantation options for these patients.

%B Blood %V 132 %P 89-100 %8 2018 Jul 05 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/29632024?dopt=Abstract %R 10.1182/blood-2017-11-814244 %0 Journal Article %J Am J Hum Genet %D 2018 %T Heterozygous Truncating Variants in POMP Escape Nonsense-Mediated Decay and Cause a Unique Immune Dysregulatory Syndrome. %A Poli, M Cecilia %A Ebstein, Frédéric %A Nicholas, Sarah K %A de Guzman, Marietta M %A Forbes, Lisa R %A Chinn, Ivan K %A Mace, Emily M %A Vogel, Tiphanie P %A Carisey, Alexandre F %A Benavides, Felipe %A Coban-Akdemir, Zeynep H %A Gibbs, Richard A %A Jhangiani, Shalini N %A Muzny, Donna M %A Carvalho, Claudia M B %A Schady, Deborah A %A Jain, Mahim %A Rosenfeld, Jill A %A Emrick, Lisa %A Lewis, Richard A %A Lee, Brendan %A Zieba, Barbara A %A Küry, Sébastien %A Krüger, Elke %A Lupski, James R %A Bostwick, Bret L %A Orange, Jordan S %K Base Sequence %K Cell Line %K Endoplasmic Reticulum Stress %K Exons %K Family %K Frameshift Mutation %K Genetic Predisposition to Disease %K Heterozygote %K Humans %K Immunologic Deficiency Syndromes %K Immunophenotyping %K Infant, Newborn %K Inflammation %K Interferon Type I %K Male %K Molecular Chaperones %K Mutant Proteins %K Mutation %K Nonsense Mediated mRNA Decay %K Phenotype %K Proteasome Endopeptidase Complex %K RNA, Messenger %K Syndrome %K Unfolded Protein Response %X

The proteasome processes proteins to facilitate immune recognition and host defense. When inherently defective, it can lead to aberrant immunity resulting in a dysregulated response that can cause autoimmunity and/or autoinflammation. Biallelic or digenic loss-of-function variants in some of the proteasome subunits have been described as causing a primary immunodeficiency disease that manifests as a severe dysregulatory syndrome: chronic atypical neutrophilic dermatosis with lipodystrophy and elevated temperature (CANDLE). Proteasome maturation protein (POMP) is a chaperone for proteasome assembly and is critical for the incorporation of catalytic subunits into the proteasome. Here, we characterize and describe POMP-related autoinflammation and immune dysregulation disease (PRAID) discovered in two unrelated individuals with a unique constellation of early-onset combined immunodeficiency, inflammatory neutrophilic dermatosis, and autoimmunity. We also begin to delineate a complex genetic mechanism whereby de novo heterozygous frameshift variants in the penultimate exon of POMP escape nonsense-mediated mRNA decay (NMD) and result in a truncated protein that perturbs proteasome assembly by a dominant-negative mechanism. To our knowledge, this mechanism has not been reported in any primary immunodeficiencies, autoinflammatory syndromes, or autoimmune diseases. Here, we define a unique hypo- and hyper-immune phenotype and report an immune dysregulation syndrome caused by frameshift mutations that escape NMD.

%B Am J Hum Genet %V 102 %P 1126-1142 %8 2018 Jun 07 %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/29805043?dopt=Abstract %R 10.1016/j.ajhg.2018.04.010 %0 Journal Article %J Mol Genet Metab %D 2018 %T Identification of a pathogenic PMP2 variant in a multi-generational family with CMT type 1: Clinical gene panels versus genome-wide approaches to molecular diagnosis. %A Punetha, Jaya %A Mackay-Loder, Loren %A Harel, Tamar %A Coban-Akdemir, Zeynep %A Jhangiani, Shalini N %A Richard A Gibbs %A Lee, Ian %A Terespolsky, Deborah %A Lupski, James R %A Posey, Jennifer E %K Charcot-Marie-Tooth Disease %K Demyelinating Diseases %K Humans %K Mutation %K Myelin P2 Protein %K Neural Conduction %K Pathology, Molecular %K Peripheral Nervous System Diseases %X

Charcot-Marie-Tooth (CMT) disease type 1 is an inherited peripheral neuropathy characterized by demyelination and reduced nerve conduction velocities. We present a multi-generational family with peripheral neuropathy in whom clinical CMT panel testing failed to conclude a molecular diagnosis. We found a PMP2 pathogenic variant c.155T > C, p.(Ile52Thr) that segregates with disease suggesting that PMP2 variants should be considered in patients with neuropathy and that it may be prudent to include in clinical CMT gene panels.

%B Mol Genet Metab %V 125 %P 302-304 %8 2018 Nov %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/30249361?dopt=Abstract %R 10.1016/j.ymgme.2018.08.005 %0 Journal Article %J Hum Genet %D 2018 %T Identification of likely pathogenic and known variants in TSPEAR, LAMB3, BCOR, and WNT10A in four Turkish families with tooth agenesis. %A Du, Renqian %A Dinckan, Nuriye %A Song, Xiaofei %A Coban-Akdemir, Zeynep %A Jhangiani, Shalini N %A Guven, Yeliz %A Aktoren, Oya %A Kayserili, Hulya %A Petty, Lauren E %A Donna M Muzny %A Below, Jennifer E %A Eric Boerwinkle %A Wu, Nan %A Richard A Gibbs %A Posey, Jennifer E %A Lupski, James R %A Letra, Ariadne %A Uyguner, Z Oya %K Anodontia %K Cell Adhesion Molecules %K Child %K Child, Preschool %K Female %K Genetic Markers %K Humans %K Kalinin %K Male %K Mutation %K Pedigree %K Phenotype %K Proteins %K Proto-Oncogene Proteins %K Repressor Proteins %K Turkey %K Wnt Proteins %X

Tooth agenesis (TA), the failure of development of one or more permanent teeth, is a common craniofacial abnormality observed in different world populations. The genetic etiology of TA is heterogeneous; more than a dozen genes have been associated with isolated or nonsyndromic TA, and more than 80 genes with syndromic forms. In this study, we applied whole exome sequencing (WES) to identify candidate genes contributing to TA in four Turkish families. Likely pathogenic variants with a low allele frequency in the general population were identified in four disease-associated genes, including two distinct variants in TSPEAR, associated with syndromic and isolated TA in one family each; a variant in LAMB3 associated with syndromic TA in one family; and a variant in BCOR plus a disease-associated WNT10A variant in one family with syndromic TA. With the notable exception of WNT10A (Tooth agenesis, selective, 4, MIM #150400), the genotype-phenotype relationships described in the present cohort represent an expansion of the clinical spectrum associated with these genes: TSPEAR (Deafness, autosomal recessive 98, MIM #614861), LAMB3 (Amelogenesis imperfecta, type IA, MIM #104530; Epidermolysis bullosa, junctional, MIMs #226700 and #226650), and BCOR (Microphthalmia, syndromic 2, MIM #300166). We provide evidence supporting the candidacy of these genes with TA, and propose TSPEAR as a novel nonsyndromic TA gene. Our data also suggest potential multilocus genomic variation, or mutational burden, in a single family, involving the BCOR and WNT10A loci, underscoring the complexity of the genotype-phenotype relationship in the common complex trait of TA.

%B Hum Genet %V 137 %P 689-703 %8 2018 Sep %G eng %N 9 %1 https://www.ncbi.nlm.nih.gov/pubmed/30046887?dopt=Abstract %R 10.1007/s00439-018-1907-y %0 Journal Article %J Am J Hum Genet %D 2018 %T Identifying Genes Whose Mutant Transcripts Cause Dominant Disease Traits by Potential Gain-of-Function Alleles. %A Coban-Akdemir, Zeynep %A White, Janson J %A Song, Xiaofei %A Jhangiani, Shalini N %A Fatih, Jawid M %A Gambin, Tomasz %A Bayram, Yavuz %A Chinn, Ivan K %A Karaca, Ender %A Punetha, Jaya %A Poli, Cecilia %A Eric Boerwinkle %A Shaw, Chad A %A Orange, Jordan S %A Richard A Gibbs %A Lappalainen, Tuuli %A James R Lupski %A Carvalho, Claudia M B %K Alleles %K Codon, Nonsense %K Databases, Genetic %K Exome %K Gain of Function Mutation %K Humans %K Mutation %K Nonsense Mediated mRNA Decay %K Phenotype %X

Premature termination codon (PTC)-bearing transcripts are often degraded by nonsense-mediated decay (NMD) resulting in loss-of-function (LoF) alleles. However, not all PTCs result in LoF mutations, i.e., some such transcripts escape NMD and are translated to truncated peptide products that result in disease due to gain-of-function (GoF) effects. Since the location of the PTC is a major factor determining transcript fate, we hypothesized that depletion of protein-truncating variants (PTVs) within the gene region predicted to escape NMD in control databases could provide a rank for genic susceptibility for disease through GoF versus LoF. We developed an NMD escape intolerance score to rank genes based on the depletion of PTVs that would render them able to escape NMD using the Atherosclerosis Risk in Communities Study (ARIC) and the Exome Aggregation Consortium (ExAC) control databases, which was further used to screen the Baylor-Center for Mendelian Genomics disease database. This analysis revealed 1,996 genes significantly depleted for PTVs that are predicted to escape from NMD, i.e., PTVesc; further studies provided evidence that revealed a subset as candidate genes underlying Mendelian phenotypes. Importantly, these genes have characteristically low pLI scores, which can cause them to be overlooked as candidates for dominant diseases. Collectively, we demonstrate that this NMD escape intolerance score is an effective and efficient tool for gene discovery in Mendelian diseases due to production of truncated or altered proteins. More importantly, we provide a complementary analytical tool to aid identification of genes associated with dominant traits through a mechanism distinct from LoF.

%B Am J Hum Genet %V 103 %P 171-187 %8 2018 Aug 02 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/30032986?dopt=Abstract %R 10.1016/j.ajhg.2018.06.009 %0 Journal Article %J Hum Mutat %D 2018 %T Marker chromosome genomic structure and temporal origin implicate a chromoanasynthesis event in a family with pleiotropic psychiatric phenotypes. %A Grochowski, Christopher M %A Gu, Shen %A Yuan, Bo %A Tcw, Julia %A Brennand, Kristen J %A Sebat, Jonathan %A Malhotra, Dheeraj %A McCarthy, Shane %A Rudolph, Uwe %A Lindstrand, Anna %A Chong, Zechen %A Levy, Deborah L %A Lupski, James R %A Carvalho, Claudia M B %K Bipolar Disorder %K Chromosome Aberrations %K Chromosome Disorders %K Chromosome Duplication %K Chromosomes, Human, Pair 9 %K Comparative Genomic Hybridization %K Female %K Genetic Markers %K Humans %K In Situ Hybridization, Fluorescence %K Karyotyping %K Male %K Pedigree %K Phenotype %K Psychotic Disorders %K Whole Genome Sequencing %X

Small supernumerary marker chromosomes (sSMC) are chromosomal fragments difficult to characterize genomically. Here, we detail a proband with schizoaffective disorder and a mother with bipolar disorder with psychotic features who present with a marker chromosome that segregates with disease. We explored the architecture of this marker and investigated its temporal origin. Array comparative genomic hybridization (aCGH) analysis revealed three duplications and three triplications that spanned the short arm of chromosome 9, suggestive of a chromoanasynthesis-like event. Segregation of marker genotypes, phased using sSMC mosaicism in the mother, provided evidence that it was generated during a germline-level event in the proband's maternal grandmother. Whole-genome sequencing (WGS) was performed to resolve the structure and junctions of the chromosomal fragments, revealing further complexities. While structural variations have been previously associated with neuropsychiatric disorders and marker chromosomes, here we detail the precise architecture, human life-cycle genesis, and propose a DNA replicative/repair mechanism underlying formation.

%B Hum Mutat %V 39 %P 939-946 %8 2018 Jul %G eng %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/29696747?dopt=Abstract %R 10.1002/humu.23537 %0 Journal Article %J PLoS Genet %D 2018 %T Mutation in the intracellular chloride channel CLCC1 associated with autosomal recessive retinitis pigmentosa. %A Li, Lin %A Jiao, Xiaodong %A D'Atri, Ilaria %A Ono, Fumihito %A Nelson, Ralph %A Chan, Chi-Chao %A Nakaya, Naoki %A Ma, Zhiwei %A Ma, Yan %A Cai, Xiaoying %A Zhang, Longhua %A Lin, Siying %A Hameed, Abdul %A Chioza, Barry A %A Hardy, Holly %A Arno, Gavin %A Hull, Sarah %A Khan, Muhammad Imran %A Fasham, James %A Harlalka, Gaurav V %A Michaelides, Michel %A Moore, Anthony T %A Coban Akdemir, Zeynep Hande %A Jhangiani, Shalini %A James R Lupski %A Cremers, Frans P M %A Qamar, Raheel %A Salman, Ahmed %A Chilton, John %A Self, Jay %A Ayyagari, Radha %A Kabir, Firoz %A Naeem, Muhammad Asif %A Ali, Muhammad %A Akram, Javed %A Sieving, Paul A %A Riazuddin, Sheikh %A Baple, Emma L %A Riazuddin, S Amer %A Crosby, Andrew H %A Hejtmancik, J Fielding %K Animals %K Asian People %K Cell Line %K Chloride Channels %K Cytoplasm %K Eye Proteins %K HEK293 Cells %K Homozygote %K Humans %K Mice %K Mice, Knockout %K Mutation, Missense %K Pakistan %K Retina %K Retinal Cone Photoreceptor Cells %K Retinal Rod Photoreceptor Cells %K Retinitis Pigmentosa %K Zebrafish %X

We identified a homozygous missense alteration (c.75C>A, p.D25E) in CLCC1, encoding a presumptive intracellular chloride channel highly expressed in the retina, associated with autosomal recessive retinitis pigmentosa (arRP) in eight consanguineous families of Pakistani descent. The p.D25E alteration decreased CLCC1 channel function accompanied by accumulation of mutant protein in granules within the ER lumen, while siRNA knockdown of CLCC1 mRNA induced apoptosis in cultured ARPE-19 cells. TALEN KO in zebrafish was lethal 11 days post fertilization. The depressed electroretinogram (ERG) cone response and cone spectral sensitivity of 5 dpf KO zebrafish and reduced eye size, retinal thickness, and expression of rod and cone opsins could be rescued by injection of wild type CLCC1 mRNA. Clcc1+/- KO mice showed decreased ERGs and photoreceptor number. Together these results strongly suggest that intracellular chloride transport by CLCC1 is a critical process in maintaining retinal integrity, and CLCC1 is crucial for survival and function of retinal cells.

%B PLoS Genet %V 14 %P e1007504 %8 2018 Aug %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/30157172?dopt=Abstract %R 10.1371/journal.pgen.1007504 %0 Journal Article %J J Allergy Clin Immunol %D 2018 %T Mutations in PI3K110δ cause impaired natural killer cell function partially rescued by rapamycin treatment. %A Ruiz-García, Raquel %A Vargas-Hernandez, Alexander %A Chinn, Ivan K %A Angelo, Laura S %A Cao, Tram N %A Coban-Akdemir, Zeynep %A Jhangiani, Shalini N %A Meng, Qingchang %A Forbes, Lisa R %A Muzny, Donna M %A Allende, Luis M %A Ehlayel, Mohammed S %A Gibbs, Richard A %A Lupski, James R %A Uzel, Gulbu %A Orange, Jordan S %A Mace, Emily M %K Cell Differentiation %K Cells, Cultured %K Class I Phosphatidylinositol 3-Kinases %K Cytomegalovirus %K Cytomegalovirus Infections %K Cytotoxicity, Immunologic %K Epstein-Barr Virus Infections %K Exome Sequencing %K Herpesvirus 4, Human %K Heterozygote %K Humans %K Immunologic Deficiency Syndromes %K Immunological Synapses %K Immunophenotyping %K Killer Cells, Natural %K Lymphocyte Activation %K Microscopy, Confocal %K Mutation %K Phosphatidylinositol 3-Kinases %K Sirolimus %K Viremia %X

BACKGROUND: Heterozygous gain-of-function mutations in PI3K110δ lead to lymphadenopathy, lymphoid hyperplasia, EBV and cytomegalovirus viremia, and sinopulmonary infections.

OBJECTIVE: The known role of natural killer (NK) cell function in the control of EBV and cytomegalovirus prompted us to investigate the functional and phenotypic effects of PI3K110δ mutations on NK cell subsets and cytotoxic function.

METHODS: Mutations in patients were identified by using whole-exome or targeted sequencing. We performed NK cell phenotyping and functional analysis of patients' cells using flow cytometry, standard Cr cytotoxicity assays, and quantitative confocal microscopy.

RESULTS: PI3K110δ mutations led to an altered NK cell developmental phenotype and cytotoxic dysfunction. Impaired NK cell cytotoxicity was due to decreased conjugate formation with susceptible target cells and abrogated activation of cell machinery required for target cell killing. These defects were restored partially after initiation of treatment with rapamycin in 3 patients.

CONCLUSION: We describe novel NK cell functional deficiency caused by PI3K110δ mutation, which is a likely contributor to the severe viremia observed in these patients. Rapamycin treatment partially restores NK cell function, providing a further rationale for its use in patients with this disease.

%B J Allergy Clin Immunol %V 142 %P 605-617.e7 %8 2018 Aug %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/29330011?dopt=Abstract %R 10.1016/j.jaci.2017.11.042 %0 Journal Article %J Hum Mol Genet %D 2018 %T Mutations in the mitochondrial ribosomal protein MRPS22 lead to primary ovarian insufficiency. %A Chen, Anlu %A Tiosano, Dov %A Guran, Tulay %A Baris, Hagit N %A Bayram, Yavuz %A Mory, Adi %A Shapiro-Kulnane, Laura %A Hodges, Craig A %A Akdemir, Zeynep C %A Turan, Serap %A Jhangiani, Shalini N %A van den Akker, Focco %A Hoppel, Charles L %A Salz, Helen K %A Lupski, James R %A Buchner, David A %K Adolescent %K Adult %K Amenorrhea %K Animals %K Disease Models, Animal %K Drosophila %K Drosophila Proteins %K Female %K Fertility %K Homozygote %K Humans %K Menopause, Premature %K Mitochondrial Proteins %K Mutation, Missense %K Ovarian Follicle %K Primary Ovarian Insufficiency %K Ribosomal Proteins %K Young Adult %X

Primary ovarian insufficiency (POI) is characterized by amenorrhea and loss or dysfunction of ovarian follicles prior to the age of 40. POI has been associated with autosomal recessive mutations in genes involving hormonal signaling and folliculogenesis, however, the genetic etiology of POI most often remains unknown. Here we report MRPS22 homozygous missense variants c.404G>A (p.R135Q) and c.605G>A (p.R202H) identified in four females from two independent consanguineous families as a novel genetic cause of POI in adolescents. Both missense mutations identified in MRPS22 are rare, occurred in highly evolutionarily conserved residues, and are predicted to be deleterious to protein function. In contrast to prior reports of mutations in MRPS22 associated with severe mitochondrial disease, the POI phenotype is far less severe. Consistent with this genotype-phenotype correlation, mitochondrial defects in oxidative phosphorylation or rRNA levels were not detected in fibroblasts derived from the POI patients, suggesting a non-bioenergetic or tissue-specific mitochondrial defect. Furthermore, we demonstrate in a Drosophila model that mRpS22 deficiency specifically in somatic cells of the ovary had no effect on fertility, whereas flies with mRpS22 deficiency specifically in germ cells were infertile and agametic, demonstrating a cell autonomous requirement for mRpS22 in germ cell development. These findings collectively identify that MRPS22, a component of the small mitochondrial ribosome subunit, is critical for ovarian development and may therefore provide insight into the pathophysiology and treatment of ovarian dysfunction.

%B Hum Mol Genet %V 27 %P 1913-1926 %8 2018 Jun 01 %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/29566152?dopt=Abstract %R 10.1093/hmg/ddy098 %0 Journal Article %J Eur J Hum Genet %D 2018 %T A novel NAA10 variant with impaired acetyltransferase activity causes developmental delay, intellectual disability, and hypertrophic cardiomyopathy. %A Støve, Svein Isungset %A Blenski, Marina %A Stray-Pedersen, Asbjørg %A Wierenga, Klaas J %A Jhangiani, Shalini N %A Akdemir, Zeynep Coban %A Crawford, David %A McTiernan, Nina %A Myklebust, Line M %A Purcarin, Gabriela %A McNall-Knapp, Rene %A Wadley, Alexandrea %A Belmont, John W %A Kim, Jeffrey J %A Lupski, James R %A Arnesen, Thomas %K Cardiomyopathy, Hypertrophic %K Child, Preschool %K Developmental Disabilities %K Enzyme Stability %K HeLa Cells %K Humans %K Infant %K Intellectual Disability %K Male %K Mutation %K N-Terminal Acetyltransferase A %K N-Terminal Acetyltransferase E %K Phenotype %K Protein Binding %K Syndrome %X

The NAA10-NAA15 complex (NatA) is an N-terminal acetyltransferase that catalyzes N-terminal acetylation of ~40% of all human proteins. N-terminal acetylation has several different roles in the cell, including altering protein stability and degradation, protein localization and protein-protein interactions. In recent years several X-linked NAA10 variants have been associated with genetic disorders. We have identified a previously undescribed NAA10 c.215T>C p.(Ile72Thr) variant in three boys from two unrelated families with a milder phenotypic spectrum in comparison to most of the previously described patients with NAA10 variants. These boys have development delay, intellectual disability, and cardiac abnormalities as overlapping phenotypes. Functional studies reveal that NAA10 Ile72Thr is destabilized, while binding to NAA15 most likely is intact. Surprisingly, the NatA activity of NAA10 Ile72Thr appears normal while its monomeric activity is decreased. This study further broadens the phenotypic spectrum associated with NAA10 deficiency, and adds to the evidence that genotype-phenotype correlations for NAA10 variants are much more complex than initially anticipated.

%B Eur J Hum Genet %V 26 %P 1294-1305 %8 2018 Sep %G eng %N 9 %1 https://www.ncbi.nlm.nih.gov/pubmed/29748569?dopt=Abstract %R 10.1038/s41431-018-0136-0 %0 Journal Article %J Genet Med %D 2018 %T Phenotypic expansion illuminates multilocus pathogenic variation. %A Karaca, Ender %A Posey, Jennifer E %A Coban Akdemir, Zeynep %A Pehlivan, Davut %A Harel, Tamar %A Jhangiani, Shalini N %A Bayram, Yavuz %A Song, Xiaofei %A Bahrambeigi, Vahid %A Yuregir, Ozge Ozalp %A Bozdogan, Sevcan %A Yesil, Gozde %A Isikay, Sedat %A Muzny, Donna %A Gibbs, Richard A %A Lupski, James R %K Child, Preschool %K Exome %K Exome Sequencing %K Female %K Genetic Association Studies %K Genetic Diseases, Inborn %K Genetic Variation %K Genotype %K Heterozygote %K High-Throughput Nucleotide Sequencing %K Humans %K Infant %K Infant, Newborn %K Male %K Mutation %K Pathology, Molecular %K Pedigree %K Phenotype %X

PURPOSE: Multilocus variation-pathogenic variants in two or more disease genes-can potentially explain the underlying genetic basis for apparent phenotypic expansion in cases for which the observed clinical features extend beyond those reported in association with a "known" disease gene.

METHODS: Analyses focused on 106 patients, 19 for whom apparent phenotypic expansion was previously attributed to variation at known disease genes. We performed a retrospective computational reanalysis of whole-exome sequencing data using stringent Variant Call File filtering criteria to determine whether molecular diagnoses involving additional disease loci might explain the observed expanded phenotypes.

RESULTS: Multilocus variation was identified in 31.6% (6/19) of families with phenotypic expansion and 2.3% (2/87) without phenotypic expansion. Intrafamilial clinical variability within two families was explained by multilocus variation identified in the more severely affected sibling.

CONCLUSION: Our findings underscore the role of multiple rare variants at different loci in the etiology of genetically and clinically heterogeneous cohorts. Intrafamilial phenotypic and genotypic variability allowed a dissection of genotype-phenotype relationships in two families. Our data emphasize the critical role of the clinician in diagnostic genomic analyses and demonstrate that apparent phenotypic expansion may represent blended phenotypes resulting from pathogenic variation at more than one locus.

%B Genet Med %V 20 %P 1528-1537 %8 2018 Dec %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/29790871?dopt=Abstract %R 10.1038/gim.2018.33 %0 Journal Article %J Ann Clin Transl Neurol %D 2018 %T Phenotypic expansion in - a common cause of intellectual disability in females. %A Wang, Xia %A Posey, Jennifer E %A Rosenfeld, Jill A %A Bacino, Carlos A %A Scaglia, Fernando %A Immken, Ladonna %A Harris, Jill M %A Hickey, Scott E %A Mosher, Theresa M %A Slavotinek, Anne %A Zhang, Jing %A Beuten, Joke %A Leduc, Magalie S %A He, Weimin %A Vetrini, Francesco %A Walkiewicz, Magdalena A %A Bi, Weimin %A Xiao, Rui %A Liu, Pengfei %A Shao, Yunru %A Gezdirici, Alper %A Gulec, Elif Y %A Jiang, Yunyun %A Darilek, Sandra A %A Hansen, Adam W %A Khayat, Michael M %A Pehlivan, Davut %A Piard, Juliette %A Donna M Muzny %A Hanchard, Neil %A Belmont, John W %A Van Maldergem, Lionel %A Richard A Gibbs %A Eldomery, Mohammad K %A Akdemir, Zeynep C %A Adesina, Adekunle M %A Chen, Shan %A Lee, Yi-Chien %A Lee, Brendan %A James R Lupski %A Eng, Christine M %A Xia, Fan %A Yang, Yaping %A Graham, Brett H %A Moretti, Paolo %X

De variants in account for 1-3% of unexplained intellectual disability (ID) cases and are amongst the most common causes of ID especially in females. Forty-seven patients (44 females, 3 males) have been described. We identified 31 additional individuals carrying 29 unique variants, including 30 postnatal individuals with complex clinical presentations of developmental delay or ID, and one fetus with abnormal ultrasound findings. Rare or novel phenotypes observed include respiratory problems, congenital heart disease, skeletal muscle mitochondrial DNA depletion, and late-onset neurologic decline. Our findings expand the spectrum of DNA variants and phenotypes associated with disorders.

%B Ann Clin Transl Neurol %V 5 %P 1277-1285 %8 2018 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/30349862?dopt=Abstract %R 10.1002/acn3.622 %0 Journal Article %J Am J Med Genet A %D 2018 %T The phenotypic spectrum of Xia-Gibbs syndrome. %A Jiang, Yunyun %A Wangler, Michael F %A McGuire, Amy L %A Lupski, James R %A Posey, Jennifer E %A Khayat, Michael M %A Murdock, David R %A Sanchez-Pulido, Luis %A Ponting, Chris P %A Xia, Fan %A Hunter, Jill V %A Meng, Qingchang %A Murugan, Mullai %A Gibbs, Richard A %K Autism Spectrum Disorder %K Child %K Cognition %K Corpus Callosum %K Developmental Disabilities %K DNA-Binding Proteins %K Face %K Female %K Humans %K Male %K Mutation %K Pedigree %K Phenotype %K Registries %K Seizures %K Syndrome %K Young Adult %X

Xia-Gibbs syndrome (XGS: OMIM # 615829) results from de novo truncating mutations within the AT-Hook DNA Binding Motif Containing 1 gene (AHDC1). To further define the phenotypic and molecular spectrum of this disorder, we established an XGS Registry and recruited patients from a worldwide pool of approximately 60 probands. Additional de novo truncating mutations were observed among 25 individuals, extending both the known number of mutation sites and the range of positions within the coding region that were sensitive to alteration. Detailed phenotypic examination of 20 of these patients via clinical records review and data collection from additional surveys showed a wider age range than previously described. Data from developmental milestones showed evidence for delayed speech and that males were more severely affected. Neuroimaging from six available patients showed an associated thinning of the corpus callosum and posterior fossa cysts. An increased risk of both scoliosis and seizures relative to the population burden was also observed. Data from a modified autism screening tool revealed that XGS shares significant overlap with autism spectrum disorders. These details of the phenotypic heterogeneity of XGS implicate specific genotype/phenotype correlations and suggest potential clinical management guidelines.

%B Am J Med Genet A %V 176 %P 1315-1326 %8 2018 Jun %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/29696776?dopt=Abstract %R 10.1002/ajmg.a.38699 %0 Journal Article %J Genome Res %D 2018 %T Predicting human genes susceptible to genomic instability associated with /-mediated rearrangements. %A Song, Xiaofei %A Beck, Christine R %A Du, Renqian %A Campbell, Ian M %A Coban-Akdemir, Zeynep %A Gu, Shen %A Breman, Amy M %A Stankiewicz, Pawel %A Ira, Grzegorz %A Shaw, Chad A %A Lupski, James R %K Alu Elements %K DNA Copy Number Variations %K Gene Duplication %K Genome, Human %K Genomic Instability %K Humans %K Sequence Deletion %X

elements, the short interspersed element numbering more than 1 million copies per human genome, can mediate the formation of copy number variants (CNVs) between substrate pairs. These /-mediated rearrangements (AAMRs) can result in pathogenic variants that cause diseases. To investigate the impact of AAMR on gene variation and human health, we first characterized s that are involved in mediating CNVs (CNV-s) and observed that these s tend to be evolutionarily younger. We then computationally generated, with the assistance of a supercomputer, a test data set consisting of 78 million pairs and predicted ∼18% of them are potentially susceptible to AAMR. We further determined the relative risk of AAMR in 12,074 OMIM genes using the count of predicted CNV- pairs and experimentally validated the predictions with 89 samples selected by correlating predicted hotspots with a database of CNVs identified by clinical chromosomal microarrays (CMAs) on the genomes of approximately 54,000 subjects. We fine-mapped 47 duplications, 40 deletions, and two complex rearrangements and examined a total of 52 breakpoint junctions of simple CNVs. Overall, 94% of the candidate breakpoints were at least partially mediated. We successfully predicted all (100%) of pairs that mediated deletions ( = 21) and achieved an 87% positive predictive value overall when including AAMR-generated deletions and duplications. We provided a tool, AluAluCNVpredictor, for assessing AAMR hotspots and their role in human disease. These results demonstrate the utility of our predictive model and provide insights into the genomic features and molecular mechanisms underlying AAMR.

%B Genome Res %V 28 %P 1228-1242 %8 2018 Aug %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/29907612?dopt=Abstract %R 10.1101/gr.229401.117 %0 Journal Article %J J Pediatr Genet %D 2018 %T Prioritization of Candidate Genes for Congenital Diaphragmatic Hernia in a Critical Region on Chromosome 4p16 using a Machine-Learning Algorithm. %A Callaway, Danielle A %A Campbell, Ian M %A Stover, Samantha R %A Hernandez-Garcia, Andres %A Jhangiani, Shalini N %A Punetha, Jaya %A Paine, Ingrid S %A Posey, Jennifer E %A Donna M Muzny %A Lally, Kevin P %A James R Lupski %A Shaw, Chad A %A Fernandes, Caraciolo J %A Scott, Daryl A %X

Wolf-Hirschhorn syndrome (WHS) is caused by partial deletion of the short arm of chromosome 4 and is characterized by dysmorphic facies, congenital heart defects, intellectual/developmental disability, and increased risk for congenital diaphragmatic hernia (CDH). In this report, we describe a stillborn girl with WHS and a large CDH. A literature review revealed 15 cases of WHS with CDH, which overlap a 2.3-Mb CDH critical region. We applied a machine-learning algorithm that integrates large-scale genomic knowledge to genes within the 4p16.3 CDH critical region and identified , , , , , , , and as genes whose haploinsufficiency may contribute to the development of CDH.

%B J Pediatr Genet %V 7 %P 164-173 %8 2018 Dec %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/30430034?dopt=Abstract %R 10.1055/s-0038-1655755 %0 Journal Article %J Cell Rep %D 2018 %T Pro-inflammation Associated with a Gain-of-Function Mutation (R284S) in the Innate Immune Sensor STING. %A Konno, Hiroyasu %A Chinn, Ivan K %A Hong, Diana %A Orange, Jordan S %A Lupski, James R %A Mendoza, Alejandra %A Pedroza, Luis A %A Barber, Glen N %K Animals %K Autophagy %K Autophagy-Related Protein-1 Homolog %K Gain of Function Mutation %K HEK293 Cells %K Humans %K Inflammation %K Intracellular Signaling Peptides and Proteins %K Membrane Proteins %K Mice %K Mice, Knockout %X

The cellular sensor stimulator of interferon genes (STING) initiates type I interferon (IFN) and cytokine production following association with cyclic dinucleotides (CDNs) generated from intracellular bacteria or via a cellular synthase, cGAS, after binding microbial or self-DNA. Although essential for protecting the host against infection, unscheduled STING signaling is now known to be responsible for a variety of autoinflammatory disorders. Here, we report a gain-of-function mutation in STING (R284S), isolated from a patient who did not require CDNs to augment activity and who manifested a constitutively active phenotype. Control of the Unc-51-like autophagy activating kinase 1 (ULK1) pathway, which has previously been shown to influence STING function, was potently able to suppress STING (R284S) activity to alleviate cytokine production. Our findings add to the growing list of inflammatory syndromes associated with spontaneous STING signaling and provide a therapeutic strategy for the treatment of STING-induced inflammatory disease.

%B Cell Rep %V 23 %P 1112-1123 %8 2018 Apr 24 %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/29694889?dopt=Abstract %R 10.1016/j.celrep.2018.03.115 %0 Journal Article %J Hum Mol Genet %D 2018 %T The role of FREM2 and FRAS1 in the development of congenital diaphragmatic hernia. %A Jordan, Valerie K %A Beck, Tyler F %A Hernandez-Garcia, Andres %A Kundert, Peter N %A Kim, Bum-Jun %A Jhangiani, Shalini N %A Gambin, Tomasz %A Starkovich, Molly %A Punetha, Jaya %A Paine, Ingrid S %A Posey, Jennifer E %A Li, Alexander H %A Muzny, Donna %A Hsu, Chih-Wei %A Lashua, Amber J %A Sun, Xin %A Fernandes, Caraciolo J %A Dickinson, Mary E %A Lally, Kevin P %A Gibbs, Richard A %A Boerwinkle, Eric %A Lupski, James R %A Scott, Daryl A %K Animals %K Child %K Child, Preschool %K Epithelium %K Extracellular Matrix Proteins %K Female %K Hernias, Diaphragmatic, Congenital %K Humans %K Infant %K Infant, Newborn %K Male %K Mice %K Mice, Knockout %K Mutation %K Pregnancy %K Receptors, Interleukin %X

Congenital diaphragmatic hernia (CDH) has been reported twice in individuals with a clinical diagnosis of Fraser syndrome, a genetic disorder that can be caused by recessive mutations affecting FREM2 and FRAS1. In the extracellular matrix, FREM2 and FRAS1 form a self-stabilizing complex with FREM1, a protein whose deficiency causes sac CDH in humans and mice. By sequencing FREM2 and FRAS1 in a CDH cohort, and searching online databases, we identified five individuals who carried recessive or double heterozygous, putatively deleterious variants in these genes which may represent susceptibility alleles. Three of these alleles were significantly enriched in our CDH cohort compared with ethnically matched controls. We subsequently demonstrated that 8% of Frem2ne/ne and 1% of Fras1Q1263*/Q1263* mice develop the same type of anterior sac CDH seen in FREM1-deficient mice. We went on to show that development of sac hernias in FREM1-deficient mice is preceded by failure of anterior mesothelial fold progression resulting in the persistence of an amuscular, poorly vascularized anterior diaphragm that is abnormally adherent to the underlying liver. Herniation occurs in the perinatal period when the expanding liver protrudes through this amuscular region of the anterior diaphragm that is juxtaposed to areas of muscular diaphragm. Based on these data, we conclude that deficiency of FREM2, and possibly FRAS1, are associated with an increased risk of developing CDH and that loss of the FREM1/FREM2/FRAS1 complex, or its function, leads to anterior sac CDH development through its effects on mesothelial fold progression.

%B Hum Mol Genet %V 27 %P 2064-2075 %8 2018 Jun 15 %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/29618029?dopt=Abstract %R 10.1093/hmg/ddy110 %0 Journal Article %J Am J Hum Genet %D 2018 %T Truncating Variants in NAA15 Are Associated with Variable Levels of Intellectual Disability, Autism Spectrum Disorder, and Congenital Anomalies. %A Cheng, Hanyin %A Dharmadhikari, Avinash V %A Varland, Sylvia %A Ma, Ning %A Domingo, Deepti %A Kleyner, Robert %A Rope, Alan F %A Yoon, Margaret %A Stray-Pedersen, Asbjørg %A Posey, Jennifer E %A Crews, Sarah R %A Eldomery, Mohammad K %A Akdemir, Zeynep Coban %A Lewis, Andrea M %A Sutton, Vernon R %A Rosenfeld, Jill A %A Conboy, Erin %A Agre, Katherine %A Xia, Fan %A Walkiewicz, Magdalena %A Longoni, Mauro %A High, Frances A %A van Slegtenhorst, Marjon A %A Mancini, Grazia M S %A Finnila, Candice R %A van Haeringen, Arie %A den Hollander, Nicolette %A Ruivenkamp, Claudia %A Naidu, Sakkubai %A Mahida, Sonal %A Palmer, Elizabeth E %A Murray, Lucinda %A Lim, Derek %A Jayakar, Parul %A Parker, Michael J %A Giusto, Stefania %A Stracuzzi, Emanuela %A Romano, Corrado %A Beighley, Jennifer S %A Bernier, Raphael A %A Küry, Sébastien %A Nizon, Mathilde %A Corbett, Mark A %A Shaw, Marie %A Gardner, Alison %A Barnett, Christopher %A Armstrong, Ruth %A Kassahn, Karin S %A Van Dijck, Anke %A Vandeweyer, Geert %A Kleefstra, Tjitske %A Schieving, Jolanda %A Jongmans, Marjolijn J %A de Vries, Bert B A %A Pfundt, Rolph %A Kerr, Bronwyn %A Rojas, Samantha K %A Boycott, Kym M %A Person, Richard %A Willaert, Rebecca %A Eichler, Evan E %A Kooy, R Frank %A Yang, Yaping %A Wu, Joseph C %A Lupski, James R %A Arnesen, Thomas %A Cooper, Gregory M %A Chung, Wendy K %A Gecz, Jozef %A Stessman, Holly A F %A Meng, Linyan %A Lyon, Gholson J %K Abnormalities, Multiple %K Adolescent %K Adult %K Autism Spectrum Disorder %K Cell Line %K Child %K Exons %K Female %K Gene Expression Regulation %K Genetic Predisposition to Disease %K Genetic Variation %K Humans %K Intellectual Disability %K Male %K Middle Aged %K Mutation %K N-Terminal Acetyltransferase A %K N-Terminal Acetyltransferase E %K Pedigree %K Phenotype %K RNA, Messenger %K Saccharomyces cerevisiae %X

N-alpha-acetylation is a common co-translational protein modification that is essential for normal cell function in humans. We previously identified the genetic basis of an X-linked infantile lethal Mendelian disorder involving a c.109T>C (p.Ser37Pro) missense variant in NAA10, which encodes the catalytic subunit of the N-terminal acetyltransferase A (NatA) complex. The auxiliary subunit of the NatA complex, NAA15, is the dimeric binding partner for NAA10. Through a genotype-first approach with whole-exome or genome sequencing (WES/WGS) and targeted sequencing analysis, we identified and phenotypically characterized 38 individuals from 33 unrelated families with 25 different de novo or inherited, dominantly acting likely gene disrupting (LGD) variants in NAA15. Clinical features of affected individuals with LGD variants in NAA15 include variable levels of intellectual disability, delayed speech and motor milestones, and autism spectrum disorder. Additionally, mild craniofacial dysmorphology, congenital cardiac anomalies, and seizures are present in some subjects. RNA analysis in cell lines from two individuals showed degradation of the transcripts with LGD variants, probably as a result of nonsense-mediated decay. Functional assays in yeast confirmed a deleterious effect for two of the LGD variants in NAA15. Further supporting a mechanism of haploinsufficiency, individuals with copy-number variant (CNV) deletions involving NAA15 and surrounding genes can present with mild intellectual disability, mild dysmorphic features, motor delays, and decreased growth. We propose that defects in NatA-mediated N-terminal acetylation (NTA) lead to variable levels of neurodevelopmental disorders in humans, supporting the importance of the NatA complex in normal human development.

%B Am J Hum Genet %V 102 %P 985-994 %8 2018 May 03 %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/29656860?dopt=Abstract %R 10.1016/j.ajhg.2018.03.004 %0 Journal Article %J Am J Hum Genet %D 2018 %T WNT Signaling Perturbations Underlie the Genetic Heterogeneity of Robinow Syndrome. %A White, Janson J %A Mazzeu, Juliana F %A Coban-Akdemir, Zeynep %A Bayram, Yavuz %A Bahrambeigi, Vahid %A Hoischen, Alexander %A van Bon, Bregje W M %A Gezdirici, Alper %A Gulec, Elif Yilmaz %A Ramond, Francis %A Touraine, Renaud %A Thevenon, Julien %A Shinawi, Marwan %A Beaver, Erin %A Heeley, Jennifer %A Hoover-Fong, Julie %A Durmaz, Ceren D %A Karabulut, Halil Gurhan %A Marzioglu-Ozdemir, Ebru %A Cayir, Atilla %A Duz, Mehmet B %A Seven, Mehmet %A Price, Susan %A Ferreira, Barbara Merfort %A Vianna-Morgante, Angela M %A Ellard, Sian %A Parrish, Andrew %A Stals, Karen %A Flores-Daboub, Josue %A Jhangiani, Shalini N %A Gibbs, Richard A %A Brunner, Han G %A Sutton, V Reid %A Lupski, James R %A Carvalho, Claudia M B %K Adolescent %K Adult %K Base Sequence %K Child %K Child, Preschool %K Chromosome Segregation %K Craniofacial Abnormalities %K Diagnosis, Differential %K Dwarfism %K Female %K Genes, Dominant %K Genetic Association Studies %K Genetic Heterogeneity %K Humans %K Limb Deformities, Congenital %K Male %K Middle Aged %K Mutation, Missense %K Phenotype %K Urogenital Abnormalities %K Wnt Signaling Pathway %X

Locus heterogeneity characterizes a variety of skeletal dysplasias often due to interacting or overlapping signaling pathways. Robinow syndrome is a skeletal disorder historically refractory to molecular diagnosis, potentially stemming from substantial genetic heterogeneity. All current known pathogenic variants reside in genes within the noncanonical Wnt signaling pathway including ROR2, WNT5A, and more recently, DVL1 and DVL3. However, ∼70% of autosomal-dominant Robinow syndrome cases remain molecularly unsolved. To investigate this missing heritability, we recruited 21 families with at least one family member clinically diagnosed with Robinow or Robinow-like phenotypes and performed genetic and genomic studies. In total, four families with variants in FZD2 were identified as well as three individuals from two families with biallelic variants in NXN that co-segregate with the phenotype. Importantly, both FZD2 and NXN are relevant protein partners in the WNT5A interactome, supporting their role in skeletal development. In addition to confirming that clustered -1 frameshifting variants in DVL1 and DVL3 are the main contributors to dominant Robinow syndrome, we also found likely pathogenic variants in candidate genes GPC4 and RAC3, both linked to the Wnt signaling pathway. These data support an initial hypothesis that Robinow syndrome results from perturbation of the Wnt/PCP pathway, suggest specific relevant domains of the proteins involved, and reveal key contributors in this signaling cascade during human embryonic development. Contrary to the view that non-allelic genetic heterogeneity hampers gene discovery, this study demonstrates the utility of rare disease genomic studies to parse gene function in human developmental pathways.

%B Am J Hum Genet %V 102 %P 27-43 %8 2018 Jan 04 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/29276006?dopt=Abstract %R 10.1016/j.ajhg.2017.10.002 %0 Journal Article %J J Endocr Soc %D 2018 %T Xq26.3 Duplication in a Boy With Motor Delay and Low Muscle Tone Refines the X-Linked Acrogigantism Genetic Locus. %A Trivellin, Giampaolo %A Sharwood, Erin %A Hijazi, Hadia %A Carvalho, Claudia M B %A Bo Yuan %A Tatton-Brown, Katrina %A Coman, David %A James R Lupski %A Cotterill, Andrew M %A Lodish, Maya B %A Stratakis, Constantine A %X

We describe a 4-year-old boy with developmental delay who was found to carry by clinical grade (CG) molecular cytogenetics (MCs) a chromosome Xq26 microduplication. The report prompted a referral of the patient for possible X-linked acrogigantism (X-LAG), a well-defined condition (MIM300942) due to chromosomal microduplication of a nearby region. The patient was evaluated clinically and investigated for endocrine abnormalities related to X-LAG and not only did he not have acrogigantism, but his growth parameters and other hormones were all normal. We then performed high definition MCs and the duplication copy number variant (CNV) was confirmed to precisely map outside the X-LAG critical region and definitely did not harbor the X-LAG candidate gene, . The patient's phenotype resembled that of other patients with Xq26 CNVs. The case is instructive for the need for high definition MCs when CG MCs' results are inconsistent with the patient's phenotype. It is also useful for further supporting the contention that is the gene responsible for X-LAG.

%B J Endocr Soc %V 2 %P 1100-1108 %8 2018 Oct 01 %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/30525125?dopt=Abstract %R 10.1210/js.2018-00156 %0 Journal Article %J Am J Med Genet A %D 2017 %T 22q11.2q13 duplication including SOX10 causes sex-reversal and peripheral demyelinating neuropathy, central dysmyelinating leukodystrophy, Waardenburg syndrome, and Hirschsprung disease. %A Falah, Nadia %A Posey, Jennifer E %A Thorson, Willa %A Benke, Paul %A Tekin, Mustafa %A Tarshish, Brocha %A Lupski, James R %A Harel, Tamar %K 46, XX Testicular Disorders of Sex Development %K Black or African American %K Chromosome Duplication %K Chromosomes, Human, Pair 22 %K Demyelinating Diseases %K Hirschsprung Disease %K Humans %K Kidney Failure, Chronic %K Male %K Pelizaeus-Merzbacher Disease %K SOXE Transcription Factors %K Waardenburg Syndrome %X

Diagnosis of genetic syndromes may be difficult when specific components of a disorder manifest at a later age. We present a follow up of a previous report [Seeherunvong et al., (2004); AJMGA 127: 149-151], of an individual with 22q duplication and sex-reversal syndrome. The subject's phenotype evolved to include peripheral and central demyelination, Waardenburg syndrome type IV, and Hirschsprung disease (PCWH; MIM 609136). DNA microarray analysis defined the duplication at 22q11.2q13, including SOX10. Sequencing of the coding region of SOX10 did not reveal any mutations. Our data suggest that SOX10 duplication can cause disorders of sex development and PCWH, supporting the hypothesis that SOX10 toxic gain of function rather than dominant negative activity underlies PCWH.

%B Am J Med Genet A %V 173 %P 1066-1070 %8 2017 Apr %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/28328136?dopt=Abstract %R 10.1002/ajmg.a.38109 %0 Journal Article %J J Child Adolesc Psychopharmacol %D 2017 %T CHRNA7 Deletions are Enriched in Risperidone-Treated Children and Adolescents. %A Gillentine, Madelyn A %A White, Janson J %A Grochowski, Christopher M %A Lupski, James R %A Schaaf, Christian P %A Calarge, Chadi A %K Adolescent %K alpha7 Nicotinic Acetylcholine Receptor %K Antipsychotic Agents %K Child %K Cohort Studies %K Female %K Gene Deletion %K Humans %K Male %K Neurodevelopmental Disorders %K Prospective Studies %K Risperidone %K Treatment Outcome %X

OBJECTIVE: Aggression is among the most common indications for referral to child and adolescent mental health services and is often challenging to treat. Understanding the biological underpinnings of aggression could help optimize treatment efficacy. Neuronal nicotinic acetylcholine receptors (nAChRs), specifically the α7 nAChR, encoded by the gene CHRNA7, have been implicated in aggressive behaviors in animal models as well as humans. Copy number variants (CNVs) of CHRNA7 are found in individuals with neuropsychiatric disorders, often with comorbid aggression. In this study, we aimed to determine the prevalence of CHRNA7 CNVs among individuals treated with risperidone, predominantly for irritability and aggression.

METHODS: Risperidone-treated children and adolescents were assessed for CHRNA7 copy number state using droplet digital PCR and genomic quantitative PCR. Demographic, anthropometric, and clinical data, including the Child Behavior Checklist (CBCL), were collected and compared across individuals with and without the CHRNA7 deletion.

RESULTS: Of 218 individuals (90% males, mean age: 12.3 ± 2.3 years), 7 (3.2%) were found to carry a CHRNA7 deletion and one proband carried a CHRNA7 duplication (0.46%). T-scores for rule breaking, aggression, and externalizing behavior factors of the CBCL were higher in the deletion group, despite taking 58% higher dose of risperidone.

CONCLUSIONS: CHRNA7 loss may contribute to a phenotype of severe aggression. Given the high prevalence of the deletion among risperidone-treated youth, future studies should examine the therapeutic potential of α7 nAChR-targeting drugs to target aggression associated with CHRNA7 deletions.

%B J Child Adolesc Psychopharmacol %V 27 %P 908-915 %8 2017 Dec %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/28817303?dopt=Abstract %R 10.1089/cap.2017.0068 %0 Journal Article %J J Med Genet %D 2017 %T Congenital heart defects and left ventricular non-compaction in males with loss-of-function variants in NONO. %A Scott, Daryl A %A Hernandez-Garcia, Andres %A Azamian, Mahshid S %A Jordan, Valerie K %A Kim, Bum Jun %A Starkovich, Molly %A Zhang, Jinglan %A Wong, Lee-Jun %A Darilek, Sandra A %A Breman, Amy M %A Yang, Yaping %A Lupski, James R %A Jiwani, Amyn K %A Das, Bibhuti %A Lalani, Seema R %A Iglesias, Alejandro D %A Rosenfeld, Jill A %A Xia, Fan %K Child %K Child, Preschool %K Developmental Disabilities %K DNA-Binding Proteins %K Exome %K Heart Defects, Congenital %K Heart Ventricles %K Humans %K Infant %K Male %K Nuclear Matrix-Associated Proteins %K Octamer Transcription Factors %K RNA-Binding Proteins %X

BACKGROUND: The non-POU domain containing octamer-binding gene (NONO) is located on chromosome Xq13.1 and encodes a member of a small family of RNA-binding and DNA-binding proteins that perform a variety of tasks involved in RNA synthesis, transcriptional regulation and DNA repair. Loss-of-function variants in NONO have been described as a cause of intellectual disability in males but have not been described in association with congenital heart defects or cardiomyopathy. In this article, we seek to further define the phenotypic consequences of NONO depletion in human subjects.

METHODS: We searched a clinical database of over 6000 individuals referred for exome sequencing and over 60 000 individuals referred for CNV analysis.

RESULTS: We identified two males with atrial and ventricular septal defects, left ventricular non-compaction (LVNC), developmental delay and intellectual disability, who harboured de novo, loss-of-function variants in NONO. We also identified a male infant with developmental delay, congenital brain anomalies and severe LVNC requiring cardiac transplantation, who inherited a single-gene deletion of NONO from his asymptomatic mother.

CONCLUSIONS: We conclude that in addition to global developmental delay and intellectual disability, males with loss-of-function variants in NONO may also be predisposed to developing congenital heart defects and LVNC with the penetrance of these cardiac-related problems being influenced by genetic, epigenetic, environmental or stochastic factors. Brain imaging of males with NONO deficiency may reveal structural defects with abnormalities of the corpus callosum being the most common. Although dysmorphic features vary between affected individuals, relative macrocephaly is a common feature.

%B J Med Genet %V 54 %P 47-53 %8 2017 Jan %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/27550220?dopt=Abstract %R 10.1136/jmedgenet-2016-104039 %0 Journal Article %J Am J Hum Genet %D 2017 %T De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder. %A Küry, Sébastien %A Besnard, Thomas %A Ebstein, Frédéric %A Khan, Tahir N %A Gambin, Tomasz %A Douglas, Jessica %A Bacino, Carlos A %A Craigen, William J %A Sanders, Stephan J %A Lehmann, Andrea %A Latypova, Xénia %A Khan, Kamal %A Pacault, Mathilde %A Sacharow, Stephanie %A Glaser, Kimberly %A Bieth, Eric %A Perrin-Sabourin, Laurence %A Jacquemont, Marie-Line %A Cho, Megan T %A Roeder, Elizabeth %A Denommé-Pichon, Anne-Sophie %A Monaghan, Kristin G %A Yuan, Bo %A Xia, Fan %A Simon, Sylvain %A Bonneau, Dominique %A Parent, Philippe %A Gilbert-Dussardier, Brigitte %A Odent, Sylvie %A Toutain, Annick %A Pasquier, Laurent %A Barbouth, Deborah %A Shaw, Chad A %A Patel, Ankita %A Smith, Janice L %A Bi, Weimin %A Schmitt, Sébastien %A Deb, Wallid %A Nizon, Mathilde %A Mercier, Sandra %A Vincent, Marie %A Rooryck, Caroline %A Malan, Valérie %A Briceño, Ignacio %A Gómez, Alberto %A Nugent, Kimberly M %A Gibson, James B %A Cogné, Benjamin %A Lupski, James R %A Stessman, Holly A F %A Eichler, Evan E %A Retterer, Kyle %A Yang, Yaping %A Redon, Richard %A Katsanis, Nicholas %A Rosenfeld, Jill A %A Kloetzel, Peter-Michael %A Golzio, Christelle %A Bézieau, Stéphane %A Stankiewicz, Paweł %A Isidor, Bertrand %K Adolescent %K Animals %K Child %K Child, Preschool %K Disease Models, Animal %K DNA Copy Number Variations %K Down-Regulation %K Female %K Gene Deletion %K Humans %K Infant %K Intellectual Disability %K Male %K Microcephaly %K Neurodevelopmental Disorders %K Polymorphism, Single Nucleotide %K Proteasome Endopeptidase Complex %K Zebrafish %X

Degradation of proteins by the ubiquitin-proteasome system (UPS) is an essential biological process in the development of eukaryotic organisms. Dysregulation of this mechanism leads to numerous human neurodegenerative or neurodevelopmental disorders. Through a multi-center collaboration, we identified six de novo genomic deletions and four de novo point mutations involving PSMD12, encoding the non-ATPase subunit PSMD12 (aka RPN5) of the 19S regulator of 26S proteasome complex, in unrelated individuals with intellectual disability, congenital malformations, ophthalmologic anomalies, feeding difficulties, deafness, and subtle dysmorphic facial features. We observed reduced PSMD12 levels and an accumulation of ubiquitinated proteins without any impairment of proteasome catalytic activity. Our PSMD12 loss-of-function zebrafish CRISPR/Cas9 model exhibited microcephaly, decreased convolution of the renal tubules, and abnormal craniofacial morphology. Our data support the biological importance of PSMD12 as a scaffolding subunit in proteasome function during development and neurogenesis in particular; they enable the definition of a neurodevelopmental disorder due to PSMD12 variants, expanding the phenotypic spectrum of UPS-dependent disorders.

%B Am J Hum Genet %V 100 %P 352-363 %8 2017 Feb 02 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/28132691?dopt=Abstract %R 10.1016/j.ajhg.2017.01.003 %0 Journal Article %J Am J Hum Genet %D 2017 %T De Novo Missense Mutations in DHX30 Impair Global Translation and Cause a Neurodevelopmental Disorder. %A Lessel, Davor %A Schob, Claudia %A Küry, Sébastien %A Reijnders, Margot R F %A Harel, Tamar %A Eldomery, Mohammad K %A Coban-Akdemir, Zeynep %A Denecke, Jonas %A Edvardson, Shimon %A Colin, Estelle %A Stegmann, Alexander P A %A Gerkes, Erica H %A Tessarech, Marine %A Bonneau, Dominique %A Barth, Magalie %A Besnard, Thomas %A Cogné, Benjamin %A Revah-Politi, Anya %A Strom, Tim M %A Rosenfeld, Jill A %A Yang, Yaping %A Posey, Jennifer E %A Immken, Ladonna %A Oundjian, Nelly %A Helbig, Katherine L %A Meeks, Naomi %A Zegar, Kelsey %A Morton, Jenny %A Schieving, Jolanda H %A Claasen, Ana %A Huentelman, Matthew %A Narayanan, Vinodh %A Ramsey, Keri %A Brunner, Han G %A Elpeleg, Orly %A Mercier, Sandra %A Bézieau, Stéphane %A Kubisch, Christian %A Kleefstra, Tjitske %A Kindler, Stefan %A Lupski, James R %A Kreienkamp, Hans-Jürgen %K Adenosine Triphosphatases %K Adolescent %K Amino Acids %K Cell Line %K Cell Line, Tumor %K Central Nervous System %K Child %K Child, Preschool %K Developmental Disabilities %K Female %K HEK293 Cells %K Humans %K Intellectual Disability %K Male %K Mutation, Missense %K RNA %K RNA Helicases %X

DHX30 is a member of the family of DExH-box helicases, which use ATP hydrolysis to unwind RNA secondary structures. Here we identified six different de novo missense mutations in DHX30 in twelve unrelated individuals affected by global developmental delay (GDD), intellectual disability (ID), severe speech impairment and gait abnormalities. While four mutations are recurrent, two are unique with one affecting the codon of one recurrent mutation. All amino acid changes are located within highly conserved helicase motifs and were found to either impair ATPase activity or RNA recognition in different in vitro assays. Moreover, protein variants exhibit an increased propensity to trigger stress granule (SG) formation resulting in global translation inhibition. Thus, our findings highlight the prominent role of translation control in development and function of the central nervous system and also provide molecular insight into how DHX30 dysfunction might cause a neurodevelopmental disorder.

%B Am J Hum Genet %V 101 %P 716-724 %8 2017 Nov 02 %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/29100085?dopt=Abstract %R 10.1016/j.ajhg.2017.09.014 %0 Journal Article %J Stem Cell Reports %D 2017 %T Divergent Levels of Marker Chromosomes in an hiPSC-Based Model of Psychosis. %A Tcw, Julia %A Carvalho, Claudia M B %A Yuan, Bo %A Gu, Shen %A Altheimer, Alyssa N %A McCarthy, Shane %A Malhotra, Dheeraj %A Sebat, Jonathan %A Siegel, Arthur J %A Rudolph, Uwe %A Lupski, James R %A Levy, Deborah L %A Brennand, Kristen J %K Chromosome Duplication %K Chromosomes, Human %K Chromosomes, Human, Pair 9 %K Comparative Genomic Hybridization %K Genetic Association Studies %K Genetic Markers %K Genetic Predisposition to Disease %K Heterozygote %K Humans %K Induced Pluripotent Stem Cells %K Matrix Attachment Regions %K Mosaicism %K Psychotic Disorders %K Trisomy %X

In the process of generating presumably clonal human induced pluripotent stem cells (hiPSCs) from two carriers of a complex structural rearrangement, each having a psychotic disorder, we also serendipitously generated isogenic non-carrier control hiPSCs, finding that the rearrangement occurs as an extrachromosomal marker (mar) element. All confirmed carrier hiPSCs and differentiated neural progenitor cell lines were found to be mosaic. We caution that mar elements may be difficult to functionally evaluate in hiPSC cultures using currently available methods, as it is difficult to distinguish cells with and without mar elements in live mosaic cultures.

%B Stem Cell Reports %V 8 %P 519-528 %8 2017 Mar 14 %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/28216146?dopt=Abstract %R 10.1016/j.stemcr.2017.01.010 %0 Journal Article %J Pediatr Neurol %D 2017 %T Dominant Transmission Observed in Adolescents and Families With Orthostatic Intolerance. %A Posey, Jennifer E %A Martinez, Rebecca %A Lankford, Jeremy E %A Lupski, James R %A Numan, Mohammed T %A Butler, Ian J %K Adolescent %K Cohort Studies %K Family %K Female %K Genetic Testing %K Humans %K Male %K Orthostatic Intolerance %K Pedigree %K Posture %K Surveys and Questionnaires %K Tilt-Table Test %X

BACKGROUND: Orthostatic intolerance is typically thought to be sporadic and attributed to cerebral autonomic dysfunction. We sought to identify families with inherited autonomic dysfunction manifest as symptomatic orthostatic intolerance to characterize mode of inheritance and clinical features.

METHODS: Sixteen families with two or more first- or second-degree relatives with autonomic dysfunction and orthostatic intolerance were enrolled. A clinical diagnosis of autonomic dysfunction defined by symptomatic orthostatic intolerance diagnosed by head-up tilt table testing was confirmed for each proband. Clinical features and evaluation were obtained from each proband using a standardized intake questionnaire, and family history information was obtained from probands and available relatives.

RESULTS: Comprehensive pedigree analysis of 16 families (39 individuals with orthostatic intolerance and 40 individuals suspected of having orthostatic intolerance) demonstrated dominant transmission of autonomic dysfunction with incomplete penetrance. Affected individuals were predominantly female (71.8%, 28/39; F:M, 2.5:1). Male-to-male transmission, although less common, was observed and demonstrated to transmit through unaffected males with an affected parent. Similar to sporadic orthostatic intolerance, probands report a range of symptoms across multiple organ systems, with headaches and neuromuscular features being most common.

CONCLUSIONS: Familial occurrence and vertical transmission of autonomic dysfunction in 16 families suggest a novel genetic syndrome with dominant transmission, incomplete penetrance, and skewing of the sex ratio. Elucidation of potential genetic contributions to orthostatic intolerance may inform therapeutic management and identification of individuals at risk. Adolescent evaluation should include identification and treatment of potential at-risk relatives.

%B Pediatr Neurol %V 66 %P 53-58.e5 %8 2017 Jan %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/27773421?dopt=Abstract %R 10.1016/j.pediatrneurol.2016.09.013 %0 Journal Article %J Am J Med Genet A %D 2017 %T Dual molecular diagnosis contributes to atypical Prader-Willi phenotype in monozygotic twins. %A Jehee, Fernanda S %A de Oliveira, Valdirene T %A Gurgel-Giannetti, Juliana %A Pietra, Rafaella X %A Rubatino, Fernando V M %A Carobin, Natália V %A Vianna, Gabrielle S %A de Freitas, Mariana L %A Fernandes, Karla S %A Ribeiro, Beatriz S V %A Brüggenwirth, Hennie T %A Ali-Amin, Roza %A White, Janson J %A Akdemir, Zeynep C %A Jhangiani, Shalini N %A Gibbs, Richard A %A Lupski, James R %A Varela, Monica C %A Koiffmann, Célia %A Rosenberg, Carla %A Carvalho, Claudia M B %K Adolescent %K Base Sequence %K Child %K Chromosome Deletion %K Chromosomes, Human, Pair 15 %K Comparative Genomic Hybridization %K Exome %K Facies %K Female %K Humans %K Hyperventilation %K Intellectual Disability %K Obesity %K Pathology, Molecular %K Phenotype %K Prader-Willi Syndrome %K Transcription Factor 4 %K Twins, Monozygotic %X

We describe monozygotic twin girls with genetic variation at two separate loci resulting in a blended phenotype of Prader-Willi syndrome and Pitt-Hopkins syndrome. These girls were diagnosed in early infancy with Prader-Willi syndrome, but developed an atypical phenotype, with apparent intellectual deficiency and lack of obesity. Array-comparative genomic hybridization confirmed a de novo paternal deletion of the 15q11.2q13 region and exome sequencing identified a second mutational event in both girls, which was a novel variant c.145+1G>A affecting a TCF4 canonical splicing site inherited from the mosaic mother. RNA studies showed that the variant abolished the donor splicing site, which was accompanied by activation of an alternative non-canonical splicing-site which then predicts a premature stop codon in the following exon. Clinical re-evaluation of the twins indicated that both variants are likely contributing to the more severe phenotypic presentation. Our data show that atypical clinical presentations may actually be the expression of blended clinical phenotypes arising from independent pathogenic events at two loci.

%B Am J Med Genet A %V 173 %P 2451-2455 %8 2017 Sep %G eng %N 9 %1 https://www.ncbi.nlm.nih.gov/pubmed/28631899?dopt=Abstract %R 10.1002/ajmg.a.38315 %0 Journal Article %J Genet Med %D 2017 %T Enrichment of mutations in chromatin regulators in people with Rett syndrome lacking mutations in MECP2. %A Sajan, Samin A %A Jhangiani, Shalini N %A Muzny, Donna M %A Gibbs, Richard A %A Lupski, James R %A Glaze, Daniel G %A Kaufmann, Walter E %A Skinner, Steven A %A Annese, Fran %A Friez, Michael J %A Lane, Jane %A Percy, Alan K %A Neul, Jeffrey L %K Adolescent %K Adult %K Child %K Child, Preschool %K Chromatin %K DNA Copy Number Variations %K Exome Sequencing %K Female %K Forkhead Transcription Factors %K Humans %K Infant %K Male %K Methyl-CpG-Binding Protein 2 %K Mutation %K Nerve Tissue Proteins %K Polymorphism, Single Nucleotide %K Protein Serine-Threonine Kinases %K Rett Syndrome %X

PURPOSE: Rett syndrome (RTT) is a neurodevelopmental disorder caused primarily by de novo mutations in MECP2 and sometimes in CDKL5 and FOXG1. However, some RTT patients lack mutations in these genes.

METHODS: Twenty-two RTT patients without apparent MECP2, CDKL5, and FOXG1 mutations were subjected to both whole-exome sequencing and single-nucleotide polymorphism array-based copy-number variant (CNV) analyses.

RESULTS: Three patients had MECP2 mutations initially missed by clinical testing. Of the remaining 19, 17 (89.5%) had 29 other likely pathogenic intragenic mutations and/or CNVs (10 patients had 2 or more). Interestingly, 13 patients had mutations in a gene/region previously reported in other neurodevelopmental disorders (NDDs), thereby providing a potential diagnostic yield of 68.4%. These mutations were significantly enriched in chromatin regulators (corrected P = 0.0068) and moderately enriched in postsynaptic cell membrane molecules (corrected P = 0.076), implicating glutamate receptor signaling.

CONCLUSION: The genetic etiology of RTT without MECP2, CDKL5, and FOXG1 mutations is heterogeneous, overlaps with other NDDs, and complicated by a high mutation burden. Dysregulation of chromatin structure and abnormal excitatory synaptic signaling may form two common pathological bases of RTT.Genet Med 19 1, 13-19.

%B Genet Med %V 19 %P 13-19 %8 2017 Jan %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/27171548?dopt=Abstract %R 10.1038/gim.2016.42 %0 Journal Article %J Hum Genet %D 2017 %T Erratum to: Haploinsufficiency of the E3 ubiquitin-protein ligase gene TRIP12 causes intellectual disability with or without autism spectrum disorders, speech delay, and dysmorphic features. %A Zhang, Jing %A Gambin, Tomasz %A Bo Yuan %A Szafranski, Przemyslaw %A Rosenfeld, Jill A %A Balwi, Mohammed Al %A Alswaid, Abdulrahman %A Al-Gazali, Lihadh %A Shamsi, Aisha M Al %A Komara, Makanko %A Ali, Bassam R %A Roeder, Elizabeth %A McAuley, Laura %A Roy, Daniel S %A Manchester, David K %A Magoulas, Pilar %A King, Lauren E %A Hannig, Vickie %A Bonneau, Dominique %A Denommé-Pichon, Anne-Sophie %A Charif, Majida %A Besnard, Thomas %A Bézieau, Stéphane %A Cogné, Benjamin %A Andrieux, Joris %A Zhu, Wenmiao %A He, Weimin %A Vetrini, Francesco %A Ward, Patricia A %A Cheung, Sau Wai %A Bi, Weimin %A Eng, Christine M %A Lupski, James R %A Yang, Yaping %A Patel, Ankita %A Lalani, Seema R %A Xia, Fan %A Stankiewicz, Paweł %B Hum Genet %V 136 %P 1009-1011 %8 2017 Aug %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/28660352?dopt=Abstract %R 10.1007/s00439-017-1828-1 %0 Journal Article %J Cold Spring Harb Mol Case Stud %D 2017 %T An exome sequencing study of Moebius syndrome including atypical cases reveals an individual with CFEOM3A and a mutation. %A Patel, Ronak M %A Liu, David %A Gonzaga-Jauregui, Claudia %A Jhangiani, Shalini %A Lu, James T %A Sutton, V Reid %A Fernbach, Susan D %A Azamian, Mahshid %A White, Lisa %A Edmond, Jane C %A Paysse, Evelyn A %A Belmont, John W %A Muzny, Donna %A Lupski, James R %A Gibbs, Richard A %A Lewis, Richard Alan %A Lee, Brendan H %A Lalani, Seema R %A Campeau, Philippe M %K Child %K Child, Preschool %K Cohort Studies %K Exome %K Exome Sequencing %K Eye Diseases, Hereditary %K Facial Paralysis %K Female %K Humans %K Infant %K Male %K Malformations of Cortical Development %K Mobius Syndrome %K Muscular Diseases %K Mutation %K Ocular Motility Disorders %K Ophthalmoplegia %K Orbital Diseases %K Pedigree %K Tubulin %X

Moebius syndrome is characterized by congenital unilateral or bilateral facial and abducens nerve palsies (sixth and seventh cranial nerves) causing facial weakness, feeding difficulties, and restricted ocular movements. Abnormalities of the chest wall such as Poland anomaly and variable limb defects are frequently associated with this syndrome. Most cases are isolated; however, rare families with autosomal dominant transmission with incomplete penetrance and variable expressivity have been described. The genetic basis of this condition remains unknown. In a cohort study of nine individuals suspected to have Moebius syndrome (six typical, three atypical), we performed whole-exome sequencing to try to identify a commonly mutated gene. Although no such gene was identified and we did not find mutations in and , we found a de novo heterozygous mutation, p.E410K, in the gene encoding tubulin beta 3 class III (), in an individual with atypical Moebius syndrome. This individual was diagnosed with near-complete ophthalmoplegia, agenesis of the corpus callosum, and absence of the septum pellucidum. No substantial limb abnormalities were noted. Mutations in have been associated with complex cortical dysplasia and other brain malformations and congenital fibrosis of extraocular muscles type 3A (CFEOM3A). Our report highlights the overlap of genetic etiology and clinical differences between CFEOM and Moebius syndrome and describes our approach to identifying candidate genes for typical and atypical Moebius syndrome.

%B Cold Spring Harb Mol Case Stud %V 3 %P a000984 %8 2017 Mar %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/28299356?dopt=Abstract %R 10.1101/mcs.a000984 %0 Journal Article %J Front Pediatr %D 2017 %T First Case of Deficiency in Ecuador, Diagnosed after Whole Exome Sequencing in a Patient with Severe Cutaneous Histoplasmosis. %A Pedroza, Luis Alberto %A Guerrero, Nina %A Stray-Pedersen, Asbjørg %A Tafur, Cristina %A Macias, Roque %A Muñoz, Greta %A Akdemir, Zeynep Coban %A Jhangiani, Shalini N %A Watkin, Levi B %A Chinn, Ivan K %A Lupski, James R %A Orange, Jordan S %X

Severe infections with are commonly observed in patient with secondary immunodeficiency disorders. We report a two and a half years old boy previously healthy with disseminated cutaneous histoplasmosis. Using whole exome sequencing, we found an mutation at the gene, suggesting a diagnosis of hyper-IgM (HIGM) syndrome, even in the absence of the usual features for the disease. Interestingly, the patient lives in a region endemic for histoplasmosis. The unusual infections in our case suggest that in children with severe histoplasmosis and resident in endemic areas, HIGM syndrome should be considered as a diagnosis.

%B Front Pediatr %V 5 %P 17 %8 2017 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/28239602?dopt=Abstract %R 10.3389/fped.2017.00017 %0 Journal Article %J Nat Genet %D 2017 %T Germline mutations in ABL1 cause an autosomal dominant syndrome characterized by congenital heart defects and skeletal malformations. %A Wang, Xia %A Charng, Wu-Lin %A Chen, Chun-An %A Rosenfeld, Jill A %A Al Shamsi, Aisha %A Al-Gazali, Lihadh %A McGuire, Marianne %A Mew, Nicholas Ah %A Arnold, Georgianne L %A Qu, Chunjing %A Ding, Yan %A Muzny, Donna M %A Gibbs, Richard A %A Eng, Christine M %A Walkiewicz, Magdalena %A Xia, Fan %A Plon, Sharon E %A Lupski, James R %A Schaaf, Christian P %A Yang, Yaping %K Abnormalities, Multiple %K Animals %K Bone Diseases, Developmental %K Cell Line %K Chromosome Disorders %K Craniofacial Abnormalities %K Feeding and Eating Disorders %K Female %K Fusion Proteins, bcr-abl %K Germ-Line Mutation %K Heart Defects, Congenital %K HEK293 Cells %K Humans %K Leukemia, Myelogenous, Chronic, BCR-ABL Positive %K Limb Deformities, Congenital %K Male %K Mice %K Mice, Knockout %K Philadelphia Chromosome %K Phosphorylation %K Proto-Oncogene Mas %K Signal Transduction %X

ABL1 is a proto-oncogene well known as part of the fusion gene BCR-ABL1 in the Philadelphia chromosome of leukemia cancer cells. Inherited germline ABL1 changes have not been associated with genetic disorders. Here we report ABL1 germline variants cosegregating with an autosomal dominant disorder characterized by congenital heart disease, skeletal abnormalities, and failure to thrive. The variant c.734A>G (p.Tyr245Cys) was found to occur de novo or cosegregate with disease in five individuals (families 1-3). Additionally, a de novo c.1066G>A (p.Ala356Thr) variant was identified in a sixth individual (family 4). We overexpressed the mutant constructs in HEK 293T cells and observed increased tyrosine phosphorylation, suggesting increased ABL1 kinase activities associated with both the p.Tyr245Cys and p.Ala356Thr substitutions. Our clinical and experimental findings, together with previously reported teratogenic effects of selective BCR-ABL inhibitors in humans and developmental defects in Abl1 knockout mice, suggest that ABL1 has an important role during organismal development.

%B Nat Genet %V 49 %P 613-617 %8 2017 Apr %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/28288113?dopt=Abstract %R 10.1038/ng.3815 %0 Journal Article %J Hum Genet %D 2017 %T Haploinsufficiency of the E3 ubiquitin-protein ligase gene TRIP12 causes intellectual disability with or without autism spectrum disorders, speech delay, and dysmorphic features. %A Zhang, Jing %A Gambin, Tomasz %A Yuan, Bo %A Szafranski, Przemyslaw %A Rosenfeld, Jill A %A Balwi, Mohammed Al %A Alswaid, Abdulrahman %A Al-Gazali, Lihadh %A Shamsi, Aisha M Al %A Komara, Makanko %A Ali, Bassam R %A Roeder, Elizabeth %A McAuley, Laura %A Roy, Daniel S %A Manchester, David K %A Magoulas, Pilar %A King, Lauren E %A Hannig, Vickie %A Bonneau, Dominique %A Denommé-Pichon, Anne-Sophie %A Charif, Majida %A Besnard, Thomas %A Bézieau, Stéphane %A Cogné, Benjamin %A Andrieux, Joris %A Zhu, Wenmiao %A He, Weimin %A Vetrini, Francesco %A Ward, Patricia A %A Cheung, Sau Wai %A Bi, Weimin %A Eng, Christine M %A Lupski, James R %A Yang, Yaping %A Patel, Ankita %A Lalani, Seema R %A Xia, Fan %A Stankiewicz, Paweł %K Adolescent %K Autism Spectrum Disorder %K Carrier Proteins %K Child %K Child, Preschool %K Cohort Studies %K DNA Copy Number Variations %K Facies %K Female %K Haploinsufficiency %K Humans %K Infant %K Intellectual Disability %K Language Development Disorders %K Male %K Ubiquitin-Protein Ligases %X

Impairment of ubiquitin-proteasome system activity involving ubiquitin ligase genes UBE3A, UBE3B, and HUWE1 and deubiquitinating enzyme genes USP7 and USP9X has been reported in patients with neurodevelopmental delays. To date, only a handful of single-nucleotide variants (SNVs) and copy-number variants (CNVs) involving TRIP12, encoding a member of the HECT domain E3 ubiquitin ligases family on chromosome 2q36.3 have been reported. Using chromosomal microarray analysis and whole-exome sequencing (WES), we have identified, respectively, five deletion CNVs and four inactivating SNVs (two frameshifts, one missense, and one splicing) in TRIP12. Seven of these variants were found to be de novo; parental studies could not be completed in two families. Quantitative PCR analyses of the splicing mutation showed a dramatically decreased level of TRIP12 mRNA in the proband compared to the family controls, indicating a loss-of-function mechanism. The shared clinical features include intellectual disability with or without autistic spectrum disorders, speech delay, and facial dysmorphism. Our findings demonstrate that E3 ubiquitin ligase TRIP12 plays an important role in nervous system development and function. The nine presented pathogenic variants further document that TRIP12 haploinsufficiency causes a childhood-onset neurodevelopmental disorder. Finally, our data enable expansion of the phenotypic spectrum of ubiquitin-proteasome dependent disorders.

%B Hum Genet %V 136 %P 377-386 %8 2017 Apr %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/28251352?dopt=Abstract %R 10.1007/s00439-017-1763-1 %0 Journal Article %J Nucleic Acids Res %D 2017 %T Homozygous and hemizygous CNV detection from exome sequencing data in a Mendelian disease cohort. %A Gambin, Tomasz %A Akdemir, Zeynep C %A Yuan, Bo %A Gu, Shen %A Chiang, Theodore %A Carvalho, Claudia M B %A Shaw, Chad %A Jhangiani, Shalini %A Boone, Philip M %A Eldomery, Mohammad K %A Karaca, Ender %A Bayram, Yavuz %A Stray-Pedersen, Asbjørg %A Muzny, Donna %A Charng, Wu-Lin %A Bahrambeigi, Vahid %A Belmont, John W %A Boerwinkle, Eric %A Beaudet, Arthur L %A Gibbs, Richard A %A Lupski, James R %K Algorithms %K Alternative Splicing %K Cohort Studies %K Computational Biology %K Consanguinity %K Datasets as Topic %K DNA Copy Number Variations %K Exome %K Genetic Diseases, Inborn %K Hemizygote %K High-Throughput Nucleotide Sequencing %K Homozygote %K Humans %K Inheritance Patterns %K Models, Genetic %K Pedigree %K Reproducibility of Results %K Sequence Deletion %K Workflow %X

We developed an algorithm, HMZDelFinder, that uses whole exome sequencing (WES) data to identify rare and intragenic homozygous and hemizygous (HMZ) deletions that may represent complete loss-of-function of the indicated gene. HMZDelFinder was applied to 4866 samples in the Baylor-Hopkins Center for Mendelian Genomics (BHCMG) cohort and detected 773 HMZ deletion calls (567 homozygous or 206 hemizygous) with an estimated sensitivity of 86.5% (82% for single-exonic and 88% for multi-exonic calls) and precision of 78% (53% single-exonic and 96% for multi-exonic calls). Out of 773 HMZDelFinder-detected deletion calls, 82 were subjected to array comparative genomic hybridization (aCGH) and/or breakpoint PCR and 64 were confirmed. These include 18 single-exon deletions out of which 8 were exclusively detected by HMZDelFinder and not by any of seven other CNV detection tools examined. Further investigation of the 64 validated deletion calls revealed at least 15 pathogenic HMZ deletions. Of those, 7 accounted for 17-50% of pathogenic CNVs in different disease cohorts where 7.1-11% of the molecular diagnosis solved rate was attributed to CNVs. In summary, we present an algorithm to detect rare, intragenic, single-exon deletion CNVs using WES data; this tool can be useful for disease gene discovery efforts and clinical WES analyses.

%B Nucleic Acids Res %V 45 %P 1633-1648 %8 2017 Feb 28 %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/27980096?dopt=Abstract %R 10.1093/nar/gkw1237 %0 Journal Article %J Genome Med %D 2017 %T Identification of novel candidate disease genes from de novo exonic copy number variants. %A Gambin, Tomasz %A Bo Yuan %A Bi, Weimin %A Liu, Pengfei %A Rosenfeld, Jill A %A Coban-Akdemir, Zeynep %A Pursley, Amber N %A Nagamani, Sandesh C S %A Marom, Ronit %A Golla, Sailaja %A Dengle, Lauren %A Petrie, Heather G %A Matalon, Reuben %A Emrick, Lisa %A Proud, Monica B %A Treadwell-Deering, Diane %A Chao, Hsiao-Tuan %A Koillinen, Hannele %A Brown, Chester %A Urraca, Nora %A Mostafavi, Roya %A Bernes, Saunder %A Roeder, Elizabeth R %A Nugent, Kimberly M %A Bader, Patricia I %A Bellus, Gary %A Cummings, Michael %A Northrup, Hope %A Ashfaq, Myla %A Westman, Rachel %A Wildin, Robert %A Beck, Anita E %A Immken, Ladonna %A Elton, Lindsay %A Varghese, Shaun %A Buchanan, Edward %A Faivre, Laurence %A Lefebvre, Mathilde %A Schaaf, Christian P %A Walkiewicz, Magdalena %A Yang, Yaping %A Kang, Sung-Hae L %A Lalani, Seema R %A Bacino, Carlos A %A Beaudet, Arthur L %A Breman, Amy M %A Smith, Janice L %A Cheung, Sau Wai %A James R Lupski %A Patel, Ankita %A Shaw, Chad A %A Stankiewicz, Paweł %K Cohort Studies %K DNA Copy Number Variations %K Exons %K Genetic Diseases, Inborn %K Genome, Human %K Homeodomain Proteins %K Humans %K Intracellular Signaling Peptides and Proteins %K Membrane Proteins %K Neurodevelopmental Disorders %K Protein Serine-Threonine Kinases %K Retrospective Studies %K Serine-Threonine Kinase 3 %K Transcription Factors %K Whole Genome Sequencing %X

BACKGROUND: Exon-targeted microarrays can detect small (<1000 bp) intragenic copy number variants (CNVs), including those that affect only a single exon. This genome-wide high-sensitivity approach increases the molecular diagnosis for conditions with known disease-associated genes, enables better genotype-phenotype correlations, and facilitates variant allele detection allowing novel disease gene discovery.

METHODS: We retrospectively analyzed data from 63,127 patients referred for clinical chromosomal microarray analysis (CMA) at Baylor Genetics laboratories, including 46,755 individuals tested using exon-targeted arrays, from 2007 to 2017. Small CNVs harboring a single gene or two to five non-disease-associated genes were identified; the genes involved were evaluated for a potential disease association.

RESULTS: In this clinical population, among rare CNVs involving any single gene reported in 7200 patients (11%), we identified 145 de novo autosomal CNVs (117 losses and 28 intragenic gains), 257 X-linked deletion CNVs in males, and 1049 inherited autosomal CNVs (878 losses and 171 intragenic gains); 111 known disease genes were potentially disrupted by de novo autosomal or X-linked (in males) single-gene CNVs. Ninety-one genes, either recently proposed as candidate disease genes or not yet associated with diseases, were disrupted by 147 single-gene CNVs, including 37 de novo deletions and ten de novo intragenic duplications on autosomes and 100 X-linked CNVs in males. Clinical features in individuals with de novo or X-linked CNVs encompassing at most five genes (224 bp to 1.6 Mb in size) were compared to those in individuals with larger-sized deletions (up to 5 Mb in size) in the internal CMA database or loss-of-function single nucleotide variants (SNVs) detected by clinical or research whole-exome sequencing (WES). This enabled the identification of recently published genes (BPTF, NONO, PSMD12, TANGO2, and TRIP12), novel candidate disease genes (ARGLU1 and STK3), and further confirmation of disease association for two recently proposed disease genes (MEIS2 and PTCHD1). Notably, exon-targeted CMA detected several pathogenic single-exon CNVs missed by clinical WES analyses.

CONCLUSIONS: Together, these data document the efficacy of exon-targeted CMA for detection of genic and exonic CNVs, complementing and extending WES in clinical diagnostics, and the potential for discovery of novel disease genes by genome-wide assay.

%B Genome Med %V 9 %P 83 %8 2017 09 21 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/28934986?dopt=Abstract %R 10.1186/s13073-017-0472-7 %0 Journal Article %J Genome Med %D 2017 %T Lessons learned from additional research analyses of unsolved clinical exome cases. %A Eldomery, Mohammad K %A Coban-Akdemir, Zeynep %A Harel, Tamar %A Rosenfeld, Jill A %A Gambin, Tomasz %A Stray-Pedersen, Asbjørg %A Küry, Sébastien %A Mercier, Sandra %A Lessel, Davor %A Denecke, Jonas %A Wiszniewski, Wojciech %A Penney, Samantha %A Liu, Pengfei %A Bi, Weimin %A Lalani, Seema R %A Schaaf, Christian P %A Wangler, Michael F %A Bacino, Carlos A %A Lewis, Richard Alan %A Potocki, Lorraine %A Graham, Brett H %A Belmont, John W %A Scaglia, Fernando %A Orange, Jordan S %A Jhangiani, Shalini N %A Chiang, Theodore %A Doddapaneni, Harsha %A Hu, Jianhong %A Muzny, Donna M %A Xia, Fan %A Beaudet, Arthur L %A Boerwinkle, Eric %A Eng, Christine M %A Plon, Sharon E %A Sutton, V Reid %A Gibbs, Richard A %A Posey, Jennifer E %A Yang, Yaping %A Lupski, James R %K Adenosine Triphosphatases %K ATPases Associated with Diverse Cellular Activities %K Computational Biology %K DNA Copy Number Variations %K DNA-Binding Proteins %K Exome %K Female %K Genetic Diseases, Inborn %K Genomics %K GTP-Binding Protein beta Subunits %K Humans %K Male %K Membrane Proteins %K Metalloendopeptidases %K Mitochondrial Proteins %K Pilot Projects %K Polymorphism, Single Nucleotide %K Sequence Analysis, DNA %K Transcription Factors %X

BACKGROUND: Given the rarity of most single-gene Mendelian disorders, concerted efforts of data exchange between clinical and scientific communities are critical to optimize molecular diagnosis and novel disease gene discovery.

METHODS: We designed and implemented protocols for the study of cases for which a plausible molecular diagnosis was not achieved in a clinical genomics diagnostic laboratory (i.e. unsolved clinical exomes). Such cases were recruited to a research laboratory for further analyses, in order to potentially: (1) accelerate novel disease gene discovery; (2) increase the molecular diagnostic yield of whole exome sequencing (WES); and (3) gain insight into the genetic mechanisms of disease. Pilot project data included 74 families, consisting mostly of parent-offspring trios. Analyses performed on a research basis employed both WES from additional family members and complementary bioinformatics approaches and protocols.

RESULTS: Analysis of all possible modes of Mendelian inheritance, focusing on both single nucleotide variants (SNV) and copy number variant (CNV) alleles, yielded a likely contributory variant in 36% (27/74) of cases. If one includes candidate genes with variants identified within a single family, a potential contributory variant was identified in a total of ~51% (38/74) of cases enrolled in this pilot study. The molecular diagnosis was achieved in 30/63 trios (47.6%). Besides this, the analysis workflow yielded evidence for pathogenic variants in disease-associated genes in 4/6 singleton cases (66.6%), 1/1 multiplex family involving three affected siblings, and 3/4 (75%) quartet families. Both the analytical pipeline and the collaborative efforts between the diagnostic and research laboratories provided insights that allowed recent disease gene discoveries (PURA, TANGO2, EMC1, GNB5, ATAD3A, and MIPEP) and increased the number of novel genes, defined in this study as genes identified in more than one family (DHX30 and EBF3).

CONCLUSION: An efficient genomics pipeline in which clinical sequencing in a diagnostic laboratory is followed by the detailed reanalysis of unsolved cases in a research environment, supplemented with WES data from additional family members, and subject to adjuvant bioinformatics analyses including relaxed variant filtering parameters in informatics pipelines, can enhance the molecular diagnostic yield and provide mechanistic insights into Mendelian disorders. Implementing these approaches requires collaborative clinical molecular diagnostic and research efforts.

%B Genome Med %V 9 %P 26 %8 2017 Mar 21 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/28327206?dopt=Abstract %R 10.1186/s13073-017-0412-6 %0 Journal Article %J Neuron %D 2017 %T Loss of Nardilysin, a Mitochondrial Co-chaperone for α-Ketoglutarate Dehydrogenase, Promotes mTORC1 Activation and Neurodegeneration. %A Yoon, Wan Hee %A Sandoval, Hector %A Nagarkar-Jaiswal, Sonal %A Jaiswal, Manish %A Yamamoto, Shinya %A Haelterman, Nele A %A Putluri, Nagireddy %A Putluri, Vasanta %A Sreekumar, Arun %A Tos, Tulay %A Aksoy, Ayse %A Donti, Taraka %A Graham, Brett H %A Ohno, Mikiko %A Nishi, Eiichiro %A Hunter, Jill %A Muzny, Donna M %A Carmichael, Jason %A Shen, Joseph %A Arboleda, Valerie A %A Nelson, Stanley F %A Wangler, Michael F %A Karaca, Ender %A Lupski, James R %A Bellen, Hugo J %K Animals %K Autophagy %K Drosophila %K Drosophila melanogaster %K Drosophila Proteins %K Ketoglutarate Dehydrogenase Complex %K Ketoglutaric Acids %K Lysine %K Mechanistic Target of Rapamycin Complex 1 %K Metalloendopeptidases %K Mitochondria %K Molecular Chaperones %K Multiprotein Complexes %K Neurodegenerative Diseases %K TOR Serine-Threonine Kinases %X

We previously identified mutations in Nardilysin (dNrd1) in a forward genetic screen designed to isolate genes whose loss causes neurodegeneration in Drosophila photoreceptor neurons. Here we show that NRD1 is localized to mitochondria, where it recruits mitochondrial chaperones and assists in the folding of α-ketoglutarate dehydrogenase (OGDH), a rate-limiting enzyme in the Krebs cycle. Loss of Nrd1 or Ogdh leads to an increase in α-ketoglutarate, a substrate for OGDH, which in turn leads to mTORC1 activation and a subsequent reduction in autophagy. Inhibition of mTOR activity by rapamycin or partially restoring autophagy delays neurodegeneration in dNrd1 mutant flies. In summary, this study reveals a novel role for NRD1 as a mitochondrial co-chaperone for OGDH and provides a mechanistic link between mitochondrial metabolic dysfunction, mTORC1 signaling, and impaired autophagy in neurodegeneration.

%B Neuron %V 93 %P 115-131 %8 2017 Jan 04 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/28017472?dopt=Abstract %R 10.1016/j.neuron.2016.11.038 %0 Journal Article %J Am J Hum Genet %D 2017 %T Loss-of-Function Variants in MYLK Cause Recessive Megacystis Microcolon Intestinal Hypoperistalsis Syndrome. %A Halim, Danny %A Brosens, Erwin %A Muller, Françoise %A Wangler, Michael F %A Beaudet, Arthur L %A Lupski, James R %A Akdemir, Zeynep H Coban %A Doukas, Michael %A Stoop, Hans J %A de Graaf, Bianca M %A Brouwer, Rutger W W %A van IJcken, Wilfred F J %A Oury, Jean-François %A Rosenblatt, Jonathan %A Burns, Alan J %A Tibboel, Dick %A Hofstra, Robert M W %A Alves, Maria M %K Abnormalities, Multiple %K Base Sequence %K Colon %K Female %K Genes, Recessive %K Homozygote %K Humans %K Intestinal Pseudo-Obstruction %K Male %K Mutation %K Myosin-Light-Chain Kinase %K Pedigree %K Urinary Bladder %X

Megacystis microcolon intestinal hypoperistalsis syndrome (MMIHS) is a congenital disorder characterized by loss of smooth muscle contraction in the bladder and intestine. To date, three genes are known to be involved in MMIHS pathogenesis: ACTG2, MYH11, and LMOD1. However, for approximately 10% of affected individuals, the genetic cause of the disease is unknown, suggesting that other loci are most likely involved. Here, we report on three MMIHS-affected subjects from two consanguineous families with no variants in the known MMIHS-associated genes. By performing homozygosity mapping and whole-exome sequencing, we found homozygous variants in myosin light chain kinase (MYLK) in both families. We identified a 7 bp duplication (c.3838_3844dupGAAAGCG [p.Glu1282_Glyfs51]) in one family and a putative splice-site variant (c.3985+5C>A) in the other. Expression studies and splicing assays indicated that both variants affect normal MYLK expression. Because MYLK encodes an important kinase required for myosin activation and subsequent interaction with actin filaments, it is likely that in its absence, contraction of smooth muscle cells is impaired. The existence of a conditional-Mylk-knockout mouse model with severe gut dysmotility and abnormal function of the bladder supports the involvement of this gene in MMIHS pathogenesis. In aggregate, our findings implicate MYLK as a gene involved in the recessive form of MMIHS, confirming that this disease of the visceral organs is heterogeneous with a myopathic origin.

%B Am J Hum Genet %V 101 %P 123-129 %8 2017 Jul 06 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/28602422?dopt=Abstract %R 10.1016/j.ajhg.2017.05.011 %0 Journal Article %J Am J Hum Genet %D 2017 %T Mutations in EBF3 Disturb Transcriptional Profiles and Cause Intellectual Disability, Ataxia, and Facial Dysmorphism. %A Harms, Frederike Leonie %A Girisha, Katta M %A Hardigan, Andrew A %A Kortüm, Fanny %A Shukla, Anju %A Alawi, Malik %A Dalal, Ashwin %A Brady, Lauren %A Tarnopolsky, Mark %A Bird, Lynne M %A Ceulemans, Sophia %A Bebin, Martina %A Bowling, Kevin M %A Hiatt, Susan M %A Lose, Edward J %A Primiano, Michelle %A Chung, Wendy K %A Juusola, Jane %A Akdemir, Zeynep C %A Bainbridge, Matthew %A Charng, Wu-Lin %A Drummond-Borg, Margaret %A Eldomery, Mohammad K %A El-Hattab, Ayman W %A Saleh, Mohammed A M %A Bézieau, Stéphane %A Cogné, Benjamin %A Isidor, Bertrand %A Küry, Sébastien %A Lupski, James R %A Myers, Richard M %A Cooper, Gregory M %A Kutsche, Kerstin %K Adolescent %K Adult %K Amino Acid Substitution %K Ataxia %K Child %K Child, Preschool %K Chromatin %K Cyclin-Dependent Kinase Inhibitor p21 %K Developmental Disabilities %K Exome %K Face %K Female %K Gene Expression Regulation %K Genes, Reporter %K HEK293 Cells %K Humans %K Intellectual Disability %K Language Development Disorders %K Male %K Models, Molecular %K Mosaicism %K Mutation %K Neurodevelopmental Disorders %K Protein Transport %K Syndrome %K Transcription Factors %K Transcription, Genetic %X

From a GeneMatcher-enabled international collaboration, we identified ten individuals affected by intellectual disability, speech delay, ataxia, and facial dysmorphism and carrying a deleterious EBF3 variant detected by whole-exome sequencing. One 9-bp duplication and one splice-site, five missense, and two nonsense variants in EBF3 were found; the mutations occurred de novo in eight individuals, and the missense variant c.625C>T (p.Arg209Trp) was inherited by two affected siblings from their healthy mother, who is mosaic. EBF3 belongs to the early B cell factor family (also known as Olf, COE, or O/E) and is a transcription factor involved in neuronal differentiation and maturation. Structural assessment predicted that the five amino acid substitutions have damaging effects on DNA binding of EBF3. Transient expression of EBF3 mutant proteins in HEK293T cells revealed mislocalization of all but one mutant in the cytoplasm, as well as nuclear localization. By transactivation assays, all EBF3 mutants showed significantly reduced or no ability to activate transcription of the reporter gene CDKN1A, and in situ subcellular fractionation experiments demonstrated that EBF3 mutant proteins were less tightly associated with chromatin. Finally, in RNA-seq and ChIP-seq experiments, EBF3 acted as a transcriptional regulator, and mutant EBF3 had reduced genome-wide DNA binding and gene-regulatory activity. Our findings demonstrate that variants disrupting EBF3-mediated transcriptional regulation cause intellectual disability and developmental delay and are present in ∼0.1% of individuals with unexplained neurodevelopmental disorders.

%B Am J Hum Genet %V 100 %P 117-127 %8 2017 Jan 05 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/28017373?dopt=Abstract %R 10.1016/j.ajhg.2016.11.012 %0 Journal Article %J Front Immunol %D 2017 %T Novel Combined Immune Deficiency and Radiation Sensitivity Blended Phenotype in an Adult with Biallelic Variations in and . %A Chinn, Ivan K %A Sanders, Robert P %A Stray-Pedersen, Asbjørg %A Coban-Akdemir, Zeynep H %A Kim, Vy Hong-Diep %A Dadi, Harjit %A Roifman, Chaim M %A Quigg, Troy %A Lupski, James R %A Orange, Jordan S %A Hanson, I Celine %X

With the advent of high-throughput genomic sequencing techniques, novel genetic etiologies are being uncovered for previously unexplained Mendelian phenotypes, and the underlying genetic architecture of disease is being unraveled. Although most of these "mendelizing" disease traits represent phenotypes caused by single-gene defects, a percentage of patients have blended phenotypes caused by pathogenic variants in multiple genes. We describe an adult patient with susceptibility to bacterial, herpesviral, and fungal infections. Immunologic defects included CD8 T cell lymphopenia, decreased T cell proliferative responses to mitogens, hypogammaglobulinemia, and radiation sensitivity. Whole-exome sequencing revealed compound heterozygous variants in . Biallelic mutations in are known to produce a spectrum of immune deficiency that includes the T cell abnormalities observed in this patient. Analyses for variants in genes associated with radiation sensitivity identified the presence of a homozygous variant of unknown significance. deficiency causes radiosensitivity, immunodeficiency, dysmorphic features, and learning difficulties syndrome and may account for the radiation sensitivity. Thus, the patient was found to have a novel blended phenotype associated with multilocus genomic variation: i.e., separate and distinct genetic defects. These findings further illustrate the clinical utility of applying genomic testing in patients with primary immunodeficiency diseases.

%B Front Immunol %V 8 %P 576 %8 2017 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/28603521?dopt=Abstract %R 10.3389/fimmu.2017.00576 %0 Journal Article %J Cell %D 2017 %T An Organismal CNV Mutator Phenotype Restricted to Early Human Development. %A Liu, Pengfei %A Yuan, Bo %A Carvalho, Claudia M B %A Wuster, Arthur %A Walter, Klaudia %A Zhang, Ling %A Gambin, Tomasz %A Chong, Zechen %A Campbell, Ian M %A Coban Akdemir, Zeynep %A Gelowani, Violet %A Writzl, Karin %A Bacino, Carlos A %A Lindsay, Sarah J %A Withers, Marjorie %A Gonzaga-Jauregui, Claudia %A Wiszniewska, Joanna %A Scull, Jennifer %A Stankiewicz, Paweł %A Jhangiani, Shalini N %A Muzny, Donna M %A Zhang, Feng %A Chen, Ken %A Gibbs, Richard A %A Rautenstrauss, Bernd %A Cheung, Sau Wai %A Smith, Janice %A Breman, Amy %A Shaw, Chad A %A Patel, Ankita %A Hurles, Matthew E %A Lupski, James R %K Chromosome Aberrations %K Chromosome Breakpoints %K Chromosome Duplication %K DNA Copy Number Variations %K DNA Replication %K Embryonic Development %K Female %K Gametogenesis %K Genetic Diseases, Inborn %K Genomic Instability %K Humans %K Male %K Mutation %X

De novo copy number variants (dnCNVs) arising at multiple loci in a personal genome have usually been considered to reflect cancer somatic genomic instabilities. We describe a multiple dnCNV (MdnCNV) phenomenon in which individuals with genomic disorders carry five to ten constitutional dnCNVs. These CNVs originate from independent formation incidences, are predominantly tandem duplications or complex gains, exhibit breakpoint junction features reminiscent of replicative repair, and show increased de novo point mutations flanking the rearrangement junctions. The active CNV mutation shower appears to be restricted to a transient perizygotic period. We propose that a defect in the CNV formation process is responsible for the "CNV-mutator state," and this state is dampened after early embryogenesis. The constitutional MdnCNV phenomenon resembles chromosomal instability in various cancers. Investigations of this phenomenon may provide unique access to understanding genomic disorders, structural variant mutagenesis, human evolution, and cancer biology.

%B Cell %V 168 %P 830-842.e7 %8 2017 Feb 23 %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/28235197?dopt=Abstract %R 10.1016/j.cell.2017.01.037 %0 Journal Article %J Genome Med %D 2017 %T Phenotypic and molecular characterisation of CDK13-related congenital heart defects, dysmorphic facial features and intellectual developmental disorders. %A Bostwick, Bret L %A McLean, Scott %A Posey, Jennifer E %A Streff, Haley E %A Gripp, Karen W %A Blesson, Alyssa %A Powell-Hamilton, Nina %A Tusi, Jessica %A Stevenson, David A %A Farrelly, Ellyn %A Hudgins, Louanne %A Yang, Yaping %A Xia, Fan %A Wang, Xia %A Liu, Pengfei %A Walkiewicz, Magdalena %A McGuire, Marianne %A Grange, Dorothy K %A Andrews, Marisa V %A Hummel, Marybeth %A Madan-Khetarpal, Suneeta %A Infante, Elena %A Coban-Akdemir, Zeynep %A Miszalski-Jamka, Karol %A Jefferies, John L %A Rosenfeld, Jill A %A Emrick, Lisa %A Nugent, Kimberly M %A Lupski, James R %A Belmont, John W %A Lee, Brendan %A Lalani, Seema R %K Adolescent %K Adult %K CDC2 Protein Kinase %K Child %K Child, Preschool %K Face %K Female %K Heart Defects, Congenital %K Humans %K Infant %K Intellectual Disability %K Male %K Mutation %K Phenotype %K Syndrome %X

BACKGROUND: De novo missense variants in CDK13 have been described as the cause of syndromic congenital heart defects in seven individuals ascertained from a large congenital cardiovascular malformations cohort. We aimed to further define the phenotypic and molecular spectrum of this newly described disorder.

METHODS: To minimise ascertainment bias, we recruited nine additional individuals with CDK13 pathogenic variants from clinical and research exome laboratory sequencing cohorts. Each individual underwent dysmorphology exam and comprehensive medical history review.

RESULTS: We demonstrate greater than expected phenotypic heterogeneity, including 33% (3/9) of individuals without structural heart disease on echocardiogram. There was a high penetrance for a unique constellation of facial dysmorphism and global developmental delay, as well as less frequently seen renal and sacral anomalies. Two individuals had novel CDK13 variants (p.Asn842Asp, p.Lys734Glu), while the remaining seven unrelated individuals had a recurrent, previously published p.Asn842Ser variant. Summary of all variants published to date demonstrates apparent restriction of pathogenic variants to the protein kinase domain with clustering in the ATP and magnesium binding sites.

CONCLUSIONS: Here we provide detailed phenotypic and molecular characterisation of individuals with pathogenic variants in CDK13 and propose management guidelines based upon the estimated prevalence of anomalies identified.

%B Genome Med %V 9 %P 73 %8 2017 Aug 14 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/28807008?dopt=Abstract %R 10.1186/s13073-017-0463-8 %0 Journal Article %J J Allergy Clin Immunol %D 2017 %T Primary immunodeficiency diseases: Genomic approaches delineate heterogeneous Mendelian disorders. %A Stray-Pedersen, Asbjørg %A Sorte, Hanne Sørmo %A Samarakoon, Pubudu %A Gambin, Tomasz %A Chinn, Ivan K %A Coban Akdemir, Zeynep H %A Erichsen, Hans Christian %A Forbes, Lisa R %A Gu, Shen %A Yuan, Bo %A Jhangiani, Shalini N %A Muzny, Donna M %A Rødningen, Olaug Kristin %A Sheng, Ying %A Nicholas, Sarah K %A Noroski, Lenora M %A Seeborg, Filiz O %A Davis, Carla M %A Canter, Debra L %A Mace, Emily M %A Vece, Timothy J %A Allen, Carl E %A Abhyankar, Harshal A %A Boone, Philip M %A Beck, Christine R %A Wiszniewski, Wojciech %A Fevang, Børre %A Aukrust, Pål %A Tjønnfjord, Geir E %A Gedde-Dahl, Tobias %A Hjorth-Hansen, Henrik %A Dybedal, Ingunn %A Nordøy, Ingvild %A Jørgensen, Silje F %A Abrahamsen, Tore G %A Øverland, Torstein %A Bechensteen, Anne Grete %A Skogen, Vegard %A Osnes, Liv T N %A Kulseth, Mari Ann %A Prescott, Trine E %A Rustad, Cecilie F %A Heimdal, Ketil R %A Belmont, John W %A Rider, Nicholas L %A Chinen, Javier %A Cao, Tram N %A Smith, Eric A %A Caldirola, Maria Soledad %A Bezrodnik, Liliana %A Lugo Reyes, Saul Oswaldo %A Espinosa Rosales, Francisco J %A Guerrero-Cursaru, Nina Denisse %A Pedroza, Luis Alberto %A Poli, Cecilia M %A Franco, Jose L %A Trujillo Vargas, Claudia M %A Aldave Becerra, Juan Carlos %A Wright, Nicola %A Issekutz, Thomas B %A Issekutz, Andrew C %A Abbott, Jordan %A Caldwell, Jason W %A Bayer, Diana K %A Chan, Alice Y %A Aiuti, Alessandro %A Cancrini, Caterina %A Holmberg, Eva %A West, Christina %A Burstedt, Magnus %A Karaca, Ender %A Yesil, Gozde %A Artac, Hasibe %A Bayram, Yavuz %A Atik, Mehmed Musa %A Eldomery, Mohammad K %A Ehlayel, Mohammad S %A Jolles, Stephen %A Flatø, Berit %A Bertuch, Alison A %A Hanson, I Celine %A Zhang, Victor W %A Wong, Lee-Jun %A Hu, Jianhong %A Walkiewicz, Magdalena %A Yang, Yaping %A Eng, Christine M %A Boerwinkle, Eric %A Gibbs, Richard A %A Shearer, William T %A Lyle, Robert %A Orange, Jordan S %A Lupski, James R %K Adolescent %K Adult %K Aged %K Child %K Child, Preschool %K DNA Copy Number Variations %K Female %K Genomics %K High-Throughput Nucleotide Sequencing %K Humans %K Immunologic Deficiency Syndromes %K Infant %K Male %K Middle Aged %K Young Adult %X

BACKGROUND: Primary immunodeficiency diseases (PIDDs) are clinically and genetically heterogeneous disorders thus far associated with mutations in more than 300 genes. The clinical phenotypes derived from distinct genotypes can overlap. Genetic etiology can be a prognostic indicator of disease severity and can influence treatment decisions.

OBJECTIVE: We sought to investigate the ability of whole-exome screening methods to detect disease-causing variants in patients with PIDDs.

METHODS: Patients with PIDDs from 278 families from 22 countries were investigated by using whole-exome sequencing. Computational copy number variant (CNV) prediction pipelines and an exome-tiling chromosomal microarray were also applied to identify intragenic CNVs. Analytic approaches initially focused on 475 known or candidate PIDD genes but were nonexclusive and further tailored based on clinical data, family history, and immunophenotyping.

RESULTS: A likely molecular diagnosis was achieved in 110 (40%) unrelated probands. Clinical diagnosis was revised in about half (60/110) and management was directly altered in nearly a quarter (26/110) of families based on molecular findings. Twelve PIDD-causing CNVs were detected, including 7 smaller than 30 Kb that would not have been detected with conventional diagnostic CNV arrays.

CONCLUSION: This high-throughput genomic approach enabled detection of disease-related variants in unexpected genes; permitted detection of low-grade constitutional, somatic, and revertant mosaicism; and provided evidence of a mutational burden in mixed PIDD immunophenotypes.

%B J Allergy Clin Immunol %V 139 %P 232-245 %8 2017 Jan %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/27577878?dopt=Abstract %R 10.1016/j.jaci.2016.05.042 %0 Journal Article %J Brain %D 2017 %T PRUNE is crucial for normal brain development and mutated in microcephaly with neurodevelopmental impairment. %A Zollo, Massimo %A Ahmed, Mustafa %A Ferrucci, Veronica %A Salpietro, Vincenzo %A Asadzadeh, Fatemeh %A Carotenuto, Marianeve %A Maroofian, Reza %A Al-Amri, Ahmed %A Singh, Royana %A Scognamiglio, Iolanda %A Mojarrad, Majid %A Musella, Luca %A Duilio, Angela %A Di Somma, Angela %A Karaca, Ender %A Rajab, Anna %A Al-Khayat, Aisha %A Mohan Mohapatra, Tribhuvan %A Eslahi, Atieh %A Ashrafzadeh, Farah %A Rawlins, Lettie E %A Prasad, Rajniti %A Gupta, Rashmi %A Kumari, Preeti %A Srivastava, Mona %A Cozzolino, Flora %A Kumar Rai, Sunil %A Monti, Maria %A Harlalka, Gaurav V %A Simpson, Michael A %A Rich, Philip %A Al-Salmi, Fatema %A Patton, Michael A %A Chioza, Barry A %A Efthymiou, Stephanie %A Granata, Francesca %A Di Rosa, Gabriella %A Wiethoff, Sarah %A Borgione, Eugenia %A Scuderi, Carmela %A Mankad, Kshitij %A Hanna, Michael G %A Pucci, Piero %A Houlden, Henry %A Lupski, James R %A Crosby, Andrew H %A Baple, Emma L %K Adolescent %K Brain %K Carrier Proteins %K Cell Differentiation %K Cell Movement %K Cerebral Cortex %K Child %K Child, Preschool %K Cytoskeleton %K Developmental Disabilities %K Female %K Genes, Recessive %K Heredodegenerative Disorders, Nervous System %K Humans %K Infant %K Male %K Microcephaly %K Microtubules %K Mutation %K Pedigree %K Phosphoric Monoester Hydrolases %K Young Adult %X

PRUNE is a member of the DHH (Asp-His-His) phosphoesterase protein superfamily of molecules important for cell motility, and implicated in cancer progression. Here we investigated multiple families from Oman, India, Iran and Italy with individuals affected by a new autosomal recessive neurodevelopmental and degenerative disorder in which the cardinal features include primary microcephaly and profound global developmental delay. Our genetic studies identified biallelic mutations of PRUNE1 as responsible. Our functional assays of disease-associated variant alleles revealed impaired microtubule polymerization, as well as cell migration and proliferation properties, of mutant PRUNE. Additionally, our studies also highlight a potential new role for PRUNE during microtubule polymerization, which is essential for the cytoskeletal rearrangements that occur during cellular division and proliferation. Together these studies define PRUNE as a molecule fundamental for normal human cortical development and define cellular and clinical consequences associated with PRUNE mutation.

%B Brain %V 140 %P 940-952 %8 2017 Apr 01 %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/28334956?dopt=Abstract %R 10.1093/brain/awx014 %0 Journal Article %J Am J Hum Genet %D 2017 %T A Recurrent De Novo Variant in NACC1 Causes a Syndrome Characterized by Infantile Epilepsy, Cataracts, and Profound Developmental Delay. %A Schoch, Kelly %A Meng, Linyan %A Szelinger, Szabolcs %A Bearden, David R %A Stray-Pedersen, Asbjorg %A Busk, Oyvind L %A Stong, Nicholas %A Liston, Eriskay %A Cohn, Ronald D %A Scaglia, Fernando %A Rosenfeld, Jill A %A Tarpinian, Jennifer %A Skraban, Cara M %A Deardorff, Matthew A %A Friedman, Jeremy N %A Akdemir, Zeynep Coban %A Walley, Nicole %A Mikati, Mohamad A %A Kranz, Peter G %A Jasien, Joan %A McConkie-Rosell, Allyn %A McDonald, Marie %A Wechsler, Stephanie Burns %A Freemark, Michael %A Kansagra, Sujay %A Freedman, Sharon %A Bali, Deeksha %A Millan, Francisca %A Bale, Sherri %A Nelson, Stanley F %A Lee, Hane %A Dorrani, Naghmeh %A Goldstein, David B %A Xiao, Rui %A Yang, Yaping %A Posey, Jennifer E %A Martinez-Agosto, Julian A %A Lupski, James R %A Wangler, Michael F %A Shashi, Vandana %K Alleles %K Amino Acid Sequence %K Brain %K Cataract %K Child %K Child, Preschool %K Female %K Genetic Variation %K Genome-Wide Association Study %K Humans %K Infant %K Intellectual Disability %K Magnetic Resonance Imaging %K Male %K Microcephaly %K Mutation, Missense %K Neoplasm Proteins %K Pedigree %K Phenotype %K Repressor Proteins %K Spasms, Infantile %X

Whole-exome sequencing (WES) has increasingly enabled new pathogenic gene variant identification for undiagnosed neurodevelopmental disorders and provided insights into both gene function and disease biology. Here, we describe seven children with a neurodevelopmental disorder characterized by microcephaly, profound developmental delays and/or intellectual disability, cataracts, severe epilepsy including infantile spasms, irritability, failure to thrive, and stereotypic hand movements. Brain imaging in these individuals reveals delay in myelination and cerebral atrophy. We observe an identical recurrent de novo heterozygous c.892C>T (p.Arg298Trp) variant in the nucleus accumbens associated 1 (NACC1) gene in seven affected individuals. One of the seven individuals is mosaic for this variant. NACC1 encodes a transcriptional repressor implicated in gene expression and has not previously been associated with germline disorders. The probability of finding the same missense NACC1 variant by chance in 7 out of 17,228 individuals who underwent WES for diagnoses of neurodevelopmental phenotypes is extremely small and achieves genome-wide significance (p = 1.25 × 10). Selective constraint against missense variants in NACC1 makes this excess of an identical missense variant in all seven individuals more remarkable. Our findings are consistent with a germline recurrent mutational hotspot associated with an allele-specific neurodevelopmental phenotype in NACC1.

%B Am J Hum Genet %V 100 %P 343-351 %8 2017 Feb 02 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/28132692?dopt=Abstract %R 10.1016/j.ajhg.2016.12.013 %0 Journal Article %J N Engl J Med %D 2017 %T Resolution of Disease Phenotypes Resulting from Multilocus Genomic Variation. %A Posey, Jennifer E %A Harel, Tamar %A Liu, Pengfei %A Rosenfeld, Jill A %A James, Regis A %A Coban Akdemir, Zeynep H %A Walkiewicz, Magdalena %A Bi, Weimin %A Xiao, Rui %A Ding, Yan %A Xia, Fan %A Beaudet, Arthur L %A Muzny, Donna M %A Gibbs, Richard A %A Boerwinkle, Eric %A Eng, Christine M %A Sutton, V Reid %A Shaw, Chad A %A Plon, Sharon E %A Yang, Yaping %A Lupski, James R %K Exome %K Genetic Diseases, Inborn %K Genetic Variation %K Genotyping Techniques %K High-Throughput Nucleotide Sequencing %K Humans %K Phenotype %K Retrospective Studies %K Sequence Analysis, DNA %X

BACKGROUND: Whole-exome sequencing can provide insight into the relationship between observed clinical phenotypes and underlying genotypes.

METHODS: We conducted a retrospective analysis of data from a series of 7374 consecutive unrelated patients who had been referred to a clinical diagnostic laboratory for whole-exome sequencing; our goal was to determine the frequency and clinical characteristics of patients for whom more than one molecular diagnosis was reported. The phenotypic similarity between molecularly diagnosed pairs of diseases was calculated with the use of terms from the Human Phenotype Ontology.

RESULTS: A molecular diagnosis was rendered for 2076 of 7374 patients (28.2%); among these patients, 101 (4.9%) had diagnoses that involved two or more disease loci. We also analyzed parental samples, when available, and found that de novo variants accounted for 67.8% (61 of 90) of pathogenic variants in autosomal dominant disease genes and 51.7% (15 of 29) of pathogenic variants in X-linked disease genes; both variants were de novo in 44.7% (17 of 38) of patients with two monoallelic variants. Causal copy-number variants were found in 12 patients (11.9%) with multiple diagnoses. Phenotypic similarity scores were significantly lower among patients in whom the phenotype resulted from two distinct mendelian disorders that affected different organ systems (50 patients) than among patients with disorders that had overlapping phenotypic features (30 patients) (median score, 0.21 vs. 0.36; P=1.77×10).

CONCLUSIONS: In our study, we found multiple molecular diagnoses in 4.9% of cases in which whole-exome sequencing was informative. Our results show that structured clinical ontologies can be used to determine the degree of overlap between two mendelian diseases in the same patient; the diseases can be distinct or overlapping. Distinct disease phenotypes affect different organ systems, whereas overlapping disease phenotypes are more likely to be caused by two genes encoding proteins that interact within the same pathway. (Funded by the National Institutes of Health and the Ting Tsung and Wei Fong Chao Foundation.).

%B N Engl J Med %V 376 %P 21-31 %8 2017 Jan 05 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/27959697?dopt=Abstract %R 10.1056/NEJMoa1516767 %0 Journal Article %J Am J Hum Genet %D 2017 %T REST Final-Exon-Truncating Mutations Cause Hereditary Gingival Fibromatosis. %A Bayram, Yavuz %A White, Janson J %A Elcioglu, Nursel %A Cho, Megan T %A Zadeh, Neda %A Gedikbasi, Asuman %A Palanduz, Sukru %A Ozturk, Sukru %A Cefle, Kivanc %A Kasapcopur, Ozgur %A Coban Akdemir, Zeynep %A Pehlivan, Davut %A Begtrup, Amber %A Carvalho, Claudia M B %A Paine, Ingrid Sophie %A Mentes, Ali %A Bektas-Kayhan, Kivanc %A Karaca, Ender %A Jhangiani, Shalini N %A Muzny, Donna M %A Gibbs, Richard A %A Lupski, James R %K Adolescent %K Base Sequence %K Chromosome Segregation %K Exons %K Family %K Female %K Fibromatosis, Gingival %K Genetic Predisposition to Disease %K Humans %K Male %K Middle Aged %K Mutation %K Pedigree %K Repressor Proteins %X

Hereditary gingival fibromatosis (HGF) is the most common genetic form of gingival fibromatosis that develops as a slowly progressive, benign, localized or generalized enlargement of keratinized gingiva. HGF is a genetically heterogeneous disorder and can be transmitted either as an autosomal-dominant or autosomal-recessive trait or appear sporadically. To date, four loci (2p22.1, 2p23.3-p22.3, 5q13-q22, and 11p15) have been mapped to autosomes and one gene (SOS1) has been associated with the HGF trait observed to segregate in a dominant inheritance pattern. Here we report 11 individuals with HGF from three unrelated families. Whole-exome sequencing (WES) revealed three different truncating mutations including two frameshifts and one nonsense variant in RE1-silencing transcription factor (REST) in the probands from all families and further genetic and genomic analyses confirmed the WES-identified findings. REST is a transcriptional repressor that is expressed throughout the body; it has different roles in different cellular contexts, such as oncogenic and tumor-suppressor functions and hematopoietic and cardiac differentiation. Here we show the consequences of germline final-exon-truncating mutations in REST for organismal development and the association with the HGF phenotype.

%B Am J Hum Genet %V 101 %P 149-156 %8 2017 Jul 06 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/28686854?dopt=Abstract %R 10.1016/j.ajhg.2017.06.006 %0 Journal Article %J BMC Genomics %D 2017 %T SVachra: a tool to identify genomic structural variation in mate pair sequencing data containing inward and outward facing reads. %A Hampton, Oliver A %A English, Adam C %A Wang, Mark %A Salerno, William J %A Liu, Yue %A Muzny, Donna M %A Han, Yi %A Wheeler, David A %A Worley, Kim C %A Lupski, James R %A Gibbs, Richard A %K Genetic Variation %K Genomics %K Sequence Analysis, DNA %X

BACKGROUND: Characterization of genomic structural variation (SV) is essential to expanding the research and clinical applications of genome sequencing. Reliance upon short DNA fragment paired end sequencing has yielded a wealth of single nucleotide variants and internal sequencing read insertions-deletions, at the cost of limited SV detection. Multi-kilobase DNA fragment mate pair sequencing has supplemented the void in SV detection, but introduced new analytic challenges requiring SV detection tools specifically designed for mate pair sequencing data. Here, we introduce SVachra - Structural Variation Assessment of CHRomosomal Aberrations, a breakpoint calling program that identifies large insertions-deletions, inversions, inter- and intra-chromosomal translocations utilizing both inward and outward facing read types generated by mate pair sequencing.

RESULTS: We demonstrate SVachra's utility by executing the program on large-insert (Illumina Nextera) mate pair sequencing data from the personal genome of a single subject (HS1011). An additional data set of long-read (Pacific BioSciences RSII) was also generated to validate SV calls from SVachra and other comparison SV calling programs. SVachra exhibited the highest validation rate and reported the widest distribution of SV types and size ranges when compared to other SV callers.

CONCLUSIONS: SVachra is a highly specific breakpoint calling program that exhibits a more unbiased SV detection methodology than other callers.

%B BMC Genomics %V 18 %P 691 %8 2017 Oct 03 %G eng %N Suppl 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/28984202?dopt=Abstract %R 10.1186/s12864-017-4021-y %0 Journal Article %J Eur J Hum Genet %D 2017 %T Unraveling genetic predisposition to familial or early onset gastric cancer using germline whole-exome sequencing. %A Vogelaar, Ingrid P %A van der Post, Rachel S %A van Krieken, J Han Jm %A Spruijt, Liesbeth %A van Zelst-Stams, Wendy Ag %A Kets, C Marleen %A Lubinski, Jan %A Jakubowska, Anna %A Teodorczyk, Urszula %A Aalfs, Cora M %A van Hest, Liselotte P %A Pinheiro, Hugo %A Oliveira, Carla %A Jhangiani, Shalini N %A Muzny, Donna M %A Gibbs, Richard A %A Lupski, James R %A de Ligt, Joep %A Vissers, Lisenka E L M %A Hoischen, Alexander %A Gilissen, Christian %A van de Vorst, Maartje %A Goeman, Jelle J %A Schackert, Hans K %A Ranzani, Guglielmina N %A Molinaro, Valeria %A Gómez García, Encarna B %A Hes, Frederik J %A Holinski-Feder, Elke %A Genuardi, Maurizio %A Ausems, Margreet G E M %A Sijmons, Rolf H %A Wagner, Anja %A van der Kolk, Lizet E %A Bjørnevoll, Inga %A Høberg-Vetti, Hildegunn %A van Kessel, Ad Geurts %A Kuiper, Roland P %A Ligtenberg, Marjolijn J L %A Hoogerbrugge, Nicoline %K Adult %K Aged %K Antigens, CD %K Cadherins %K Early Detection of Cancer %K Exome %K Female %K Genetic Predisposition to Disease %K Genetic Testing %K Germ-Line Mutation %K Humans %K Male %K Middle Aged %K Sequence Analysis, DNA %K Stomach Neoplasms %X

Recognition of individuals with a genetic predisposition to gastric cancer (GC) enables preventive measures. However, the underlying cause of genetic susceptibility to gastric cancer remains largely unexplained. We performed germline whole-exome sequencing on leukocyte DNA of 54 patients from 53 families with genetically unexplained diffuse-type and intestinal-type GC to identify novel GC-predisposing candidate genes. As young age at diagnosis and familial clustering are hallmarks of genetic tumor susceptibility, we selected patients that were diagnosed below the age of 35, patients from families with two cases of GC at or below age 60 and patients from families with three GC cases at or below age 70. All included individuals were tested negative for germline CDH1 mutations before or during the study. Variants that were possibly deleterious according to in silico predictions were filtered using several independent approaches that were based on gene function and gene mutation burden in controls. Despite a rigorous search, no obvious candidate GC predisposition genes were identified. This negative result stresses the importance of future research studies in large, homogeneous cohorts.

%B Eur J Hum Genet %V 25 %P 1246-1252 %8 2017 Nov %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/28875981?dopt=Abstract %R 10.1038/ejhg.2017.138 %0 Journal Article %J JAMA Pediatr %D 2017 %T Use of Exome Sequencing for Infants in Intensive Care Units: Ascertainment of Severe Single-Gene Disorders and Effect on Medical Management. %A Meng, Linyan %A Pammi, Mohan %A Saronwala, Anirudh %A Magoulas, Pilar %A Ghazi, Andrew Ray %A Vetrini, Francesco %A Zhang, Jing %A He, Weimin %A Dharmadhikari, Avinash V %A Qu, Chunjing %A Ward, Patricia %A Braxton, Alicia %A Narayanan, Swetha %A Ge, Xiaoyan %A Tokita, Mari J %A Santiago-Sim, Teresa %A Dai, Hongzheng %A Chiang, Theodore %A Smith, Hadley %A Azamian, Mahshid S %A Robak, Laurie %A Bostwick, Bret L %A Schaaf, Christian P %A Potocki, Lorraine %A Scaglia, Fernando %A Bacino, Carlos A %A Hanchard, Neil A %A Wangler, Michael F %A Scott, Daryl %A Brown, Chester %A Hu, Jianhong %A Belmont, John W %A Burrage, Lindsay C %A Graham, Brett H %A Sutton, Vernon Reid %A Craigen, William J %A Plon, Sharon E %A Lupski, James R %A Beaudet, Arthur L %A Gibbs, Richard A %A Muzny, Donna M %A Miller, Marcus J %A Wang, Xia %A Leduc, Magalie S %A Xiao, Rui %A Liu, Pengfei %A Shaw, Chad %A Walkiewicz, Magdalena %A Bi, Weimin %A Xia, Fan %A Lee, Brendan %A Eng, Christine M %A Yang, Yaping %A Lalani, Seema R %K Adult %K Critical Care %K Disease Management %K Exome %K Exome Sequencing %K Genetic Counseling %K Genetic Diseases, Inborn %K Humans %K Infant %K Infant Care %K Infant, Newborn %K Intensive Care Units, Pediatric %K Length of Stay %K Retrospective Studies %K Texas %X

IMPORTANCE: While congenital malformations and genetic diseases are a leading cause of early infant death, to our knowledge, the contribution of single-gene disorders in this group is undetermined.

OBJECTIVE: To determine the diagnostic yield and use of clinical exome sequencing in critically ill infants.

DESIGN, SETTING, AND PARTICIPANTS: Clinical exome sequencing was performed for 278 unrelated infants within the first 100 days of life who were admitted to Texas Children's Hospital in Houston, Texas, during a 5-year period between December 2011 and January 2017. Exome sequencing types included proband exome, trio exome, and critical trio exome, a rapid genomic assay for seriously ill infants.

MAIN OUTCOMES AND MEASURES: Indications for testing, diagnostic yield of clinical exome sequencing, turnaround time, molecular findings, patient age at diagnosis, and effect on medical management among a group of critically ill infants who were suspected to have genetic disorders.

RESULTS: The mean (SEM) age for infants participating in the study was 28.5 (1.7) days; of these, the mean (SEM) age was 29.0 (2.2) days for infants undergoing proband exome sequencing, 31.5 (3.9) days for trio exome, and 22.7 (3.9) days for critical trio exome. Clinical indications for exome sequencing included a range of medical concerns. Overall, a molecular diagnosis was achieved in 102 infants (36.7%) by clinical exome sequencing, with relatively low yield for cardiovascular abnormalities. The diagnosis affected medical management for 53 infants (52.0%) and had a substantial effect on informed redirection of care, initiation of new subspecialist care, medication/dietary modifications, and furthering life-saving procedures in select patients. Critical trio exome sequencing revealed a molecular diagnosis in 32 of 63 infants (50.8%) at a mean (SEM) of 33.1 (5.6) days of life with a mean (SEM) turnaround time of 13.0 (0.4) days. Clinical care was altered by the diagnosis in 23 of 32 patients (71.9%). The diagnostic yield, patient age at diagnosis, and medical effect in the group that underwent critical trio exome sequencing were significantly different compared with the group who underwent regular exome testing. For deceased infants (n = 81), genetic disorders were molecularly diagnosed in 39 (48.1%) by exome sequencing, with implications for recurrence risk counseling.

CONCLUSIONS AND RELEVANCE: Exome sequencing is a powerful tool for the diagnostic evaluation of critically ill infants with suspected monogenic disorders in the neonatal and pediatric intensive care units and its use has a notable effect on clinical decision making.

%B JAMA Pediatr %V 171 %P e173438 %8 2017 Dec 04 %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/28973083?dopt=Abstract %R 10.1001/jamapediatrics.2017.3438 %0 Journal Article %J Eur J Hum Genet %D 2017 %T Variants in SKP1, PROB1, and IL17B genes at keratoconus 5q31.1-q35.3 susceptibility locus identified by whole-exome sequencing. %A Karolak, Justyna A %A Gambin, Tomasz %A Pitarque, Jose A %A Molinari, Andrea %A Jhangiani, Shalini %A Stankiewicz, Pawel %A Lupski, James R %A Gajecka, Marzena %K Chromosomes, Human, Pair 5 %K Exome %K Female %K Gene Frequency %K Genetic Linkage %K Genetic Predisposition to Disease %K Genome, Human %K Hexokinase %K High-Throughput Nucleotide Sequencing %K Humans %K Interleukin-17 %K Keratoconus %K Male %K Pedigree %K Phenotype %K Proteins %K S-Phase Kinase-Associated Proteins %X

Keratoconus (KTCN) is a protrusion and thinning of the cornea, resulting in impairment of visual function. The extreme genetic heterogeneity makes it difficult to discover factors unambiguously influencing the KTCN phenotype. In this study, we used whole-exome sequencing (WES) and Sanger sequencing to reduce the number of candidate genes at the 5q31.1-q35.3 locus and to prioritize other potentially relevant variants in an Ecuadorian family with KTCN. We applied WES in two affected KTCN individuals from the Ecuadorian family that showed a suggestive linkage between the KTCN phenotype and the 5q31.1-q35.3 locus. Putative variants identified by WES were further evaluated in this family using Sanger sequencing. Exome capture discovered a total of 173 rare (minor allele frequency <0.001 in control population) nonsynonymous variants in both affected individuals. Among them, 16 SNVs were selected for further evaluation. Segregation analysis revealed that variants c.475T>G in SKP1, c.671G>A in PROB1, and c.527G>A in IL17B in the 5q31.1-q35.3 linkage region, and c.850G>A in HKDC1 in the 10q22 locus completely segregated with the phenotype in the studied KTCN family. We demonstrate that a combination of various techniques significantly narrowed the studied genomic region and reduced the list of the putative exonic variants. Moreover, since this locus overlapped two other chromosomal regions previously recognized in distinct KTCN studies, our findings suggest that this 5q31.1-q35.3 locus might be linked with KTCN.

%B Eur J Hum Genet %V 25 %P 73-78 %8 2017 Jan %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/27703147?dopt=Abstract %R 10.1038/ejhg.2016.130 %0 Journal Article %J Genome Med %D 2017 %T Whole exome sequencing in 342 congenital cardiac left sided lesion cases reveals extensive genetic heterogeneity and complex inheritance patterns. %A Li, Alexander H %A Hanchard, Neil A %A Furthner, Dieter %A Fernbach, Susan %A Azamian, Mahshid %A Nicosia, Annarita %A Rosenfeld, Jill %A Muzny, Donna %A D'Alessandro, Lisa C A %A Morris, Shaine %A Jhangiani, Shalini %A Parekh, Dhaval R %A Franklin, Wayne J %A Lewin, Mark %A Towbin, Jeffrey A %A Penny, Daniel J %A Fraser, Charles D %A Martin, James F %A Eng, Christine %A Lupski, James R %A Gibbs, Richard A %A Boerwinkle, Eric %A Belmont, John W %K Exome Sequencing %K Female %K Genetic Heterogeneity %K Heart Defects, Congenital %K Humans %K Inheritance Patterns %K Male %X

BACKGROUND: Left-sided lesions (LSLs) account for an important fraction of severe congenital cardiovascular malformations (CVMs). The genetic contributions to LSLs are complex, and the mutations that cause these malformations span several diverse biological signaling pathways: TGFB, NOTCH, SHH, and more. Here, we use whole exome sequence data generated in 342 LSL cases to identify likely damaging variants in putative candidate CVM genes.

METHODS: Using a series of bioinformatics filters, we focused on genes harboring population-rare, putative loss-of-function (LOF), and predicted damaging variants in 1760 CVM candidate genes constructed a priori from the literature and model organism databases. Gene variants that were not observed in a comparably sequenced control dataset of 5492 samples without severe CVM were then subjected to targeted validation in cases and parents. Whole exome sequencing data from 4593 individuals referred for clinical sequencing were used to bolster evidence for the role of candidate genes in CVMs and LSLs.

RESULTS: Our analyses revealed 28 candidate variants in 27 genes, including 17 genes not previously associated with a human CVM disorder, and revealed diverse patterns of inheritance among LOF carriers, including 9 confirmed de novo variants in both novel and newly described human CVM candidate genes (ACVR1, JARID2, NR2F2, PLRG1, SMURF1) as well as established syndromic CVM genes (KMT2D, NF1, TBX20, ZEB2). We also identified two genes (DNAH5, OFD1) with evidence of recessive and hemizygous inheritance patterns, respectively. Within our clinical cohort, we also observed heterozygous LOF variants in JARID2 and SMAD1 in individuals with cardiac phenotypes, and collectively, carriers of LOF variants in our candidate genes had a four times higher odds of having CVM (odds ratio = 4.0, 95% confidence interval 2.5-6.5).

CONCLUSIONS: Our analytical strategy highlights the utility of bioinformatic resources, including human disease records and model organism phenotyping, in novel gene discovery for rare human disease. The results underscore the extensive genetic heterogeneity underlying non-syndromic LSLs, and posit potential novel candidate genes and complex modes of inheritance in this important group of birth defects.

%B Genome Med %V 9 %P 95 %8 2017 Oct 31 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/29089047?dopt=Abstract %R 10.1186/s13073-017-0482-5 %0 Journal Article %J Genet Med %D 2017 %T Whole-exome sequencing in the molecular diagnosis of individuals with congenital anomalies of the kidney and urinary tract and identification of a new causative gene. %A Bekheirnia, Mir Reza %A Bekheirnia, Nasim %A Bainbridge, Matthew N %A Gu, Shen %A Coban Akdemir, Zeynep Hande %A Gambin, Tomek %A Janzen, Nicolette K %A Jhangiani, Shalini N %A Muzny, Donna M %A Michael, Mini %A Brewer, Eileen D %A Elenberg, Ewa %A Kale, Arundhati S %A Riley, Alyssa A %A Swartz, Sarah J %A Scott, Daryl A %A Yang, Yaping %A Srivaths, Poyyapakkam R %A Wenderfer, Scott E %A Bodurtha, Joann %A Applegate, Carolyn D %A Velinov, Milen %A Myers, Angela %A Borovik, Lior %A Craigen, William J %A Hanchard, Neil A %A Rosenfeld, Jill A %A Lewis, Richard Alan %A Gonzales, Edmond T %A Gibbs, Richard A %A Belmont, John W %A Roth, David R %A Eng, Christine %A Braun, Michael C %A Lupski, James R %A Lamb, Dolores J %K Adolescent %K Child %K Child, Preschool %K DNA Copy Number Variations %K Exome Sequencing %K Female %K Forkhead Transcription Factors %K Genetic Predisposition to Disease %K Hepatocyte Nuclear Factor 1-beta %K Humans %K Infant %K Intracellular Signaling Peptides and Proteins %K Male %K Nuclear Proteins %K PAX2 Transcription Factor %K Pedigree %K Polymorphism, Single Nucleotide %K Protein Tyrosine Phosphatases %K Repressor Proteins %K Urogenital Abnormalities %K Vesico-Ureteral Reflux %K Young Adult %X

PURPOSE: To investigate the utility of whole-exome sequencing (WES) to define a molecular diagnosis for patients clinically diagnosed with congenital anomalies of kidney and urinary tract (CAKUT).

METHODS: WES was performed in 62 families with CAKUT. WES data were analyzed for single-nucleotide variants (SNVs) in 35 known CAKUT genes, putatively deleterious sequence changes in new candidate genes, and potentially disease-associated copy-number variants (CNVs).

RESULTS: In approximately 5% of families, pathogenic SNVs were identified in PAX2, HNF1B, and EYA1. Observed phenotypes in these families expand the current understanding about the role of these genes in CAKUT. Four pathogenic CNVs were also identified using two CNV detection tools. In addition, we found one deleterious de novo SNV in FOXP1 among the 62 families with CAKUT. The clinical database of the Baylor Miraca Genetics laboratory was queried and seven additional unrelated individuals with novel de novo SNVs in FOXP1 were identified. Six of these eight individuals with FOXP1 SNVs have syndromic urinary tract defects, implicating this gene in urinary tract development.

CONCLUSION: We conclude that WES can be used to identify molecular etiology (SNVs, CNVs) in a subset of individuals with CAKUT. WES can also help identify novel CAKUT genes.Genet Med 19 4, 412-420.

%B Genet Med %V 19 %P 412-420 %8 2017 Apr %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/27657687?dopt=Abstract %R 10.1038/gim.2016.131 %0 Journal Article %J Endocrine %D 2016 %T Aggressive tumor growth and clinical evolution in a patient with X-linked acro-gigantism syndrome. %A Naves, Luciana A %A Daly, Adrian F %A Dias, Luiz Augusto %A Yuan, Bo %A Zakir, Juliano Coelho Oliveira %A Barra, Gustavo Barcellos %A Palmeira, Leonor %A Villa, Chiara %A Trivellin, Giampaolo %A Júnior, Armindo Jreige %A Neto, Florêncio Figueiredo Cavalcante %A Liu, Pengfei %A Pellegata, Natalia S %A Stratakis, Constantine A %A Lupski, James R %A Beckers, Albert %K Adenoma %K Child %K Genetic Diseases, X-Linked %K Gigantism %K Humans %K Male %K Pituitary Neoplasms %K Treatment Outcome %X

X-linked acro-gigantism (X-LAG) syndrome is a newly described disease caused by microduplications on chromosome Xq26.3 leading to copy number gain of GPR101. We describe the clinical progress of a sporadic male X-LAG syndrome patient with an Xq26.3 microduplication, highlighting the aggressive natural history of pituitary tumor growth in the absence of treatment. The patient first presented elsewhere aged 5 years 8 months with a history of excessive growth for >2 years. His height was 163 cm, his weight was 36 kg, and he had markedly elevated GH and IGF-1. MRI showed a non-invasive sellar mass measuring 32.5 × 23.9 × 29.1 mm. Treatment was declined and the family was lost to follow-up. At the age of 10 years and 7 months, he presented again with headaches, seizures, and visual disturbance. His height had increased to 197 cm. MRI showed an invasive mass measuring 56.2 × 58.1 × 45.0 mm, with compression of optic chiasma, bilateral cavernous sinus invasion, and hydrocephalus. His thyrotrope, corticotrope, and gonadotrope axes were deficient. Surgery, somatostatin analogs, and cabergoline did not control vertical growth and pegvisomant was added, although vertical growth continues (currently 207 cm at 11 years 7 months of age). X-LAG syndrome is a new genomic disorder in which early-onset pituitary tumorigenesis can lead to marked overgrowth and gigantism. This case illustrates the aggressive nature of tumor evolution and the challenging clinical management in X-LAG syndrome.

%B Endocrine %V 51 %P 236-44 %8 2016 Feb %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/26607152?dopt=Abstract %R 10.1007/s12020-015-0804-6 %0 Journal Article %J JAMA Neurol %D 2016 %T Association of MTOR Mutations With Developmental Brain Disorders, Including Megalencephaly, Focal Cortical Dysplasia, and Pigmentary Mosaicism. %A Mirzaa, Ghayda M %A Campbell, Catarina D %A Solovieff, Nadia %A Goold, Carleton %A Jansen, Laura A %A Menon, Suchithra %A Timms, Andrew E %A Conti, Valerio %A Biag, Jonathan D %A Adams, Carissa %A Boyle, Evan August %A Collins, Sarah %A Ishak, Gisele %A Poliachik, Sandra %A Girisha, Katta M %A Yeung, Kit San %A Chung, Brian Hon Yin %A Rahikkala, Elisa %A Gunter, Sonya A %A McDaniel, Sharon S %A Macmurdo, Colleen Forsyth %A Bernstein, Jonathan A %A Martin, Beth %A Leary, Rebecca %A Mahan, Scott %A Liu, Shanming %A Weaver, Molly %A Doerschner, Michael %A Jhangiani, Shalini %A Muzny, Donna M %A Boerwinkle, Eric %A Gibbs, Richard A %A Lupski, James R %A Shendure, Jay %A Saneto, Russell P %A Novotny, Edward J %A Wilson, Christopher J %A Sellers, William R %A Morrissey, Michael %A Hevner, Robert F %A Ojemann, Jeffrey G %A Guerrini, Renzo %A Murphy, Leon O %A Winckler, Wendy %A Dobyns, William B %K Adolescent %K Adult %K Amino Acids %K Animals %K Cells, Cultured %K Cerebral Cortex %K Child %K Child, Preschool %K Developmental Disabilities %K Embryo, Mammalian %K Female %K Gene Expression Regulation %K Genetic Association Studies %K Humans %K Intercellular Signaling Peptides and Proteins %K Male %K Malformations of Cortical Development %K Mechanistic Target of Rapamycin Complex 1 %K Megalencephaly %K Mosaicism %K Multiprotein Complexes %K Mutation %K Nerve Tissue Proteins %K Neurons %K Rats %K Retrospective Studies %K TOR Serine-Threonine Kinases %K Young Adult %X

IMPORTANCE: Focal cortical dysplasia (FCD), hemimegalencephaly, and megalencephaly constitute a spectrum of malformations of cortical development with shared neuropathologic features. These disorders are associated with significant childhood morbidity and mortality.

OBJECTIVE: To identify the underlying molecular cause of FCD, hemimegalencephaly, and diffuse megalencephaly.

DESIGN, SETTING, AND PARTICIPANTS: Patients with FCD, hemimegalencephaly, or megalencephaly (mean age, 11.7 years; range, 2-32 years) were recruited from Pediatric Hospital A. Meyer, the University of Hong Kong, and Seattle Children's Research Institute from June 2012 to June 2014. Whole-exome sequencing (WES) was performed on 8 children with FCD or hemimegalencephaly using standard-depth (50-60X) sequencing in peripheral samples (blood, saliva, or skin) from the affected child and their parents and deep (150-180X) sequencing in affected brain tissue. Targeted sequencing and WES were used to screen 93 children with molecularly unexplained diffuse or focal brain overgrowth. Histopathologic and functional assays of phosphatidylinositol 3-kinase-AKT (serine/threonine kinase)-mammalian target of rapamycin (mTOR) pathway activity in resected brain tissue and cultured neurons were performed to validate mutations.

MAIN OUTCOMES AND MEASURES: Whole-exome sequencing and targeted sequencing identified variants associated with this spectrum of developmental brain disorders.

RESULTS: Low-level mosaic mutations of MTOR were identified in brain tissue in 4 children with FCD type 2a with alternative allele fractions ranging from 0.012 to 0.086. Intermediate-level mosaic mutation of MTOR (p.Thr1977Ile) was also identified in 3 unrelated children with diffuse megalencephaly and pigmentary mosaicism in skin. Finally, a constitutional de novo mutation of MTOR (p.Glu1799Lys) was identified in 3 unrelated children with diffuse megalencephaly and intellectual disability. Molecular and functional analysis in 2 children with FCD2a from whom multiple affected brain tissue samples were available revealed a mutation gradient with an epicenter in the most epileptogenic area. When expressed in cultured neurons, all MTOR mutations identified here drive constitutive activation of mTOR complex 1 and enlarged neuronal size.

CONCLUSIONS AND RELEVANCE: In this study, mutations of MTOR were associated with a spectrum of brain overgrowth phenotypes extending from FCD type 2a to diffuse megalencephaly, distinguished by different mutations and levels of mosaicism. These mutations may be sufficient to cause cellular hypertrophy in cultured neurons and may provide a demonstration of the pattern of mosaicism in brain and substantiate the link between mosaic mutations of MTOR and pigmentary mosaicism in skin.

%B JAMA Neurol %V 73 %P 836-845 %8 2016 Jul 01 %G eng %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/27159400?dopt=Abstract %R 10.1001/jamaneurol.2016.0363 %0 Journal Article %J Am J Hum Genet %D 2016 %T Bi-allelic Mutations in PKD1L1 Are Associated with Laterality Defects in Humans. %A Vetrini, Francesco %A D'Alessandro, Lisa C A %A Akdemir, Zeynep C %A Braxton, Alicia %A Azamian, Mahshid S %A Eldomery, Mohammad K %A Miller, Kathryn %A Kois, Chelsea %A Sack, Virginia %A Shur, Natasha %A Rijhsinghani, Asha %A Chandarana, Jignesh %A Ding, Yan %A Holtzman, Judy %A Jhangiani, Shalini N %A Muzny, Donna M %A Gibbs, Richard A %A Eng, Christine M %A Hanchard, Neil A %A Harel, Tamar %A Rosenfeld, Jill A %A Belmont, John W %A Lupski, James R %A Yang, Yaping %K Alleles %K Amino Acid Motifs %K Amino Acid Sequence %K Animals %K Caenorhabditis elegans %K Cysteine %K Exome %K Female %K Fetal Diseases %K Functional Laterality %K Heart Defects, Congenital %K Heterotaxy Syndrome %K Homozygote %K Humans %K Infant, Newborn %K Introns %K Male %K Membrane Proteins %K Mice %K Middle Aged %K Models, Molecular %K Mutation %K Mutation, Missense %K Oryzias %K Pedigree %K RNA Splicing %K Situs Inversus %X

Disruption of the establishment of left-right (L-R) asymmetry leads to situs anomalies ranging from situs inversus totalis (SIT) to situs ambiguus (heterotaxy). The genetic causes of laterality defects in humans are highly heterogeneous. Via whole-exome sequencing (WES), we identified homozygous mutations in PKD1L1 from three affected individuals in two unrelated families. PKD1L1 encodes a polycystin-1-like protein and its loss of function is known to cause laterality defects in mouse and medaka fish models. Family 1 had one fetus and one deceased child with heterotaxy and complex congenital heart malformations. WES identified a homozygous splicing mutation, c.6473+2_6473+3delTG, which disrupts the invariant splice donor site in intron 42, in both affected individuals. In the second family, a homozygous c.5072G>C (p.Cys1691Ser) missense mutation was detected in an individual with SIT and congenital heart disease. The p.Cys1691Ser substitution affects a highly conserved cysteine residue and is predicted by molecular modeling to disrupt a disulfide bridge essential for the proper folding of the G protein-coupled receptor proteolytic site (GPS) motif. Damaging effects associated with substitutions of this conserved cysteine residue in the GPS motif have also been reported in other genes, namely GPR56, BAI3, and PKD1 in human and lat-1 in C. elegans, further supporting the likely pathogenicity of p.Cys1691Ser in PKD1L1. The identification of bi-allelic PKD1L1 mutations recapitulates previous findings regarding phenotypic consequences of loss of function of the orthologous genes in mice and medaka fish and further expands our understanding of genetic contributions to laterality defects in humans.

%B Am J Hum Genet %V 99 %P 886-893 %8 2016 Oct 06 %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/27616478?dopt=Abstract %R 10.1016/j.ajhg.2016.07.011 %0 Journal Article %J Am J Hum Genet %D 2016 %T Biallelic Mutations in UNC80 Cause Persistent Hypotonia, Encephalopathy, Growth Retardation, and Severe Intellectual Disability. %A Stray-Pedersen, Asbjørg %A Cobben, Jan-Maarten %A Prescott, Trine E %A Lee, Sora %A Cang, Chunlei %A Aranda, Kimberly %A Ahmed, Sohnee %A Alders, Marielle %A Gerstner, Thorsten %A Aslaksen, Kathinka %A Tétreault, Martine %A Qin, Wen %A Hartley, Taila %A Jhangiani, Shalini N %A Muzny, Donna M %A Tarailo-Graovac, Maja %A van Karnebeek, Clara D M %A Lupski, James R %A Ren, Dejian %A Yoon, Grace %K Adolescent %K Alleles %K Brain Diseases %K Carrier Proteins %K Child %K Child, Preschool %K Female %K Growth Disorders %K Humans %K Intellectual Disability %K Membrane Proteins %K Muscle Hypotonia %K Mutation %K Severity of Illness Index %X

Ion channel proteins are required for both the establishment of resting membrane potentials and the generation of action potentials. Hundreds of mutations in genes encoding voltage-gated ion channels responsible for action potential generation have been found to cause severe neurological diseases. In contrast, the roles of voltage-independent "leak" channels, important for the establishment and maintenance of resting membrane potentials upon which action potentials are generated, are not well established in human disease. UNC80 is a large component of the NALCN sodium-leak channel complex that regulates the basal excitability of the nervous system. Loss-of-function mutations of NALCN cause infantile hypotonia with psychomotor retardation and characteristic facies (IHPRF). We report four individuals from three unrelated families who have homozygous missense or compound heterozygous truncating mutations in UNC80 and persistent hypotonia, encephalopathy, growth failure, and severe intellectual disability. Compared to control cells, HEK293T cells transfected with an expression plasmid containing the c.5098C>T (p.Pro1700Ser) UNC80 mutation found in one individual showed markedly decreased NALCN channel currents. Our findings demonstrate the fundamental significance of UNC80 and basal ionic conductance to human health.

%B Am J Hum Genet %V 98 %P 202-9 %8 2016 Jan 07 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/26708751?dopt=Abstract %R 10.1016/j.ajhg.2015.11.004 %0 Journal Article %J Neurol Neurochir Pol %D 2016 %T CAV3 mutation in a patient with transient hyperCKemia and myalgia. %A Macias, Anna %A Gambin, Tomasz %A Szafranski, Przemyslaw %A Jhangiani, Shalini N %A Kolasa, Anna %A Obersztyn, Ewa %A Lupski, James R %A Stankiewicz, Pawel %A Kaminska, Anna %K Caveolin 3 %K Colitis, Ulcerative %K Creatine Kinase %K Frameshift Mutation %K Humans %K Klinefelter Syndrome %K Magnetic Resonance Imaging %K Male %K Membrane Proteins %K Middle Aged %K Muscle, Skeletal %K Muscular Diseases %K Mutation, Missense %K Myalgia %K Phenotype %K Sjogren's Syndrome %K Thigh %X

Mutations in caveolin-3 (CAV3) can lead to different clinical phenotypes affecting skeletal or cardiac muscles. Here, we describe a patient with Klinefelter syndrome, ulcerative colitis and Sjögren syndrome, who developed transient hyperCKemia, myalgia and mild muscular weakness. Using whole exome sequencing (WES), a missense mutation G169A was found in the CAV3 gene. In addition, we identified a homozygous frameshift deletion in MS4A12 that may contribute to inflammatory bowel disease, further demonstrating usefulness of WES in dual molecular diagnoses.

%B Neurol Neurochir Pol %V 50 %P 468-473 %8 2016 Nov-Dec %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/27772553?dopt=Abstract %R 10.1016/j.pjnns.2016.06.008 %0 Journal Article %J Hum Genet %D 2016 %T Clinical genomics: from a truly personal genome viewpoint. %A Lupski, James R %K Genetic Diseases, Inborn %K Genetic Variation %K Genome, Human %K Genomics %K Humans %K Informed Consent %K Precision Medicine %K Privacy %K Sequence Analysis, DNA %X

The path to Clinical Genomics is punctuated by our understanding of what types of DNA structural and sequence variation contribute to disease, the many technical challenges to detect such variation genome-wide, and the initial struggles to interpret personal genome variation in the context of disease. This review describes one perspective of the development of clinical genomics; whereas the experimental challenges, and hurdles to overcoming them, might be deemed readily apparent, the non-technical issues for clinical implementation may be less obvious. Some of these latter challenges, including: (1) informed consent, (2) privacy, (3) what constitutes potentially pathogenic variation contributing to disease, (4) disease penetrance in populations, and (5) the genetic architecture of disease, and the struggles sometimes faced for solutions, are highlighted using illustrative examples.

%B Hum Genet %V 135 %P 591-601 %8 2016 Jun %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/27221143?dopt=Abstract %R 10.1007/s00439-016-1682-6 %0 Journal Article %J Hum Genet %D 2016 %T Complex inheritance of ABCA4 disease: four mutations in a family with multiple macular phenotypes. %A Lee, Winston %A Xie, Yajing %A Zernant, Jana %A Bo Yuan %A Bearelly, Srilaxmi %A Tsang, Stephen H %A James R Lupski %A Allikmets, Rando %K Adult %K Aged %K ATP-Binding Cassette Transporters %K Comparative Genomic Hybridization %K DNA Copy Number Variations %K Electroretinography %K Female %K High-Throughput Nucleotide Sequencing %K Humans %K Macula Lutea %K Macular Degeneration %K Male %K Middle Aged %K Mutation %K Pedigree %K Phenotype %K Stargardt Disease %X

Over 800 mutations in the ABCA4 gene cause autosomal recessive Stargardt disease. Due to extensive genetic heterogeneity, observed variant-associated phenotypes can manifest tremendous variability of expression. Furthermore, the high carrier frequency of pathogenic ABCA4 alleles in the general population (~1:20) often results in pseudo-dominant inheritance patterns further complicating the diagnosis and characterization of affected individuals. This study describes a genotype/phenotype analysis of an unusual family with multiple macular disease phenotypes spanning across two generations and segregating four distinct ABCA4 mutant alleles. Complete sequencing of ABCA4 discovered two known missense mutations, p.C54Y and p.G1961E. Array comparative genomic hybridization revealed a large novel deletion combined with a small insertion, c.6148-698_c.6670del/insTGTGCACCTCCCTAG, and complete sequencing of the entire ABCA4 genomic locus uncovered a new deep intronic variant, c.302+68C>T. Patients with the p.G1961E mutation had the mildest, confined maculopathy phenotype with peripheral flecks while those with all other mutant allele combinations exhibited a more advanced stage of generalized retinal and choriocapillaris atrophy. This family epitomizes the clinical and genetic complexity of ABCA4-associated diseases. It contained variants from all classes of mutations, in the coding region, deep intronic, both single nucleotide variants and copy number variants that accounted for varying phenotypes segregating in an apparent dominant fashion. Unequivocally defining disease-associated alleles in the ABCA4 locus requires a multifaceted approach that includes advanced mutation detection methods and a thorough analysis of clinical phenotypes.

%B Hum Genet %V 135 %P 9-19 %8 2016 Jan %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/26527198?dopt=Abstract %R 10.1007/s00439-015-1605-y %0 Journal Article %J Genom Data %D 2016 %T Copy number analysis of the low-copy repeats at the primate NPHP1 locus by array comparative genomic hybridization. %A Yuan, Bo %A Liu, Pengfei %A Rogers, Jeffrey %A Lupski, James R %X

Array comparative genomic hybridization (aCGH) has been widely used to detect copy number variants (CNVs) in both research and clinical settings. A customizable aCGH platform may greatly facilitate copy number analyses in genomic regions with higher-order complexity, such as low-copy repeats (LCRs). Here we present the aCGH analyses focusing on the 45 kb LCRs [1] at the NPHP1 region with diverse copy numbers in humans. Also, the interspecies aCGH analysis comparing human and nonhuman primates revealed dynamic copy number transitions of the human 45 kb LCR orthologues during primate evolution and therefore shed light on the origin of complexity at this locus. The original aCGH data are available at GEO under GSE73962.

%B Genom Data %V 8 %P 106-9 %8 2016 Jun %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/27222811?dopt=Abstract %R 10.1016/j.gdata.2016.04.008 %0 Journal Article %J Am J Hum Genet %D 2016 %T Copy-Number Variation Contributes to the Mutational Load of Bardet-Biedl Syndrome. %A Lindstrand, Anna %A Frangakis, Stephan %A Carvalho, Claudia M B %A Richardson, Ellen B %A McFadden, Kelsey A %A Willer, Jason R %A Pehlivan, Davut %A Liu, Pengfei %A Pediaditakis, Igor L %A Sabo, Aniko %A Lewis, Richard Alan %A Banin, Eyal %A Lupski, James R %A Davis, Erica E %A Katsanis, Nicholas %K Adolescent %K Adult %K Alleles %K Animals %K Bardet-Biedl Syndrome %K Child %K Child, Preschool %K Chromosome Breakpoints %K Cytoskeletal Proteins %K DNA Copy Number Variations %K Exons %K Female %K Gastrulation %K Genes, Recessive %K Humans %K Infant %K Male %K Mutation %K Pedigree %K Young Adult %K Zebrafish %K Zebrafish Proteins %X

Bardet-Biedl syndrome (BBS) is a defining ciliopathy, notable for extensive allelic and genetic heterogeneity, almost all of which has been identified through sequencing. Recent data have suggested that copy-number variants (CNVs) also contribute to BBS. We used a custom oligonucleotide array comparative genomic hybridization (aCGH) covering 20 genes that encode intraflagellar transport (IFT) components and 74 ciliopathy loci to screen 92 unrelated individuals with BBS, irrespective of their known mutational burden. We identified 17 individuals with exon-disruptive CNVs (18.5%), including 13 different deletions in eight BBS genes (BBS1, BBS2, ARL6/BBS3, BBS4, BBS5, BBS7, BBS9, and NPHP1) and a deletion and a duplication in other ciliopathy-associated genes (ALMS1 and NPHP4, respectively). By contrast, we found a single heterozygous exon-disruptive event in a BBS-associated gene (BBS9) in 229 control subjects. Superimposing these data with resequencing revealed CNVs to (1) be sufficient to cause disease, (2) Mendelize heterozygous deleterious alleles, and (3) contribute oligogenic alleles by combining point mutations and exonic CNVs in multiple genes. Finally, we report a deletion and a splice site mutation in IFT74, inherited under a recessive paradigm, defining a candidate BBS locus. Our data suggest that CNVs contribute pathogenic alleles to a substantial fraction of BBS-affected individuals and highlight how either deletions or point mutations in discrete splice isoforms can induce hypomorphic mutations in genes otherwise intolerant to deleterious variation. Our data also suggest that CNV analyses and resequencing studies unbiased for previous mutational burden is necessary to delineate the complexity of disease architecture.

%B Am J Hum Genet %V 99 %P 318-36 %8 2016 Aug 04 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/27486776?dopt=Abstract %R 10.1016/j.ajhg.2015.04.023 %0 Journal Article %J Hum Genet %D 2016 %T De novo missense variants in PPP1CB are associated with intellectual disability and congenital heart disease. %A Ma, Lijiang %A Bayram, Yavuz %A McLaughlin, Heather M %A Cho, Megan T %A Krokosky, Alyson %A Turner, Clesson E %A Lindstrom, Kristin %A Bupp, Caleb P %A Mayberry, Katey %A Mu, Weiyi %A Bodurtha, Joann %A Weinstein, Veronique %A Zadeh, Neda %A Alcaraz, Wendy %A Powis, Zöe %A Shao, Yunru %A Scott, Daryl A %A Lewis, Andrea M %A White, Janson J %A Jhangiani, Shalani N %A Gulec, Elif Yilmaz %A Lalani, Seema R %A Lupski, James R %A Retterer, Kyle %A Schnur, Rhonda E %A Wentzensen, Ingrid M %A Bale, Sherri %A Chung, Wendy K %K Adolescent %K Adult %K Child %K Child, Preschool %K Exome %K Female %K Genetic Association Studies %K Genetic Predisposition to Disease %K Heart Defects, Congenital %K Humans %K Intellectual Disability %K Male %K Mutation, Missense %K Phosphorylation %K Protein Phosphatase 1 %X

Intellectual disabilities are genetically heterogeneous and can be associated with congenital anomalies. Using whole-exome sequencing (WES), we identified five different de novo missense variants in the protein phosphatase-1 catalytic subunit beta (PPP1CB) gene in eight unrelated individuals who share an overlapping phenotype of dysmorphic features, macrocephaly, developmental delay or intellectual disability (ID), congenital heart disease, short stature, and skeletal and connective tissue abnormalities. Protein phosphatase-1 (PP1) is a serine/threonine-specific protein phosphatase involved in the dephosphorylation of a variety of proteins. The PPP1CB gene encodes a PP1 subunit that regulates the level of protein phosphorylation. All five altered amino acids we observed are highly conserved among the PP1 subunit family, and all are predicted to disrupt PP1 subunit binding and impair dephosphorylation. Our data suggest that our heterozygous de novo PPP1CB pathogenic variants are associated with syndromic intellectual disability.

%B Hum Genet %V 135 %P 1399-1409 %8 2016 Dec %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/27681385?dopt=Abstract %R 10.1007/s00439-016-1731-1 %0 Journal Article %J Am J Hum Genet %D 2016 %T DVL3 Alleles Resulting in a -1 Frameshift of the Last Exon Mediate Autosomal-Dominant Robinow Syndrome. %A White, Janson J %A Mazzeu, Juliana F %A Hoischen, Alexander %A Bayram, Yavuz %A Withers, Marjorie %A Gezdirici, Alper %A Kimonis, Virginia %A Steehouwer, Marloes %A Jhangiani, Shalini N %A Muzny, Donna M %A Gibbs, Richard A %A van Bon, Bregje W M %A Sutton, V Reid %A Lupski, James R %A Brunner, Han G %A Carvalho, Claudia M B %K Adaptor Proteins, Signal Transducing %K Alleles %K Base Sequence %K Codon, Nonsense %K Craniofacial Abnormalities %K Dishevelled Proteins %K Dwarfism %K Exons %K Female %K Frameshift Mutation %K Genetic Variation %K Humans %K Limb Deformities, Congenital %K Male %K Molecular Sequence Data %K Phosphoproteins %K Proto-Oncogene Proteins %K Receptor Tyrosine Kinase-like Orphan Receptors %K Sequence Analysis, DNA %K Sequence Deletion %K Urogenital Abnormalities %K Wnt Proteins %K Wnt-5a Protein %X

Robinow syndrome is a rare congenital disorder characterized by mesomelic limb shortening, genital hypoplasia, and distinctive facial features. Recent reports have identified, in individuals with dominant Robinow syndrome, a specific type of variant characterized by being uniformly located in the penultimate exon of DVL1 and resulting in a -1 frameshift allele with a premature termination codon that escapes nonsense-mediated decay. Here, we studied a cohort of individuals who had been clinically diagnosed with Robinow syndrome but who had not received a molecular diagnosis from variant studies of DVL1, WNT5A, and ROR2. Because of the uniform location of frameshift variants in DVL1-mediated Robinow syndrome and the functional redundancy of DVL1, DVL2, and DVL3, we elected to pursue direct Sanger sequencing of the penultimate exon of DVL1 and its paralogs DVL2 and DVL3 to search for potential disease-associated variants. Remarkably, targeted sequencing identified five unrelated individuals harboring heterozygous, de novo frameshift variants in DVL3, including two splice acceptor mutations and three 1 bp deletions. Similar to the variants observed in DVL1-mediated Robinow syndrome, all variants in DVL3 result in a -1 frameshift, indicating that these highly specific alterations might be a common cause of dominant Robinow syndrome. Here, we review the current knowledge of these peculiar variant alleles in DVL1- and DVL3-mediated Robinow syndrome and further elucidate the phenotypic features present in subjects with DVL1 and DVL3 frameshift mutations.

%B Am J Hum Genet %V 98 %P 553-561 %8 2016 Mar 03 %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/26924530?dopt=Abstract %R 10.1016/j.ajhg.2016.01.005 %0 Journal Article %J Trends Genet %D 2016 %T Erratum to: Somatic Mosaicism: Implications for Disease and Transmission Genetics. %A Campbell, Ian M %A Shaw, Chad A %A Stankiewicz, Pawel %A Lupski, James R %B Trends Genet %V 32 %P 138 %8 2016 Feb %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/29482722?dopt=Abstract %R 10.1016/j.tig.2015.07.004 %0 Journal Article %J BMC Med Genomics %D 2016 %T Exome sequencing in mostly consanguineous Arab families with neurologic disease provides a high potential molecular diagnosis rate. %A Charng, Wu-Lin %A Karaca, Ender %A Coban Akdemir, Zeynep %A Gambin, Tomasz %A Atik, Mehmed M %A Gu, Shen %A Posey, Jennifer E %A Jhangiani, Shalini N %A Muzny, Donna M %A Doddapaneni, Harsha %A Hu, Jianhong %A Boerwinkle, Eric %A Gibbs, Richard A %A Rosenfeld, Jill A %A Cui, Hong %A Xia, Fan %A Manickam, Kandamurugu %A Yang, Yaping %A Faqeih, Eissa A %A Al Asmari, Ali %A Saleh, Mohammed A M %A El-Hattab, Ayman W %A Lupski, James R %K Arabs %K Cohort Studies %K Consanguinity %K Data Mining %K Databases, Genetic %K DNA Copy Number Variations %K Exome %K Female %K High-Throughput Nucleotide Sequencing %K Humans %K Male %K Molecular Diagnostic Techniques %K Nervous System Diseases %K Pedigree %K Phenotype %K Polymorphism, Single Nucleotide %K Sequence Analysis, DNA %X

BACKGROUND: Neurodevelopment is orchestrated by a wide range of genes, and the genetic causes of neurodevelopmental disorders are thus heterogeneous. We applied whole exome sequencing (WES) for molecular diagnosis and in silico analysis to identify novel disease gene candidates in a cohort from Saudi Arabia with primarily Mendelian neurologic diseases.

METHODS: We performed WES in 31 mostly consanguineous Arab families and analyzed both single nucleotide and copy number variants (CNVs) from WES data. Interaction/expression network and pathway analyses, as well as paralog studies were utilized to investigate potential pathogenicity and disease association of novel candidate genes. Additional cases for candidate genes were identified through the clinical WES database at Baylor Miraca Genetics Laboratories and GeneMatcher.

RESULTS: We found known pathogenic or novel variants in known disease genes with phenotypic expansion in 6 families, disease-associated CNVs in 2 families, and 12 novel disease gene candidates in 11 families, including KIF5B, GRM7, FOXP4, MLLT1, and KDM2B. Overall, a potential molecular diagnosis was provided by variants in known disease genes in 17 families (54.8 %) and by novel candidate disease genes in an additional 11 families, making the potential molecular diagnostic rate ~90 %.

CONCLUSIONS: Molecular diagnostic rate from WES is improved by exome-predicted CNVs. Novel candidate disease gene discovery is facilitated by paralog studies and through the use of informatics tools and available databases to identify additional evidence for pathogenicity.

TRIAL REGISTRATION: Not applicable.

%B BMC Med Genomics %V 9 %P 42 %8 2016 Jul 19 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/27435318?dopt=Abstract %R 10.1186/s12920-016-0208-3 %0 Journal Article %J Genome Med %D 2016 %T From genomic medicine to precision medicine: highlights of 2015. %A Auffray, Charles %A Caulfield, Timothy %A Griffin, Julian L %A Khoury, Muin J %A Lupski, James R %A Schwab, Matthias %K Genomics %K Humans %K Precision Medicine %K Public Health %B Genome Med %V 8 %P 12 %8 2016 Jan 29 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/26825779?dopt=Abstract %R 10.1186/s13073-016-0265-4 %0 Journal Article %J Acta Neuropathol Commun %D 2016 %T Germline or somatic GPR101 duplication leads to X-linked acrogigantism: a clinico-pathological and genetic study. %A Iacovazzo, Donato %A Caswell, Richard %A Bunce, Benjamin %A Jose, Sian %A Yuan, Bo %A Hernández-Ramírez, Laura C %A Kapur, Sonal %A Caimari, Francisca %A Evanson, Jane %A Ferraù, Francesco %A Dang, Mary N %A Gabrovska, Plamena %A Larkin, Sarah J %A Ansorge, Olaf %A Rodd, Celia %A Vance, Mary L %A Ramírez-Renteria, Claudia %A Mercado, Moisés %A Goldstone, Anthony P %A Buchfelder, Michael %A Burren, Christine P %A Gurlek, Alper %A Dutta, Pinaki %A Choong, Catherine S %A Cheetham, Timothy %A Trivellin, Giampaolo %A Stratakis, Constantine A %A Lopes, Maria-Beatriz %A Grossman, Ashley B %A Trouillas, Jacqueline %A Lupski, James R %A Ellard, Sian %A Sampson, Julian R %A Roncaroli, Federico %A Korbonits, Márta %K Acromegaly %K Adenoma %K Adolescent %K Child %K Child, Preschool %K Female %K Gene Duplication %K Germ-Line Mutation %K Gigantism %K Humans %K Infant %K Intracellular Signaling Peptides and Proteins %K Male %K Pituitary Neoplasms %K Receptors, G-Protein-Coupled %K Treatment Outcome %K Young Adult %X

Non-syndromic pituitary gigantism can result from AIP mutations or the recently identified Xq26.3 microduplication causing X-linked acrogigantism (XLAG). Within Xq26.3, GPR101 is believed to be the causative gene, and the c.924G > C (p.E308D) variant in this orphan G protein-coupled receptor has been suggested to play a role in the pathogenesis of acromegaly.We studied 153 patients (58 females and 95 males) with pituitary gigantism. AIP mutation-negative cases were screened for GPR101 duplication through copy number variation droplet digital PCR and high-density aCGH. The genetic, clinical and histopathological features of XLAG patients were studied in detail. 395 peripheral blood and 193 pituitary tumor DNA samples from acromegaly patients were tested for GPR101 variants.We identified 12 patients (10 females and 2 males; 7.8 %) with XLAG. In one subject, the duplicated region only contained GPR101, but not the other three genes in found to be duplicated in the previously reported patients, defining a new smallest region of overlap of duplications. While females presented with germline mutations, the two male patients harbored the mutation in a mosaic state. Nine patients had pituitary adenomas, while three had hyperplasia. The comparison of the features of XLAG, AIP-positive and GPR101&AIP-negative patients revealed significant differences in sex distribution, age at onset, height, prolactin co-secretion and histological features. The pathological features of XLAG-related adenomas were remarkably similar. These tumors had a sinusoidal and lobular architecture. Sparsely and densely granulated somatotrophs were admixed with lactotrophs; follicle-like structures and calcifications were commonly observed. Patients with sporadic of familial acromegaly did not have an increased prevalence of the c.924G > C (p.E308D) GPR101 variant compared to public databases.In conclusion, XLAG can result from germline or somatic duplication of GPR101. Duplication of GPR101 alone is sufficient for the development of XLAG, implicating it as the causative gene within the Xq26.3 region. The pathological features of XLAG-associated pituitary adenomas are typical and, together with the clinical phenotype, should prompt genetic testing.

%B Acta Neuropathol Commun %V 4 %P 56 %8 2016 Jun 01 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/27245663?dopt=Abstract %R 10.1186/s40478-016-0328-1 %0 Journal Article %J Mol Genet Genomic Med %D 2016 %T Hutterite-type cataract maps to chromosome 6p21.32-p21.31, cosegregates with a homozygous mutation in LEMD2, and is associated with sudden cardiac death. %A Boone, Philip M %A Yuan, Bo %A Gu, Shen %A Ma, Zhiwei %A Gambin, Tomasz %A Gonzaga-Jauregui, Claudia %A Jain, Mahim %A Murdock, Todd J %A White, Janson J %A Jhangiani, Shalini N %A Walker, Kimberly %A Wang, Qiaoyan %A Muzny, Donna M %A Gibbs, Richard A %A Hejtmancik, J Fielding %A Lupski, James R %A Posey, Jennifer E %A Lewis, Richard A %X

BACKGROUND: Juvenile-onset cataracts are known among the Hutterites of North America. Despite being identified over 30 years ago, this autosomal recessive condition has not been mapped, and the disease gene is unknown.

METHODS: We performed whole exome sequencing of three Hutterite-type cataract trios and follow-up genotyping and mapping in four extended kindreds.

RESULTS: Trio exomes enabled genome-wide autozygosity mapping, which localized the disease gene to a 9.5-Mb region on chromosome 6p. This region contained two candidate variants, LEMD2 c.T38G and MUC21 c.665delC. Extended pedigrees recruited for variant genotyping revealed multiple additional relatives with juvenile-onset cataract, as well as six deceased relatives with both cataracts and sudden cardiac death. The candidate variants were genotyped in 84 family members, including 17 with cataracts; only the variant in LEMD2 cosegregated with cataracts (LOD = 9.62). SNP-based fine mapping within the 9.5 Mb linked region supported this finding by refining the cataract locus to a 0.5- to 2.9-Mb subregion (6p21.32-p21.31) containing LEMD2 but not MUC21. LEMD2 is expressed in mouse and human lenses and encodes a LEM domain-containing protein; the c.T38G missense mutation is predicted to mutate a highly conserved residue within this domain (p.Leu13Arg).

CONCLUSION: We performed a genetic and genomic study of Hutterite-type cataract and found evidence for an association of this phenotype with sudden cardiac death. Using combined genetic and genomic approaches, we mapped cataracts to a small portion of chromosome 6 and propose that they result from a homozygous missense mutation in LEMD2.

%B Mol Genet Genomic Med %V 4 %P 77-94 %8 2016 Jan %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/26788539?dopt=Abstract %R 10.1002/mgg3.181 %0 Journal Article %J Genome Med %D 2016 %T Identification of a RAI1-associated disease network through integration of exome sequencing, transcriptomics, and 3D genomics. %A Loviglio, Maria Nicla %A Beck, Christine R %A White, Janson J %A Leleu, Marion %A Harel, Tamar %A Guex, Nicolas %A Niknejad, Anne %A Bi, Weimin %A Chen, Edward S %A Crespo, Isaac %A Yan, Jiong %A Charng, Wu-Lin %A Gu, Shen %A Fang, Ping %A Coban-Akdemir, Zeynep %A Shaw, Chad A %A Jhangiani, Shalini N %A Muzny, Donna M %A Gibbs, Richard A %A Rougemont, Jacques %A Xenarios, Ioannis %A Lupski, James R %A Reymond, Alexandre %K Animals %K Embryo, Mammalian %K Exome %K Female %K Gene Regulatory Networks %K Genomics %K Humans %K Male %K Mice %K Mice, Inbred C57BL %K Mice, Knockout %K Mutation %K Phenotype %K Real-Time Polymerase Chain Reaction %K Reverse Transcriptase Polymerase Chain Reaction %K RNA, Messenger %K Smith-Magenis Syndrome %K Trans-Activators %K Transcription Factors %K Transcriptome %X

BACKGROUND: Smith-Magenis syndrome (SMS) is a developmental disability/multiple congenital anomaly disorder resulting from haploinsufficiency of RAI1. It is characterized by distinctive facial features, brachydactyly, sleep disturbances, and stereotypic behaviors.

METHODS: We investigated a cohort of 15 individuals with a clinical suspicion of SMS who showed neither deletion in the SMS critical region nor damaging variants in RAI1 using whole exome sequencing. A combination of network analysis (co-expression and biomedical text mining), transcriptomics, and circularized chromatin conformation capture (4C-seq) was applied to verify whether modified genes are part of the same disease network as known SMS-causing genes.

RESULTS: Potentially deleterious variants were identified in nine of these individuals using whole-exome sequencing. Eight of these changes affect KMT2D, ZEB2, MAP2K2, GLDC, CASK, MECP2, KDM5C, and POGZ, known to be associated with Kabuki syndrome 1, Mowat-Wilson syndrome, cardiofaciocutaneous syndrome, glycine encephalopathy, mental retardation and microcephaly with pontine and cerebellar hypoplasia, X-linked mental retardation 13, X-linked mental retardation Claes-Jensen type, and White-Sutton syndrome, respectively. The ninth individual carries a de novo variant in JAKMIP1, a regulator of neuronal translation that was recently found deleted in a patient with autism spectrum disorder. Analyses of co-expression and biomedical text mining suggest that these pathologies and SMS are part of the same disease network. Further support for this hypothesis was obtained from transcriptome profiling that showed that the expression levels of both Zeb2 and Map2k2 are perturbed in Rai1 mice. As an orthogonal approach to potentially contributory disease gene variants, we used chromatin conformation capture to reveal chromatin contacts between RAI1 and the loci flanking ZEB2 and GLDC, as well as between RAI1 and human orthologs of the genes that show perturbed expression in our Rai1 mouse model.

CONCLUSIONS: These holistic studies of RAI1 and its interactions allow insights into SMS and other disorders associated with intellectual disability and behavioral abnormalities. Our findings support a pan-genomic approach to the molecular diagnosis of a distinctive disorder.

%B Genome Med %V 8 %P 105 %8 2016 Nov 01 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/27799067?dopt=Abstract %R 10.1186/s13073-016-0359-z %0 Journal Article %J Hum Mutat %D 2016 %T Identification of Intellectual Disability Genes in Female Patients with a Skewed X-Inactivation Pattern. %A Fieremans, Nathalie %A Van Esch, Hilde %A Holvoet, Maureen %A Van Goethem, Gert %A Devriendt, Koenraad %A Rosello, Monica %A Mayo, Sonia %A Martinez, Francisco %A Jhangiani, Shalini %A Muzny, Donna M %A Gibbs, Richard A %A Lupski, James R %A Vermeesch, Joris R %A Marynen, Peter %A Froyen, Guy %K Carrier Proteins %K Cell Cycle Proteins %K Chromosomal Proteins, Non-Histone %K DEAD-box RNA Helicases %K Exome %K Female %K Genetic Variation %K Humans %K Intellectual Disability %K Membrane Proteins %K Methyl-CpG-Binding Protein 2 %K Nuclear Proteins %K Sequence Analysis, DNA %K X Chromosome Inactivation %X

Intellectual disability (ID) is a heterogeneous disorder with an unknown molecular etiology in many cases. Previously, X-linked ID (XLID) studies focused on males because of the hemizygous state of their X chromosome. Carrier females are generally unaffected because of the presence of a second normal allele, or inactivation of the mutant X chromosome in most of their cells (skewing). However, in female ID patients, we hypothesized that the presence of skewing of X-inactivation would be an indicator for an X chromosomal ID cause. We analyzed the X-inactivation patterns of 288 females with ID, and found that 22 (7.6%) had extreme skewing (>90%), which is significantly higher than observed in the general population (3.6%; P = 0.029). Whole-exome sequencing of 19 females with extreme skewing revealed causal variants in six females in the XLID genes DDX3X, NHS, WDR45, MECP2, and SMC1A. Interestingly, variants in genes escaping X-inactivation presumably cause both XLID and skewing of X-inactivation in three of these patients. Moreover, variants likely accounting for skewing only were detected in MED12, HDAC8, and TAF9B. All tested candidate causative variants were de novo events. Hence, extreme skewing is a good indicator for the presence of X-linked variants in female patients.

%B Hum Mutat %V 37 %P 804-11 %8 2016 Aug %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/27159028?dopt=Abstract %R 10.1002/humu.23012 %0 Journal Article %J PLoS Genet %D 2016 %T Mechanisms for Complex Chromosomal Insertions. %A Gu, Shen %A Szafranski, Przemyslaw %A Akdemir, Zeynep Coban %A Yuan, Bo %A Cooper, Mitchell L %A Magriñá, Maria A %A Bacino, Carlos A %A Lalani, Seema R %A Breman, Amy M %A Smith, Janice L %A Patel, Ankita %A Song, Rodger H %A Bi, Weimin %A Cheung, Sau Wai %A Carvalho, Claudia M B %A Stankiewicz, Paweł %A Lupski, James R %K Chromosome Aberrations %K Chromosome Inversion %K Comparative Genomic Hybridization %K DNA Copy Number Variations %K DNA Replication %K Female %K Gene Duplication %K Genome, Human %K Humans %K In Situ Hybridization, Fluorescence %K Male %K Sequence Analysis, DNA %K Translocation, Genetic %X

Chromosomal insertions are genomic rearrangements with a chromosome segment inserted into a non-homologous chromosome or a non-adjacent locus on the same chromosome or the other homologue, constituting ~2% of nonrecurrent copy-number gains. Little is known about the molecular mechanisms of their formation. We identified 16 individuals with complex insertions among 56,000 individuals tested at Baylor Genetics using clinical array comparative genomic hybridization (aCGH) and fluorescence in situ hybridization (FISH). Custom high-density aCGH was performed on 10 individuals with available DNA, and breakpoint junctions were fine-mapped at nucleotide resolution by long-range PCR and DNA sequencing in 6 individuals to glean insights into potential mechanisms of formation. We observed microhomologies and templated insertions at the breakpoint junctions, resembling the breakpoint junction signatures found in complex genomic rearrangements generated by replication-based mechanism(s) with iterative template switches. In addition, we analyzed 5 families with apparently balanced insertion in one parent detected by FISH analysis and found that 3 parents had additional small copy-number variants (CNVs) at one or both sides of the inserting fragments as well as at the inserted sites. We propose that replicative repair can result in interchromosomal complex insertions generated through chromothripsis-like chromoanasynthesis involving two or three chromosomes, and cause a significant fraction of apparently balanced insertions harboring small flanking CNVs.

%B PLoS Genet %V 12 %P e1006446 %8 2016 Nov %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/27880765?dopt=Abstract %R 10.1371/journal.pgen.1006446 %0 Journal Article %J Hum Mutat %D 2016 %T Mechanisms for the Generation of Two Quadruplications Associated with Split-Hand Malformation. %A Gu, Shen %A Posey, Jennifer E %A Yuan, Bo %A Carvalho, Claudia M B %A Luk, H M %A Erikson, Kelly %A Lo, Ivan F M %A Leung, Gordon K C %A Pickering, Curtis R %A Chung, Brian H Y %A Lupski, James R %K 14-3-3 Proteins %K Adult %K Aged %K Alu Elements %K Base Sequence %K Basic Helix-Loop-Helix Transcription Factors %K Chromosome Duplication %K Chromosomes, Human, Pair 17 %K DNA Copy Number Variations %K Female %K Genetic Loci %K Genome, Human %K Hand Deformities, Congenital %K Humans %K Infant %K Male %K Molecular Sequence Data %K Pedigree %K Sequence Alignment %K Sequence Analysis, DNA %X

Germline copy-number variants (CNVs) involving quadruplications are rare and the mechanisms generating them are largely unknown. Previously, we reported a 20-week gestation fetus with split-hand malformation; clinical microarray detected two maternally inherited triplications separated by a copy-number neutral region at 17p13.3, involving BHLHA9 and part of YWHAE. Here, we describe an 18-month-old male sibling of the previously described fetus with split-hand malformation. Custom high-density microarray and digital droplet PCR revealed the copy-number gains were actually quadruplications in the mother, the fetus, and her later born son. This quadruplication-normal-quadruplication pattern was shown to be expanded from the triplication-normal-triplication CNV at the same loci in the maternal grandmother. We mapped two breakpoint junctions and demonstrated that both are mediated by Alu repetitive elements and identical in these four individuals. We propose a three-step process combining Alu-mediated replicative-repair-based mechanism(s) and intergenerational, intrachromosomal nonallelic homologous recombination to generate the quadruplications in this family.

%B Hum Mutat %V 37 %P 160-4 %8 2016 Feb %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/26549411?dopt=Abstract %R 10.1002/humu.22929 %0 Journal Article %J Nat Rev Genet %D 2016 %T Mechanisms underlying structural variant formation in genomic disorders. %A Carvalho, Claudia M B %A Lupski, James R %K Gene Rearrangement %K Genetic Diseases, Inborn %K Genetic Predisposition to Disease %K Genetic Variation %K Genome, Human %K Genomic Instability %K Homologous Recombination %K Humans %K Models, Genetic %K Mutation %K Repetitive Sequences, Nucleic Acid %X

With the recent burst of technological developments in genomics, and the clinical implementation of genome-wide assays, our understanding of the molecular basis of genomic disorders, specifically the contribution of structural variation to disease burden, is evolving quickly. Ongoing studies have revealed a ubiquitous role for genome architecture in the formation of structural variants at a given locus, both in DNA recombination-based processes and in replication-based processes. These reports showcase the influence of repeat sequences on genomic stability and structural variant complexity and also highlight the tremendous plasticity and dynamic nature of our genome in evolution, health and disease susceptibility.

%B Nat Rev Genet %V 17 %P 224-38 %8 2016 Apr %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/26924765?dopt=Abstract %R 10.1038/nrg.2015.25 %0 Journal Article %J Genome Med %D 2016 %T MIPEP recessive variants cause a syndrome of left ventricular non-compaction, hypotonia, and infantile death. %A Eldomery, Mohammad K %A Akdemir, Zeynep C %A Vögtle, F-Nora %A Charng, Wu-Lin %A Mulica, Patrycja %A Rosenfeld, Jill A %A Gambin, Tomasz %A Gu, Shen %A Burrage, Lindsay C %A Al Shamsi, Aisha %A Penney, Samantha %A Jhangiani, Shalini N %A Zimmerman, Holly H %A Muzny, Donna M %A Wang, Xia %A Tang, Jia %A Medikonda, Ravi %A Ramachandran, Prasanna V %A Wong, Lee-Jun %A Boerwinkle, Eric %A Gibbs, Richard A %A Eng, Christine M %A Lalani, Seema R %A Hertecant, Jozef %A Rodenburg, Richard J %A Abdul-Rahman, Omar A %A Yang, Yaping %A Xia, Fan %A Wang, Meng C %A Lupski, James R %A Meisinger, Chris %A Sutton, V Reid %K Adult %K Amino Acid Sequence %K Female %K Genes, Recessive %K Heart Defects, Congenital %K Humans %K Infant %K Infant, Newborn %K Male %K Metalloendopeptidases %K Muscle Hypotonia %K Pedigree %K Phenotype %K Sequence Homology, Amino Acid %K Sudden Infant Death %K Syndrome %X

BACKGROUND: Mitochondrial presequence proteases perform fundamental functions as they process about 70 % of all mitochondrial preproteins that are encoded in the nucleus and imported posttranslationally. The mitochondrial intermediate presequence protease MIP/Oct1, which carries out precursor processing, has not yet been established to have a role in human disease.

METHODS: Whole exome sequencing was performed on four unrelated probands with left ventricular non-compaction (LVNC), developmental delay (DD), seizures, and severe hypotonia. Proposed pathogenic variants were confirmed by Sanger sequencing or array comparative genomic hybridization. Functional analysis of the identified MIP variants was performed using the model organism Saccharomyces cerevisiae as the protein and its functions are highly conserved from yeast to human.

RESULTS: Biallelic single nucleotide variants (SNVs) or copy number variants (CNVs) in MIPEP, which encodes MIP, were present in all four probands, three of whom had infantile/childhood death. Two patients had compound heterozygous SNVs (p.L582R/p.L71Q and p.E602*/p.L306F) and one patient from a consanguineous family had a homozygous SNV (p.K343E). The fourth patient, identified through the GeneMatcher tool, a part of the Matchmaker Exchange Project, was found to have inherited a paternal SNV (p.H512D) and a maternal CNV (1.4-Mb deletion of 13q12.12) that includes MIPEP. All amino acids affected in the patients' missense variants are highly conserved from yeast to human and therefore S. cerevisiae was employed for functional analysis (for p.L71Q, p.L306F, and p.K343E). The mutations p.L339F (human p.L306F) and p.K376E (human p.K343E) resulted in a severe decrease of Oct1 protease activity and accumulation of non-processed Oct1 substrates and consequently impaired viability under respiratory growth conditions. The p.L83Q (human p.L71Q) failed to localize to the mitochondria.

CONCLUSIONS: Our findings reveal for the first time the role of the mitochondrial intermediate peptidase in human disease. Loss of MIP function results in a syndrome which consists of LVNC, DD, seizures, hypotonia, and cataracts. Our approach highlights the power of data exchange and the importance of an interrelationship between clinical and research efforts for disease gene discovery.

%B Genome Med %V 8 %P 106 %8 2016 Nov 01 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/27799064?dopt=Abstract %R 10.1186/s13073-016-0360-6 %0 Journal Article %J Genet Med %D 2016 %T Molecular diagnostic experience of whole-exome sequencing in adult patients. %A Posey, Jennifer E %A Rosenfeld, Jill A %A James, Regis A %A Bainbridge, Matthew %A Niu, Zhiyv %A Wang, Xia %A Dhar, Shweta %A Wiszniewski, Wojciech %A Akdemir, Zeynep H C %A Gambin, Tomasz %A Xia, Fan %A Person, Richard E %A Walkiewicz, Magdalena %A Shaw, Chad A %A Sutton, V Reid %A Beaudet, Arthur L %A Muzny, Donna %A Eng, Christine M %A Yang, Yaping %A Gibbs, Richard A %A Lupski, James R %A Boerwinkle, Eric %A Plon, Sharon E %K Adult %K Exome %K Female %K Genetic Diseases, Inborn %K Genetic Predisposition to Disease %K Genetic Testing %K Genome, Human %K High-Throughput Nucleotide Sequencing %K Humans %K Male %K Pathology, Molecular %X

PURPOSE: Whole-exome sequencing (WES) is increasingly used as a diagnostic tool in medicine, but prior reports focus on predominantly pediatric cohorts with neurologic or developmental disorders. We describe the diagnostic yield and characteristics of WES in adults.

METHODS: We performed a retrospective analysis of consecutive WES reports for adults from a diagnostic laboratory. Phenotype composition was determined using Human Phenotype Ontology terms.

RESULTS: Molecular diagnoses were reported for 17.5% (85/486) of adults, which is lower than that for a primarily pediatric population (25.2%; P = 0.0003); the diagnostic rate was higher (23.9%) for those 18-30 years of age compared to patients older than 30 years (10.4%; P = 0.0001). Dual Mendelian diagnoses contributed to 7% of diagnoses, revealing blended phenotypes. Diagnoses were more frequent among individuals with abnormalities of the nervous system, skeletal system, head/neck, and growth. Diagnostic rate was independent of family history information, and de novo mutations contributed to 61.4% of autosomal dominant diagnoses.

CONCLUSION: Early WES experience in adults demonstrates molecular diagnoses in a substantial proportion of patients, informing clinical management, recurrence risk, and recommendations for relatives. A positive family history was not predictive, consistent with molecular diagnoses often revealed by de novo events, informing the Mendelian basis of genetic disease in adults.Genet Med 18 7, 678-685.

%B Genet Med %V 18 %P 678-85 %8 2016 Jul %G eng %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/26633545?dopt=Abstract %R 10.1038/gim.2015.142 %0 Journal Article %J Am J Hum Genet %D 2016 %T Monoallelic and Biallelic Variants in EMC1 Identified in Individuals with Global Developmental Delay, Hypotonia, Scoliosis, and Cerebellar Atrophy. %A Harel, Tamar %A Yesil, Gozde %A Bayram, Yavuz %A Coban-Akdemir, Zeynep %A Charng, Wu-Lin %A Karaca, Ender %A Al Asmari, Ali %A Eldomery, Mohammad K %A Hunter, Jill V %A Jhangiani, Shalini N %A Rosenfeld, Jill A %A Pehlivan, Davut %A El-Hattab, Ayman W %A Saleh, Mohammed A %A LeDuc, Charles A %A Muzny, Donna %A Boerwinkle, Eric %A Gibbs, Richard A %A Chung, Wendy K %A Yang, Yaping %A Belmont, John W %A Lupski, James R %K Adolescent %K Alleles %K Amino Acid Sequence %K Atrophy %K Cerebellum %K Child %K Child, Preschool %K Developmental Disabilities %K Endoplasmic Reticulum-Associated Degradation %K Female %K Genetic Association Studies %K Genetic Variation %K Heterozygote %K Humans %K Magnetic Resonance Imaging %K Male %K Membrane Proteins %K Molecular Sequence Data %K Muscle Hypotonia %K Mutation %K Pedigree %K Protein Folding %K Proteins %K Scoliosis %X

The paradigm of a single gene associated with one specific phenotype and mode of inheritance has been repeatedly challenged. Genotype-phenotype correlations can often be traced to different mutation types, localization of the variants in distinct protein domains, or the trigger of or escape from nonsense-mediated decay. Using whole-exome sequencing, we identified homozygous variants in EMC1 that segregated with a phenotype of developmental delay, hypotonia, scoliosis, and cerebellar atrophy in three families. In addition, a de novo heterozygous EMC1 variant was seen in an individual with a similar clinical and MRI imaging phenotype. EMC1 encodes a member of the endoplasmic reticulum (ER)-membrane protein complex (EMC), an evolutionarily conserved complex that has been proposed to have multiple roles in ER-associated degradation, ER-mitochondria tethering, and proper assembly of multi-pass transmembrane proteins. Perturbations of protein folding and organelle crosstalk have been implicated in neurodegenerative processes including cerebellar atrophy. We propose EMC1 as a gene in which either biallelic or monoallelic variants might lead to a syndrome including intellectual disability and preferential degeneration of the cerebellum.

%B Am J Hum Genet %V 98 %P 562-570 %8 2016 Mar 03 %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/26942288?dopt=Abstract %R 10.1016/j.ajhg.2016.01.011 %0 Journal Article %J Hum Mutat %D 2016 %T Multiallelic Positions in the Human Genome: Challenges for Genetic Analyses. %A Campbell, Ian M %A Gambin, Tomasz %A Jhangiani, Shalini %A Grove, Megan L %A Veeraraghavan, Narayanan %A Donna M Muzny %A Shaw, Chad A %A Richard A Gibbs %A Eric Boerwinkle %A Fuli Yu %A Lupski, James R %K Alleles %K Exome %K Genome, Human %K Humans %X

As the amount of human genomic sequence available from personal genomes and exomes has increased, so too has the observation of genomic positions having two or more alternative alleles, so-called multiallelic sites. For portions of the haploid genome that are present in more than one copy, including segmental duplications, variation at such multisite variant positions becomes even more complex. Despite the frequency of multiallelic variants, a number of commonly used resources and tools in genomic research and diagnostics do not support these multiallelic variants all together or require special modifications. Here, we explore the frequency of multiallelic sites in large samples with whole exome sequencing and discuss potential outcomes of failing to account for multiple variant alleles. We also briefly discuss some commonly utilized resources that fully support multiallelic sites.

%B Hum Mutat %V 37 %P 231-234 %8 2016 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/26670213?dopt=Abstract %R 10.1002/humu.22944 %0 Journal Article %J Nat Commun %D 2016 %T Mutations in the nuclear bile acid receptor FXR cause progressive familial intrahepatic cholestasis. %A Gomez-Ospina, Natalia %A Potter, Carol J %A Xiao, Rui %A Manickam, Kandamurugu %A Kim, Mi-Sun %A Kim, Kang Ho %A Shneider, Benjamin L %A Picarsic, Jennifer L %A Jacobson, Theodora A %A Zhang, Jing %A He, Weimin %A Liu, Pengfei %A Knisely, A S %A Finegold, Milton J %A Muzny, Donna M %A Boerwinkle, Eric %A Lupski, James R %A Plon, Sharon E %A Gibbs, Richard A %A Eng, Christine M %A Yang, Yaping %A Washington, Gabriel C %A Porteus, Matthew H %A Berquist, William E %A Kambham, Neeraja %A Singh, Ravinder J %A Xia, Fan %A Enns, Gregory M %A Moore, David D %K ATP Binding Cassette Transporter, Subfamily B, Member 11 %K ATP-Binding Cassette Transporters %K Bile Acids and Salts %K Cholestasis, Intrahepatic %K Female %K Humans %K Male %K Mutation %K Receptors, Cytoplasmic and Nuclear %K Young Adult %X

Neonatal cholestasis is a potentially life-threatening condition requiring prompt diagnosis. Mutations in several different genes can cause progressive familial intrahepatic cholestasis, but known genes cannot account for all familial cases. Here we report four individuals from two unrelated families with neonatal cholestasis and mutations in NR1H4, which encodes the farnesoid X receptor (FXR), a bile acid-activated nuclear hormone receptor that regulates bile acid metabolism. Clinical features of severe, persistent NR1H4-related cholestasis include neonatal onset with rapid progression to end-stage liver disease, vitamin K-independent coagulopathy, low-to-normal serum gamma-glutamyl transferase activity, elevated serum alpha-fetoprotein and undetectable liver bile salt export pump (ABCB11) expression. Our findings demonstrate a pivotal function for FXR in bile acid homeostasis and liver protection.

%B Nat Commun %V 7 %P 10713 %8 2016 Feb 18 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/26888176?dopt=Abstract %R 10.1038/ncomms10713 %0 Journal Article %J Hum Genet %D 2016 %T Nonrecurrent PMP22-RAI1 contiguous gene deletions arise from replication-based mechanisms and result in Smith-Magenis syndrome with evident peripheral neuropathy. %A Yuan, Bo %A Neira, Juanita %A Gu, Shen %A Harel, Tamar %A Liu, Pengfei %A Briceño, Ignacio %A Elsea, Sarah H %A Gómez, Alberto %A Potocki, Lorraine %A Lupski, James R %K Adolescent %K Adult %K Child %K Child, Preschool %K Chromosomes, Human, Pair 17 %K DNA Copy Number Variations %K DNA Replication %K Female %K Gene Deletion %K Haploinsufficiency %K Homologous Recombination %K Humans %K Intellectual Disability %K Male %K Mutation %K Myelin Proteins %K Smith-Magenis Syndrome %K Trans-Activators %K Transcription Factors %X

Hereditary neuropathy with liability to pressure palsies (HNPP) and Smith-Magenis syndrome (SMS) are genomic disorders associated with deletion copy number variants involving chromosome 17p12 and 17p11.2, respectively. Nonallelic homologous recombination (NAHR)-mediated recurrent deletions are responsible for the majority of HNPP and SMS cases; the rearrangement products encompass the key dosage-sensitive genes PMP22 and RAI1, respectively, and result in haploinsufficiency for these genes. Less frequently, nonrecurrent genomic rearrangements occur at this locus. Contiguous gene duplications encompassing both PMP22 and RAI1, i.e., PMP22-RAI1 duplications, have been investigated, and replication-based mechanisms rather than NAHR have been proposed for these rearrangements. In the current study, we report molecular and clinical characterizations of six subjects with the reciprocal phenomenon of deletions spanning both genes, i.e., PMP22-RAI1 deletions. Molecular studies utilizing high-resolution array comparative genomic hybridization and breakpoint junction sequencing identified mutational signatures that were suggestive of replication-based mechanisms. Systematic clinical studies revealed features consistent with SMS, including features of intellectual disability, speech and gross motor delays, behavioral problems and ocular abnormalities. Five out of six subjects presented clinical signs and/or objective electrophysiologic studies of peripheral neuropathy. Clinical profiling may improve the clinical management of this unique group of subjects, as the peripheral neuropathy can be more severe or of earlier onset as compared to SMS patients having the common recurrent deletion. Moreover, the current study, in combination with the previous report of PMP22-RAI1 duplications, contributes to the understanding of rare complex phenotypes involving multiple dosage-sensitive genes from a genetic mechanistic standpoint.

%B Hum Genet %V 135 %P 1161-74 %8 2016 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/27386852?dopt=Abstract %R 10.1007/s00439-016-1703-5 %0 Journal Article %J Eur J Hum Genet %D 2016 %T Novel genetic causes for cerebral visual impairment. %A Bosch, Daniëlle G M %A Boonstra, F Nienke %A de Leeuw, Nicole %A Pfundt, Rolph %A Nillesen, Willy M %A de Ligt, Joep %A Gilissen, Christian %A Jhangiani, Shalini %A Lupski, James R %A Cremers, Frans P M %A de Vries, Bert B A %K Adolescent %K Blindness, Cortical %K Child %K Child, Preschool %K Female %K Genetic Loci %K Humans %K Male %K Polymorphism, Single Nucleotide %K Young Adult %X

Cerebral visual impairment (CVI) is a major cause of low vision in children due to impairment in projection and/or interpretation of the visual input in the brain. Although acquired causes for CVI are well known, genetic causes underlying CVI are largely unidentified. DNAs of 25 patients with CVI and intellectual disability, but without acquired (eg, perinatal) damage, were investigated by whole-exome sequencing. The data were analyzed for de novo, autosomal-recessive, and X-linked variants, and subsequently classified into known, candidate, or unlikely to be associated with CVI. This classification was based on the Online Mendelian Inheritance in Man database, literature reports, variant characteristics, and functional relevance of the gene. After classification, variants in four genes known to be associated with CVI (AHDC1, NGLY1, NR2F1, PGAP1) in 5 patients (20%) were identified, establishing a conclusive genetic diagnosis for CVI. In addition, in 11 patients (44%) with CVI, variants in one or more candidate genes were identified (ACP6, AMOT, ARHGEF10L, ATP6V1A, DCAF6, DLG4, GABRB2, GRIN1, GRIN2B, KCNQ3, KCTD19, RERE, SLC1A1, SLC25A16, SLC35A2, SOX5, UFSP2, UHMK1, ZFP30). Our findings show that diverse genetic causes underlie CVI, some of which will provide insight into the biology underlying this disease process.

%B Eur J Hum Genet %V 24 %P 660-5 %8 2016 May %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/26350515?dopt=Abstract %R 10.1038/ejhg.2015.186 %0 Journal Article %J Genet Med %D 2016 %T Novel mutations in LRP6 highlight the role of WNT signaling in tooth agenesis. %A Ockeloen, Charlotte W %A Khandelwal, Kriti D %A Dreesen, Karoline %A Ludwig, Kerstin U %A Sullivan, Robert %A van Rooij, Iris A L M %A Thonissen, Michelle %A Swinnen, Steven %A Phan, Milien %A Conte, Federica %A Ishorst, Nina %A Gilissen, Christian %A RoaFuentes, Laury %A van de Vorst, Maartje %A Henkes, Arjen %A Steehouwer, Marloes %A van Beusekom, Ellen %A Bloemen, Marjon %A Vankeirsbilck, Bruno %A Bergé, Stefaan %A Hens, Greet %A Schoenaers, Joseph %A Poorten, Vincent Vander %A Roosenboom, Jasmien %A Verdonck, An %A Devriendt, Koen %A Roeleveldt, Nel %A Jhangiani, Shalini N %A Vissers, Lisenka E L M %A Lupski, James R %A de Ligt, Joep %A Von den Hoff, Johannes W %A Pfundt, Rolph %A Brunner, Han G %A Zhou, Huiqing %A Dixon, Jill %A Mangold, Elisabeth %A van Bokhoven, Hans %A Dixon, Michael J %A Kleefstra, Tjitske %A Hoischen, Alexander %A Carels, Carine E L %K Adolescent %K Anodontia %K Child %K Exome %K Female %K Frameshift Mutation %K Genetic Predisposition to Disease %K Humans %K Low Density Lipoprotein Receptor-Related Protein-6 %K Male %K Mutation, Missense %K Pedigree %K Sequence Analysis, DNA %K Wnt Signaling Pathway %X

PURPOSE: We aimed to identify a novel genetic cause of tooth agenesis (TA) and/or orofacial clefting (OFC) by combining whole-exome sequencing (WES) and targeted resequencing in a large cohort of TA and OFC patients.

METHODS: WES was performed in two unrelated patients: one with severe TA and OFC and another with severe TA only. After deleterious mutations were identified in a gene encoding low-density lipoprotein receptor-related protein 6 (LRP6), all its exons were resequenced with molecular inversion probes in 67 patients with TA, 1,072 patients with OFC, and 706 controls.

RESULTS: We identified a frameshift (c.4594delG, p.Cys1532fs) and a canonical splice-site mutation (c.3398-2A>C, p.?) in LRP6, respectively, in the patient with TA and OFC and in the patient with severe TA only. The targeted resequencing showed significant enrichment of unique LRP6 variants in TA patients but not in nonsyndromic OFC patients. Of the five variants in patients with TA, two affected the canonical splice site and three were missense variants; all variants segregated with the dominant phenotype, and in one case the missense mutation occurred de novo.

CONCLUSION: Mutations in LRP6 cause TA in humans.Genet Med 18 11, 1158-1162.

%B Genet Med %V 18 %P 1158-1162 %8 2016 Nov %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/26963285?dopt=Abstract %R 10.1038/gim.2016.10 %0 Journal Article %J Hum Genet %D 2016 %T Pathogenetics of alveolar capillary dysplasia with misalignment of pulmonary veins. %A Szafranski, Przemyslaw %A Gambin, Tomasz %A Dharmadhikari, Avinash V %A Akdemir, Kadir Caner %A Jhangiani, Shalini N %A Schuette, Jennifer %A Godiwala, Nihal %A Yatsenko, Svetlana A %A Sebastian, Jessica %A Madan-Khetarpal, Suneeta %A Surti, Urvashi %A Abellar, Rosanna G %A Bateman, David A %A Wilson, Ashley L %A Markham, Melinda H %A Slamon, Jill %A Santos-Simarro, Fernando %A Palomares, María %A Nevado, Julián %A Lapunzina, Pablo %A Chung, Brian Hon-Yin %A Wong, Wai-Lap %A Chu, Yoyo Wing Yiu %A Mok, Gary Tsz Kin %A Kerem, Eitan %A Reiter, Joel %A Ambalavanan, Namasivayam %A Anderson, Scott A %A Kelly, David R %A Shieh, Joseph %A Rosenthal, Taryn C %A Scheible, Kristin %A Steiner, Laurie %A Iqbal, M Anwar %A McKinnon, Margaret L %A Hamilton, Sara Jane %A Schlade-Bartusiak, Kamilla %A English, Dawn %A Hendson, Glenda %A Roeder, Elizabeth R %A DeNapoli, Thomas S %A Littlejohn, Rebecca Okashah %A Wolff, Daynna J %A Wagner, Carol L %A Yeung, Alison %A Francis, David %A Fiorino, Elizabeth K %A Edelman, Morris %A Fox, Joyce %A Hayes, Denise A %A Janssens, Sandra %A De Baere, Elfride %A Menten, Björn %A Loccufier, Anne %A Vanwalleghem, Lieve %A Moerman, Philippe %A Sznajer, Yves %A Lay, Amy S %A Kussmann, Jennifer L %A Chawla, Jasneek %A Payton, Diane J %A Phillips, Gael E %A Brosens, Erwin %A Tibboel, Dick %A de Klein, Annelies %A Maystadt, Isabelle %A Fisher, Richard %A Sebire, Neil %A Male, Alison %A Chopra, Maya %A Pinner, Jason %A Malcolm, Girvan %A Peters, Gregory %A Arbuckle, Susan %A Lees, Melissa %A Mead, Zoe %A Quarrell, Oliver %A Sayers, Richard %A Owens, Martina %A Shaw-Smith, Charles %A Lioy, Janet %A McKay, Eileen %A de Leeuw, Nicole %A Feenstra, Ilse %A Spruijt, Liesbeth %A Elmslie, Frances %A Thiruchelvam, Timothy %A Bacino, Carlos A %A Langston, Claire %A Lupski, James R %A Sen, Partha %A Popek, Edwina %A Stankiewicz, Paweł %K Chromosomes, Human, Pair 16 %K Comparative Genomic Hybridization %K Female %K Forkhead Transcription Factors %K Genes, Lethal %K Genome, Human %K Genomic Imprinting %K High-Throughput Nucleotide Sequencing %K Humans %K Infant, Newborn %K Male %K Pedigree %K Persistent Fetal Circulation Syndrome %K Pulmonary Alveoli %K Pulmonary Veins %K Sequence Deletion %X

Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) is a lethal lung developmental disorder caused by heterozygous point mutations or genomic deletion copy-number variants (CNVs) of FOXF1 or its upstream enhancer involving fetal lung-expressed long noncoding RNA genes LINC01081 and LINC01082. Using custom-designed array comparative genomic hybridization, Sanger sequencing, whole exome sequencing (WES), and bioinformatic analyses, we studied 22 new unrelated families (20 postnatal and two prenatal) with clinically diagnosed ACDMPV. We describe novel deletion CNVs at the FOXF1 locus in 13 unrelated ACDMPV patients. Together with the previously reported cases, all 31 genomic deletions in 16q24.1, pathogenic for ACDMPV, for which parental origin was determined, arose de novo with 30 of them occurring on the maternally inherited chromosome 16, strongly implicating genomic imprinting of the FOXF1 locus in human lungs. Surprisingly, we have also identified four ACDMPV families with the pathogenic variants in the FOXF1 locus that arose on paternal chromosome 16. Interestingly, a combination of the severe cardiac defects, including hypoplastic left heart, and single umbilical artery were observed only in children with deletion CNVs involving FOXF1 and its upstream enhancer. Our data demonstrate that genomic imprinting at 16q24.1 plays an important role in variable ACDMPV manifestation likely through long-range regulation of FOXF1 expression, and may be also responsible for key phenotypic features of maternal uniparental disomy 16. Moreover, in one family, WES revealed a de novo missense variant in ESRP1, potentially implicating FGF signaling in the etiology of ACDMPV.

%B Hum Genet %V 135 %P 569-586 %8 2016 May %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/27071622?dopt=Abstract %R 10.1007/s00439-016-1655-9 %0 Journal Article %J Pediatr Neurol %D 2016 %T PEHO Syndrome May Represent Phenotypic Expansion at the Severe End of the Early-Onset Encephalopathies. %A Gawlinski, Pawel %A Posmyk, Renata %A Gambin, Tomasz %A Sielicka, Danuta %A Chorazy, Monika %A Nowakowska, Beata %A Jhangiani, Shalini N %A Muzny, Donna M %A Bekiesinska-Figatowska, Monika %A Bal, Jerzy %A Boerwinkle, Eric %A Gibbs, Richard A %A Lupski, James R %A Wiszniewski, Wojciech %K Brain Edema %K Child %K Child, Preschool %K Female %K GTP-Binding Protein alpha Subunits, Gi-Go %K Humans %K Infant %K Male %K Mutation %K Neurodegenerative Diseases %K Optic Atrophy %K Phenotype %K Protein Serine-Threonine Kinases %K Spasms, Infantile %X

BACKGROUND: Progressive encephalopathy with edema, hypsarrhythmia and optic atrophy (PEHO) syndrome is a distinct neurodevelopmental disorder. Patients without optic nerve atrophy and brain imaging abnormalities but fulfilling other PEHO criteria are often described as a PEHO-like syndrome. The molecular bases of both clinically defined conditions remain unknown in spite of the widespread application of genome analyses in both clinic and research.

METHODS: We enrolled two patients with a prior diagnosis of PEHO and two individuals with PEHO-like syndrome. All four individuals subsequently underwent whole-exome sequencing and comprehensive genomic analysis.

RESULTS: We identified disease-causing mutations in known genes associated with neurodevelopmental disorders including GNAO1 and CDKL5 in two of four individuals. One patient with PEHO syndrome and a de novoGNAO1 mutation was found to have an additional de novo mutation in HESX1 that is associated with optic atrophy.

CONCLUSIONS: We hypothesize that PEHO and PEHO-like syndrome may represent a severe end of the spectrum of the early-onset encephalopathies and, in some instances, its complex phenotype may result from an aggregated effect of mutations at two loci.

%B Pediatr Neurol %V 60 %P 83-7 %8 2016 Jul %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/27343026?dopt=Abstract %R 10.1016/j.pediatrneurol.2016.03.011 %0 Journal Article %J JIMD Rep %D 2016 %T Phenotypic Expansion of Congenital Disorder of Glycosylation Due to SRD5A3 Null Mutation. %A Tuysuz, Beyhan %A Pehlivan, Davut %A Özkök, Ahmet %A Jhangiani, Shalini %A Yalcinkaya, Cengiz %A Zeybek, Çiğdem Aktuğlu %A Muzny, Donna Marie %A Lupski, James R %A Gibbs, Richard %A Jaeken, Jaak %X

We present a boy, admitted at 4 months, with facial dysmorphism, hypertrichosis, loose skin, bilateral inguinal hernia, severe hypotonia, psychomotor disability, seizures with hypsarrhythmia (West syndrome), hepatosplenomegaly, increased serum transaminases, iris coloboma, glaucoma, corneal clouding and bilateral dilated lateral ventricles, and extra-axial post-cerebellar space. Serum transferrin isoelectrofocusing (IEF) showed a type 1 pattern. Whole-exome genotyping showed a previously reported homozygous nonsense mutation c.320G>A; p.Trp107X in SRD5A3. Epilepsy and glaucoma have been reported only once in the 19 described SRD5A3-congenital glycosylation defect patients, and corneal clouding not at all.

%B JIMD Rep %V 26 %P 7-12 %8 2016 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/26219881?dopt=Abstract %R 10.1007/8904_2015_478 %0 Journal Article %J Am J Med Genet A %D 2016 %T Phenotypic expansion of TBX4 mutations to include acinar dysplasia of the lungs. %A Szafranski, Przemyslaw %A Coban-Akdemir, Zeynep H %A Rupps, Rosemarie %A Grazioli, Serge %A Wensley, David %A Jhangiani, Shalini N %A Popek, Edwina %A Lee, Anna F %A Lupski, James R %A Boerkoel, Cornelius F %A Stankiewicz, Paweł %K Alleles %K Autopsy %K Chromosomes, Human, Pair 16 %K DNA Copy Number Variations %K DNA Mutational Analysis %K Fatal Outcome %K Female %K Genetic Association Studies %K Genotype %K Heterozygote %K Humans %K Infant, Newborn %K Karyotype %K Lung %K Mutation %K Pedigree %K Phenotype %K Radiography, Thoracic %K T-Box Domain Proteins %X

Mutations in the T-box transcription factor TBX4 gene have been reported in patients with Ischiocoxopodopatellar syndrome (MIM# 147891) and childhood-onset pulmonary arterial hypertension. Whole exome sequencing of DNA from a 1 day old deceased newborn, with severe diffuse developmental lung disorder exhibiting features of acinar dysplasia, and her unaffected parents identified a de novo TBX4 missense mutation p.E86Q (c.256G>C) in the DNA-binding T-box domain. We propose phenotypic expansion of the TBX4-related clinical disease spectrum to include acinar dysplasia of the lungs. The reported mutation is the first identified genetic variant causative for acinar dysplasia. © 2016 Wiley Periodicals, Inc.

%B Am J Med Genet A %V 170 %P 2440-4 %8 2016 Sep %G eng %N 9 %1 https://www.ncbi.nlm.nih.gov/pubmed/27374786?dopt=Abstract %R 10.1002/ajmg.a.37822 %0 Journal Article %J Genome Med %D 2016 %T POGZ truncating alleles cause syndromic intellectual disability. %A White, Janson %A Beck, Christine R %A Harel, Tamar %A Posey, Jennifer E %A Jhangiani, Shalini N %A Tang, Sha %A Farwell, Kelly D %A Powis, Zöe %A Mendelsohn, Nancy J %A Baker, Janice A %A Pollack, Lynda %A Mason, Kati J %A Wierenga, Klaas J %A Arrington, Daniel K %A Hall, Melissa %A Psychogios, Apostolos %A Fairbrother, Laura %A Walkiewicz, Magdalena %A Person, Richard E %A Niu, Zhiyv %A Zhang, Jing %A Rosenfeld, Jill A %A Muzny, Donna M %A Eng, Christine %A Beaudet, Arthur L %A Lupski, James R %A Boerwinkle, Eric %A Gibbs, Richard A %A Yang, Yaping %A Xia, Fan %A Sutton, V Reid %K Adolescent %K Adult %K Alleles %K Child, Preschool %K Exome %K Female %K Heterozygote %K Humans %K Infant %K Intellectual Disability %K Male %K Mutation %K Sequence Analysis, DNA %K Transposases %X

BACKGROUND: Large-scale cohort-based whole exome sequencing of individuals with neurodevelopmental disorders (NDDs) has identified numerous novel candidate disease genes; however, detailed phenotypic information is often lacking in such studies. De novo mutations in pogo transposable element with zinc finger domain (POGZ) have been identified in six independent and diverse cohorts of individuals with NDDs ranging from autism spectrum disorder to developmental delay.

METHODS: Whole exome sequencing was performed on five unrelated individuals. Sanger sequencing was used to validate variants and segregate mutations with the phenotype in available family members.

RESULTS: We identified heterozygous truncating mutations in POGZ in five unrelated individuals, which were confirmed to be de novo or not present in available parental samples. Careful review of the phenotypes revealed shared features that included developmental delay, intellectual disability, hypotonia, behavioral abnormalities, and similar facial characteristics. Variable features included short stature, microcephaly, strabismus and hearing loss.

CONCLUSIONS: While POGZ has been associated with neurodevelopmental disorders in large cohort studies, our data suggest that loss of function variants in POGZ lead to an identifiable syndrome of NDD with specific phenotypic traits. This study exemplifies the era of human reverse clinical genomics ushered in by large disease-directed cohort studies; first defining a new syndrome molecularly and, only subsequently, phenotypically.

%B Genome Med %V 8 %P 3 %8 2016 Jan 06 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/26739615?dopt=Abstract %R 10.1186/s13073-015-0253-0 %0 Journal Article %J Mol Genet Genomic Med %D 2016 %T A potential founder variant in in three Norwegian families with warts, molluscum contagiosum, and T-cell dysfunction. %A Sorte, Hanne S %A Osnes, Liv T %A Fevang, Børre %A Aukrust, Pål %A Erichsen, Hans C %A Backe, Paul H %A Abrahamsen, Tore G %A Kittang, Ole B %A Øverland, Torstein %A Jhangiani, Shalini N %A Muzny, Donna M %A Vigeland, Magnus D %A Samarakoon, Pubudu %A Gambin, Tomasz %A Akdemir, Zeynep H C %A Gibbs, Richard A %A Rødningen, Olaug K %A Lyle, Robert %A Lupski, James R %A Stray-Pedersen, Asbjørg %X

BACKGROUND: Four patients from three Norwegian families presented with a common skin phenotype of warts, molluscum contagiosum, and dermatitis since early childhood, and various other immunological features. Warts are a common manifestation of (HPV), but when they are overwhelming, disseminated and/or persistent, and presenting together with other immunological features, a primary immunodeficiency disease (PIDD) may be suspected.

METHODS AND RESULTS: The four patients were exome sequenced as part of a larger study for detecting genetic causes of primary immunodeficiencies. No disease-causing variants were identified in known primary immunodeficiency genes or in other disease-related OMIM genes. However, the same homozygous missense variant in (also known as ) was identified in all four patients. In each family, the variant was located within a narrow region of homozygosity, representing a potential region of autozygosity. is a protein of undetermined function. A role in T-cell activation has been suggested and the mouse protein homolog (Rltpr) is essential for costimulation of T-cell activation via CD28, and for the development of regulatory T cells. Immunophenotyping demonstrated reduced regulatory, CD4+ memory, and CD4+ follicular T cells in all four patients. In addition, they all seem to have a deficiency in IFN -synthesis in CD4+ T cells and NK cells.

CONCLUSIONS: We report a novel primary immunodeficiency, and a differential molecular diagnosis to ,,,,,,, and related diseases. The specific variant may represent a Norwegian founder variant segregating on a population-specific haplotype.

%B Mol Genet Genomic Med %V 4 %P 604-616 %8 2016 Nov %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/27896283?dopt=Abstract %R 10.1002/mgg3.237 %0 Journal Article %J Am J Hum Genet %D 2016 %T Recurrent De Novo and Biallelic Variation of ATAD3A, Encoding a Mitochondrial Membrane Protein, Results in Distinct Neurological Syndromes. %A Harel, Tamar %A Yoon, Wan Hee %A Garone, Caterina %A Gu, Shen %A Coban-Akdemir, Zeynep %A Eldomery, Mohammad K %A Posey, Jennifer E %A Jhangiani, Shalini N %A Rosenfeld, Jill A %A Cho, Megan T %A Fox, Stephanie %A Withers, Marjorie %A Brooks, Stephanie M %A Chiang, Theodore %A Duraine, Lita %A Erdin, Serkan %A Yuan, Bo %A Shao, Yunru %A Moussallem, Elie %A Lamperti, Costanza %A Donati, Maria A %A Smith, Joshua D %A McLaughlin, Heather M %A Eng, Christine M %A Walkiewicz, Magdalena %A Xia, Fan %A Pippucci, Tommaso %A Magini, Pamela %A Seri, Marco %A Zeviani, Massimo %A Hirano, Michio %A Hunter, Jill V %A Srour, Myriam %A Zanigni, Stefano %A Lewis, Richard Alan %A Muzny, Donna M %A Lotze, Timothy E %A Boerwinkle, Eric %A Gibbs, Richard A %A Hickey, Scott E %A Graham, Brett H %A Yang, Yaping %A Buhas, Daniela %A Martin, Donna M %A Potocki, Lorraine %A Graziano, Claudio %A Bellen, Hugo J %A Lupski, James R %K Adenosine Triphosphatases %K Adult %K Alleles %K Animals %K ATPases Associated with Diverse Cellular Activities %K Axons %K Cardiomyopathies %K Child %K Child, Preschool %K Developmental Disabilities %K DNA Copy Number Variations %K Drosophila melanogaster %K Female %K Fibroblasts %K Homozygote %K Humans %K Infant %K Infant, Newborn %K Male %K Membrane Proteins %K Mitochondria %K Mitochondrial Proteins %K Muscle Hypotonia %K Muscles %K Mutation %K Nervous System Diseases %K Neurons %K Optic Atrophy %K Phenotype %K Polymorphism, Single Nucleotide %K Syndrome %K Young Adult %X

ATPase family AAA-domain containing protein 3A (ATAD3A) is a nuclear-encoded mitochondrial membrane protein implicated in mitochondrial dynamics, nucleoid organization, protein translation, cell growth, and cholesterol metabolism. We identified a recurrent de novo ATAD3A c.1582C>T (p.Arg528Trp) variant by whole-exome sequencing (WES) in five unrelated individuals with a core phenotype of global developmental delay, hypotonia, optic atrophy, axonal neuropathy, and hypertrophic cardiomyopathy. We also describe two families with biallelic variants in ATAD3A, including a homozygous variant in two siblings, and biallelic ATAD3A deletions mediated by nonallelic homologous recombination (NAHR) between ATAD3A and gene family members ATAD3B and ATAD3C. Tissue-specific overexpression of bor, the Drosophila mutation homologous to the human c.1582C>T (p.Arg528Trp) variant, resulted in a dramatic decrease in mitochondrial content, aberrant mitochondrial morphology, and increased autophagy. Homozygous null bor larvae showed a significant decrease of mitochondria, while overexpression of bor resulted in larger, elongated mitochondria. Finally, fibroblasts of an affected individual exhibited increased mitophagy. We conclude that the p.Arg528Trp variant functions through a dominant-negative mechanism that results in small mitochondria that trigger mitophagy, resulting in a reduction in mitochondrial content. ATAD3A variation represents an additional link between mitochondrial dynamics and recognizable neurological syndromes, as seen with MFN2, OPA1, DNM1L, and STAT2 mutations.

%B Am J Hum Genet %V 99 %P 831-845 %8 2016 Oct 06 %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/27640307?dopt=Abstract %R 10.1016/j.ajhg.2016.08.007 %0 Journal Article %J Am J Hum Genet %D 2016 %T Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations. %A Lalani, Seema R %A Liu, Pengfei %A Rosenfeld, Jill A %A Watkin, Levi B %A Chiang, Theodore %A Leduc, Magalie S %A Zhu, Wenmiao %A Ding, Yan %A Pan, Shujuan %A Vetrini, Francesco %A Miyake, Christina Y %A Shinawi, Marwan %A Gambin, Tomasz %A Eldomery, Mohammad K %A Akdemir, Zeynep Hande Coban %A Emrick, Lisa %A Wilnai, Yael %A Schelley, Susan %A Koenig, Mary Kay %A Memon, Nada %A Farach, Laura S %A Coe, Bradley P %A Azamian, Mahshid %A Hernandez, Patricia %A Zapata, Gladys %A Jhangiani, Shalini N %A Muzny, Donna M %A Lotze, Timothy %A Clark, Gary %A Wilfong, Angus %A Northrup, Hope %A Adesina, Adekunle %A Bacino, Carlos A %A Scaglia, Fernando %A Bonnen, Penelope E %A Crosson, Jane %A Duis, Jessica %A Maegawa, Gustavo H B %A Coman, David %A Inwood, Anita %A McGill, Jim %A Boerwinkle, Eric %A Graham, Brett %A Beaudet, Art %A Eng, Christine M %A Hanchard, Neil A %A Xia, Fan %A Orange, Jordan S %A Gibbs, Richard A %A Lupski, James R %A Yang, Yaping %K Alleles %K Arabs %K Arrhythmias, Cardiac %K Base Sequence %K Child %K Child, Preschool %K Endoplasmic Reticulum Stress %K Exome %K Exons %K Female %K Gene Deletion %K Golgi Apparatus %K Hispanic or Latino %K Homozygote %K Humans %K Infant %K Male %K Molecular Sequence Data %K Muscle Weakness %K Pedigree %K Rhabdomyolysis %K White People %X

The underlying genetic etiology of rhabdomyolysis remains elusive in a significant fraction of individuals presenting with recurrent metabolic crises and muscle weakness. Using exome sequencing, we identified bi-allelic mutations in TANGO2 encoding transport and Golgi organization 2 homolog (Drosophila) in 12 subjects with episodic rhabdomyolysis, hypoglycemia, hyperammonemia, and susceptibility to life-threatening cardiac tachyarrhythmias. A recurrent homozygous c.460G>A (p.Gly154Arg) mutation was found in four unrelated individuals of Hispanic/Latino origin, and a homozygous ∼34 kb deletion affecting exons 3-9 was observed in two families of European ancestry. One individual of mixed Hispanic/European descent was found to be compound heterozygous for c.460G>A (p.Gly154Arg) and the deletion of exons 3-9. Additionally, a homozygous exons 4-6 deletion was identified in a consanguineous Middle Eastern Arab family. No homozygotes have been reported for these changes in control databases. Fibroblasts derived from a subject with the recurrent c.460G>A (p.Gly154Arg) mutation showed evidence of increased endoplasmic reticulum stress and a reduction in Golgi volume density in comparison to control. Our results show that the c.460G>A (p.Gly154Arg) mutation and the exons 3-9 heterozygous deletion in TANGO2 are recurrent pathogenic alleles present in the Latino/Hispanic and European populations, respectively, causing considerable morbidity in the homozygotes in these populations.

%B Am J Hum Genet %V 98 %P 347-57 %8 2016 Feb 04 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/26805781?dopt=Abstract %R 10.1016/j.ajhg.2015.12.008 %0 Journal Article %J Genet Med %D 2016 %T The role of combined SNV and CNV burden in patients with distal symmetric polyneuropathy. %A Pehlivan, Davut %A Beck, Christine R %A Okamoto, Yuji %A Harel, Tamar %A Akdemir, Zeynep H C %A Jhangiani, Shalini N %A Withers, Marjorie A %A Goksungur, Meryem Tuba %A Carvalho, Claudia M B %A Czesnik, Dirk %A Gonzaga-Jauregui, Claudia %A Wiszniewski, Wojciech %A Muzny, Donna M %A Gibbs, Richard A %A Rautenstrauss, Bernd %A Sereda, Michael W %A Lupski, James R %K Adult %K Age of Onset %K Charcot-Marie-Tooth Disease %K Child, Preschool %K Comparative Genomic Hybridization %K DNA Copy Number Variations %K Exome %K Female %K Genetic Predisposition to Disease %K GTP Phosphohydrolases %K High-Throughput Nucleotide Sequencing %K Humans %K Male %K Mitochondrial Proteins %K Motor Neurons %K Myelin P0 Protein %K Myelin Proteins %K Neural Conduction %K Polymorphism, Single Nucleotide %K Polyneuropathies %X

PURPOSE: Charcot-Marie-Tooth (CMT) disease is a heterogeneous group of genetic disorders of the peripheral nervous system. Copy-number variants (CNVs) contribute significantly to CMT, as duplication of PMP22 underlies the majority of CMT1 cases. We hypothesized that CNVs and/or single-nucleotide variants (SNVs) might exist in patients with CMT with an unknown molecular genetic etiology.

METHODS: Two hundred patients with CMT, negative for both SNV mutations in several CMT genes and for CNVs involving PMP22, were screened for CNVs by high-resolution oligonucleotide array comparative genomic hybridization. Whole-exome sequencing was conducted on individuals with rare, potentially pathogenic CNVs.

RESULTS: Putatively causative CNVs were identified in five subjects (~2.5%); four of the five map to known neuropathy genes. Breakpoint sequencing revealed Alu-Alu-mediated junctions as a predominant contributor. Exome sequencing identified MFN2 SNVs in two of the individuals.

CONCLUSION: Neuropathy-associated CNV outside of the PMP22 locus is rare in CMT. Nevertheless, there is potential clinical utility in testing for CNVs and exome sequencing in CMT cases negative for the CMT1A duplication. These findings suggest that complex phenotypes including neuropathy can potentially be caused by a combination of SNVs and CNVs affecting more than one disease-associated locus and contributing to a mutational burden.Genet Med 18 5, 443-451.

%B Genet Med %V 18 %P 443-51 %8 2016 May %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/26378787?dopt=Abstract %R 10.1038/gim.2015.124 %0 Journal Article %J Endocr Relat Cancer %D 2016 %T Somatic mosaicism underlies X-linked acrogigantism syndrome in sporadic male subjects. %A Daly, Adrian F %A Bo Yuan %A Fina, Frederic %A Caberg, Jean-Hubert %A Trivellin, Giampaolo %A Rostomyan, Liliya %A de Herder, Wouter W %A Naves, Luciana A %A Metzger, Daniel %A Cuny, Thomas %A Rabl, Wolfgang %A Shah, Nalini %A Jaffrain-Rea, Marie-Lise %A Zatelli, Maria Chiara %A Faucz, Fabio R %A Castermans, Emilie %A Nanni-Metellus, Isabelle %A Lodish, Maya %A Muhammad, Ammar %A Palmeira, Leonor %A Potorac, Iulia %A Mantovani, Giovanna %A Neggers, Sebastian J %A Klein, Marc %A Barlier, Anne %A Liu, Pengfei %A Ouafik, L'Houcine %A Bours, Vincent %A Lupski, James R %A Stratakis, Constantine A %A Beckers, Albert %K Adult %K Female %K Genetic Diseases, X-Linked %K Gigantism %K Humans %K Male %K Middle Aged %K Mosaicism %K Polymerase Chain Reaction %K Syndrome %K Young Adult %X

Somatic mosaicism has been implicated as a causative mechanism in a number of genetic and genomic disorders. X-linked acrogigantism (XLAG) syndrome is a recently characterized genomic form of pediatric gigantism due to aggressive pituitary tumors that is caused by submicroscopic chromosome Xq26.3 duplications that include GPR101 We studied XLAG syndrome patients (n= 18) to determine if somatic mosaicism contributed to the genomic pathophysiology. Eighteen subjects with XLAG syndrome caused by Xq26.3 duplications were identified using high-definition array comparative genomic hybridization (HD-aCGH). We noted that males with XLAG had a decreased log2ratio (LR) compared with expected values, suggesting potential mosaicism, whereas females showed no such decrease. Compared with familial male XLAG cases, sporadic males had more marked evidence for mosaicism, with levels of Xq26.3 duplication between 16.1 and 53.8%. These characteristics were replicated using a novel, personalized breakpoint junction-specific quantification droplet digital polymerase chain reaction (ddPCR) technique. Using a separate ddPCR technique, we studied the feasibility of identifying XLAG syndrome cases in a distinct patient population of 64 unrelated subjects with acromegaly/gigantism, and identified one female gigantism patient who had had increased copy number variation (CNV) threshold for GPR101 that was subsequently diagnosed as having XLAG syndrome on HD-aCGH. Employing a combination of HD-aCGH and novel ddPCR approaches, we have demonstrated, for the first time, that XLAG syndrome can be caused by variable degrees of somatic mosaicism for duplications at chromosome Xq26.3. Somatic mosaicism was shown to occur in sporadic males but not in females with XLAG syndrome, although the clinical characteristics of the disease were similarly severe in both sexes.

%B Endocr Relat Cancer %V 23 %P 221-33 %8 2016 Apr %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/26935837?dopt=Abstract %R 10.1530/ERC-16-0082 %0 Journal Article %J Eur J Med Genet %D 2016 %T Two male sibs with severe micrognathia and a missense variant in MED12. %A Prescott, Trine E %A Kulseth, Mari Ann %A Heimdal, Ketil R %A Stadheim, Barbro %A Hopp, Einar %A Gambin, Tomasz %A Coban Akdemir, Zeynep H %A Jhangiani, Shalini N %A Donna M Muzny %A Richard A Gibbs %A Lupski, James R %A Stray-Pedersen, Asbjørg %K Exons %K Genes, X-Linked %K Genetic Association Studies %K Genotype %K Humans %K Infant %K Male %K Mediator Complex %K Micrognathism %K Mutation, Missense %K Pedigree %K Phenotype %K Polymorphism, Single Nucleotide %K Severity of Illness Index %K Siblings %K Tomography, X-Ray Computed %K X Chromosome Inactivation %X

Missense variants in MED12 cause three partially overlapping dysmorphic X-linked intellectual disability (XLID) syndromes: Lujan-Fryns syndrome (also known as Lujan syndrome), FG syndrome (also known as Opitz-Kaveggia syndrome) and X-linked Ohdo syndrome. We report a family with two severely micrognathic male sibs, a 10½ year old boy and a fetus, in which hemizygosity for a previously unreported missense variant in exon 13 of MED12 (NM_005120.2), c.1862G > A, p.(Arg621Gln) was detected by whole exome sequencing. The affected sibs shared no other rare variant with relevance to the phenotype. X-chromosome inactivation in blood was completely skewed (100:0) in the unaffected heterozygous mother, most likely as a result of preferential inactivation of the X-chromosome harbouring the missense variant in MED12. Neither the unaffected brother nor the unaffected maternal grandfather carried the missense variant in MED12. In the 10½ year old boy, upper airway obstruction secondary to Pierre Robin sequence necessitated a tracheostomy for the first 10 months of life. He has mild to moderate intellectual disability and some dysmorphic features seen in MED12-related syndromes. In addition, he has a horizontal gaze paresis, anomalies of the inner ear, and a cervical block vertebra. This report contributes to the expanding phenotypic range associated with MED12-mutations.

%B Eur J Med Genet %V 59 %P 367-72 %8 2016 Aug %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/27286923?dopt=Abstract %R 10.1016/j.ejmg.2016.06.001 %0 Journal Article %J Genome Med %D 2016 %T A visual and curatorial approach to clinical variant prioritization and disease gene discovery in genome-wide diagnostics. %A James, Regis A %A Campbell, Ian M %A Chen, Edward S %A Boone, Philip M %A Rao, Mitchell A %A Bainbridge, Matthew N %A Lupski, James R %A Yang, Yaping %A Eng, Christine M %A Posey, Jennifer E %A Shaw, Chad A %K Computational Biology %K Diagnosis, Differential %K Disease %K Genetic Variation %K Genome-Wide Association Study %K Humans %K Phenotype %K Pilot Projects %K Retrospective Studies %K Software %X

BACKGROUND: Genome-wide data are increasingly important in the clinical evaluation of human disease. However, the large number of variants observed in individual patients challenges the efficiency and accuracy of diagnostic review. Recent work has shown that systematic integration of clinical phenotype data with genotype information can improve diagnostic workflows and prioritization of filtered rare variants. We have developed visually interactive, analytically transparent analysis software that leverages existing disease catalogs, such as the Online Mendelian Inheritance in Man database (OMIM) and the Human Phenotype Ontology (HPO), to integrate patient phenotype and variant data into ranked diagnostic alternatives.

METHODS: Our tool, "OMIM Explorer" ( http://www.omimexplorer.com ), extends the biomedical application of semantic similarity methods beyond those reported in previous studies. The tool also provides a simple interface for translating free-text clinical notes into HPO terms, enabling clinical providers and geneticists to contribute phenotypes to the diagnostic process. The visual approach uses semantic similarity with multidimensional scaling to collapse high-dimensional phenotype and genotype data from an individual into a graphical format that contextualizes the patient within a low-dimensional disease map. The map proposes a differential diagnosis and algorithmically suggests potential alternatives for phenotype queries--in essence, generating a computationally assisted differential diagnosis informed by the individual's personal genome. Visual interactivity allows the user to filter and update variant rankings by interacting with intermediate results. The tool also implements an adaptive approach for disease gene discovery based on patient phenotypes.

RESULTS: We retrospectively analyzed pilot cohort data from the Baylor Miraca Genetics Laboratory, demonstrating performance of the tool and workflow in the re-analysis of clinical exomes. Our tool assigned to clinically reported variants a median rank of 2, placing causal variants in the top 1 % of filtered candidates across the 47 cohort cases with reported molecular diagnoses of exome variants in OMIM Morbidmap genes. Our tool outperformed Phen-Gen, eXtasy, PhenIX, PHIVE, and hiPHIVE in the prioritization of these clinically reported variants.

CONCLUSIONS: Our integrative paradigm can improve efficiency and, potentially, the quality of genomic medicine by more effectively utilizing available phenotype information, catalog data, and genomic knowledge.

%B Genome Med %V 8 %P 13 %8 2016 Feb 02 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/26838676?dopt=Abstract %R 10.1186/s13073-016-0261-8 %0 Journal Article %J JAMA Neurol %D 2016 %T Whole-Exome Sequencing in Familial Parkinson Disease. %A Farlow, Janice L %A Robak, Laurie A %A Hetrick, Kurt %A Bowling, Kevin %A Boerwinkle, Eric %A Coban-Akdemir, Zeynep H %A Gambin, Tomasz %A Gibbs, Richard A %A Gu, Shen %A Jain, Preti %A Jankovic, Joseph %A Jhangiani, Shalini %A Kaw, Kaveeta %A Lai, Dongbing %A Lin, Hai %A Ling, Hua %A Liu, Yunlong %A Lupski, James R %A Muzny, Donna %A Porter, Paula %A Pugh, Elizabeth %A White, Janson %A Doheny, Kimberly %A Myers, Richard M %A Shulman, Joshua M %A Foroud, Tatiana %K Adult %K Aged %K Cohort Studies %K Exome %K Female %K Genetic Predisposition to Disease %K Genetic Variation %K Humans %K Male %K Middle Aged %K Parkinsonian Disorders %K Protein-Tyrosine Kinases %K Sequence Analysis, DNA %K Tenascin %X

IMPORTANCE: Parkinson disease (PD) is a progressive neurodegenerative disease for which susceptibility is linked to genetic and environmental risk factors.

OBJECTIVE: To identify genetic variants contributing to disease risk in familial PD.

DESIGN, SETTING, AND PARTICIPANTS: A 2-stage study design that included a discovery cohort of families with PD and a replication cohort of familial probands was used. In the discovery cohort, rare exonic variants that segregated in multiple affected individuals in a family and were predicted to be conserved or damaging were retained. Genes with retained variants were prioritized if expressed in the brain and located within PD-relevant pathways. Genes in which prioritized variants were observed in at least 4 families were selected as candidate genes for replication in the replication cohort. The setting was among individuals with familial PD enrolled from academic movement disorder specialty clinics across the United States. All participants had a family history of PD.

MAIN OUTCOMES AND MEASURES: Identification of genes containing rare, likely deleterious, genetic variants in individuals with familial PD using a 2-stage exome sequencing study design.

RESULTS: The 93 individuals from 32 families in the discovery cohort (49.5% [46 of 93] female) had a mean (SD) age at onset of 61.8 (10.0) years. The 49 individuals with familial PD in the replication cohort (32.6% [16 of 49] female) had a mean (SD) age at onset of 50.1 (15.7) years. Discovery cohort recruitment dates were 1999 to 2009, and replication cohort recruitment dates were 2003 to 2014. Data analysis dates were 2011 to 2015. Three genes containing a total of 13 rare and potentially damaging variants were prioritized in the discovery cohort. Two of these genes (TNK2 and TNR) also had rare variants that were predicted to be damaging in the replication cohort. All 9 variants identified in the 2 replicated genes in 12 families across the discovery and replication cohorts were confirmed via Sanger sequencing.

CONCLUSIONS AND RELEVANCE: TNK2 and TNR harbored rare, likely deleterious, variants in individuals having familial PD, with similar findings in an independent cohort. To our knowledge, these genes have not been previously associated with PD, although they have been linked to critical neuronal functions. Further studies are required to confirm a potential role for these genes in the pathogenesis of PD.

%B JAMA Neurol %V 73 %P 68-75 %8 2016 Jan %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/26595808?dopt=Abstract %R 10.1001/jamaneurol.2015.3266 %0 Journal Article %J Cold Spring Harb Mol Case Stud %D 2016 %T Whole-exome sequencing reveals an inherited R566X mutation of the epithelial sodium channel β-subunit in a case of early-onset phenotype of Liddle syndrome. %A Polfus, Linda M %A Boerwinkle, Eric %A Gibbs, Richard A %A Metcalf, Ginger %A Muzny, Donna %A Veeraraghavan, Narayanan %A Grove, Megan %A Shete, Sanjay %A Wallace, Stephanie %A Milewicz, Dianna %A Hanchard, Neil %A Lupski, James R %A Hashmi, Syed Shahrukh %A Gupta-Malhotra, Monesha %K Adult %K Aldosterone %K Alleles %K Amiloride %K Child, Preschool %K Epithelial Sodium Channels %K Exome %K Exome Sequencing %K Female %K Gene Frequency %K Germ-Line Mutation %K Humans %K Hydrochlorothiazide %K Hypertension %K Hypokalemia %K Liddle Syndrome %K Male %K Mutation %K Mutation, Missense %K Renin %X

To comprehensively evaluate a European-American child with severe hypertension, whole-exome sequencing (WES) was performed on the child and parents, which identified causal variation of the proband's early-onset disease. The proband's hypertension was resistant to treatment, requiring a multiple drug regimen including amiloride, spironolactone, and hydrochlorothiazide. We suspected a monogenic form of hypertension because of the persistent hypokalemia with low plasma levels of renin and aldosterone. To address this, we focused on rare functional variants and indels, and performed gene-based tests incorporating linkage scores and allele frequency and filtered on deleterious functional mutations. Drawing upon clinical presentation, 27 genes were selected evidenced to cause monogenic hypertension and matched to the gene-based results. This resulted in the identification of a stop-gain mutation in an epithelial sodium channel (ENaC), , an established Liddle syndrome gene, shared by the child and her father. Interestingly, the father also harbored a missense mutation (p.Trp552Arg) in the α-subunit of the ENaC trimer, , possibly pointing to pseudohypoaldosteronism type I. This case is unique in that we present the early-onset disease and treatment response caused by a canonical stop-gain mutation (p.Arg566*) as well as ENaC digenic hits in the father, emphasizing the utility of WES informing precision medicine.

%B Cold Spring Harb Mol Case Stud %V 2 %P a001255 %8 2016 Nov %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/27900368?dopt=Abstract %R 10.1101/mcs.a001255 %0 Journal Article %J Am J Hum Genet %D 2015 %T Absence of heterozygosity due to template switching during replicative rearrangements. %A Carvalho, Claudia M B %A Pfundt, Rolph %A King, Daniel A %A Lindsay, Sarah J %A Zuccherato, Luciana W %A Macville, Merryn V E %A Liu, Pengfei %A Johnson, Diana %A Stankiewicz, Pawel %A Brown, Chester W %A Shaw, Chad A %A Hurles, Matthew E %A Ira, Grzegorz %A Hastings, P J %A Brunner, Han G %A Lupski, James R %K Base Sequence %K DNA Copy Number Variations %K DNA Repair %K DNA Replication %K Gene Rearrangement %K Humans %K In Situ Hybridization, Fluorescence %K Loss of Heterozygosity %K Models, Genetic %K Molecular Sequence Data %K Netherlands %K Polymerase Chain Reaction %K Polymorphism, Single Nucleotide %K Sequence Analysis, DNA %K Uniparental Disomy %X

We investigated complex genomic rearrangements (CGRs) consisting of triplication copy-number variants (CNVs) that were accompanied by extended regions of copy-number-neutral absence of heterozygosity (AOH) in subjects with multiple congenital abnormalities. Molecular analyses provided observational evidence that in humans, post-zygotically generated CGRs can lead to regional uniparental disomy (UPD) due to template switches between homologs versus sister chromatids by using microhomology to prime DNA replication-a prediction of the replicative repair model, MMBIR. Our findings suggest that replication-based mechanisms might underlie the formation of diverse types of genomic alterations (CGRs and AOH) implicated in constitutional disorders.

%B Am J Hum Genet %V 96 %P 555-64 %8 2015 Apr 02 %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/25799105?dopt=Abstract %R 10.1016/j.ajhg.2015.01.021 %0 Journal Article %J Am J Hum Genet %D 2015 %T Allelic Mutations of KITLG, Encoding KIT Ligand, Cause Asymmetric and Unilateral Hearing Loss and Waardenburg Syndrome Type 2. %A Zazo Seco, Celia %A Serrão de Castro, Luciana %A van Nierop, Josephine W %A Morín, Matías %A Jhangiani, Shalini %A Verver, Eva J J %A Schraders, Margit %A Maiwald, Nadine %A Wesdorp, Mieke %A Venselaar, Hanka %A Spruijt, Liesbeth %A Oostrik, Jaap %A Schoots, Jeroen %A van Reeuwijk, Jeroen %A Lelieveld, Stefan H %A Huygen, Patrick L M %A Insenser, María %A Admiraal, Ronald J C %A Pennings, Ronald J E %A Hoefsloot, Lies H %A Arias-Vásquez, Alejandro %A de Ligt, Joep %A Yntema, Helger G %A Jansen, Joop H %A Muzny, Donna M %A Huls, Gerwin %A van Rossum, Michelle M %A Lupski, James R %A Moreno-Pelayo, Miguel Angel %A Kunst, Henricus P M %A Kremer, Hannie %K Alleles %K Animals %K Female %K Fluorescent Antibody Technique %K Genetic Linkage %K Hearing Loss, Unilateral %K Humans %K Male %K Mice %K Mutation %K NIH 3T3 Cells %K Pedigree %K Phenotype %K Prognosis %K Real-Time Polymerase Chain Reaction %K Reverse Transcriptase Polymerase Chain Reaction %K RNA, Messenger %K Stem Cell Factor %K Waardenburg Syndrome %X

Linkage analysis combined with whole-exome sequencing in a large family with congenital and stable non-syndromic unilateral and asymmetric hearing loss (NS-UHL/AHL) revealed a heterozygous truncating mutation, c.286_303delinsT (p.Ser96Ter), in KITLG. This mutation co-segregated with NS-UHL/AHL as a dominant trait with reduced penetrance. By screening a panel of probands with NS-UHL/AHL, we found an additional mutation, c.200_202del (p.His67_Cys68delinsArg). In vitro studies revealed that the p.His67_Cys68delinsArg transmembrane isoform of KITLG is not detectable at the cell membrane, supporting pathogenicity. KITLG encodes a ligand for the KIT receptor. Also, KITLG-KIT signaling and MITF are suggested to mutually interact in melanocyte development. Because mutations in MITF are causative of Waardenburg syndrome type 2 (WS2), we screened KITLG in suspected WS2-affected probands. A heterozygous missense mutation, c.310C>G (p.Leu104Val), that segregated with WS2 was identified in a small family. In vitro studies revealed that the p.Leu104Val transmembrane isoform of KITLG is located at the cell membrane, as is wild-type KITLG. However, in culture media of transfected cells, the p.Leu104Val soluble isoform of KITLG was reduced, and no soluble p.His67_Cys68delinsArg and p.Ser96Ter KITLG could be detected. These data suggest that mutations in KITLG associated with NS-UHL/AHL have a loss-of-function effect. We speculate that the mechanism of the mutation underlying WS2 and leading to membrane incorporation and reduced secretion of KITLG occurs via a dominant-negative or gain-of-function effect. Our study unveils different phenotypes associated with KITLG, previously associated with pigmentation abnormalities, and will thereby improve the genetic counseling given to individuals with KITLG variants.

%B Am J Hum Genet %V 97 %P 647-60 %8 2015 Nov 05 %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/26522471?dopt=Abstract %R 10.1016/j.ajhg.2015.09.011 %0 Journal Article %J Hum Mol Genet %D 2015 %T Alu-mediated diverse and complex pathogenic copy-number variants within human chromosome 17 at p13.3. %A Gu, Shen %A Yuan, Bo %A Campbell, Ian M %A Beck, Christine R %A Carvalho, Claudia M B %A Nagamani, Sandesh C S %A Erez, Ayelet %A Patel, Ankita %A Bacino, Carlos A %A Shaw, Chad A %A Stankiewicz, Paweł %A Cheung, Sau Wai %A Bi, Weimin %A Lupski, James R %K Alleles %K Alu Elements %K Base Sequence %K Chromosomes, Human, Pair 17 %K Comparative Genomic Hybridization %K DNA Copy Number Variations %K Female %K Gene Duplication %K Gene Rearrangement %K Genome, Human %K Genomic Instability %K Genomics %K Homologous Recombination %K Humans %K Male %K Molecular Sequence Data %K Segmental Duplications, Genomic %K Sequence Deletion %X

Alu repetitive elements are known to be major contributors to genome instability by generating Alu-mediated copy-number variants (CNVs). Most of the reported Alu-mediated CNVs are simple deletions and duplications, and the mechanism underlying Alu-Alu-mediated rearrangement has been attributed to non-allelic homologous recombination (NAHR). Chromosome 17 at the p13.3 genomic region lacks extensive low-copy repeat architecture; however, it is highly enriched for Alu repetitive elements, with a fraction of 30% of total sequence annotated in the human reference genome, compared with the 10% genome-wide and 18% on chromosome 17. We conducted mechanistic studies of the 17p13.3 CNVs by performing high-density oligonucleotide array comparative genomic hybridization, specifically interrogating the 17p13.3 region with ∼150 bp per probe density; CNV breakpoint junctions were mapped to nucleotide resolution by polymerase chain reaction and Sanger sequencing. Studied rearrangements include 5 interstitial deletions, 14 tandem duplications, 7 terminal deletions and 13 complex genomic rearrangements (CGRs). Within the 17p13.3 region, Alu-Alu-mediated rearrangements were identified in 80% of the interstitial deletions, 46% of the tandem duplications and 50% of the CGRs, indicating that this mechanism was a major contributor for formation of breakpoint junctions. Our studies suggest that Alu repetitive elements facilitate formation of non-recurrent CNVs, CGRs and other structural aberrations of chromosome 17 at p13.3. The common observation of Alu-mediated rearrangement in CGRs and breakpoint junction sequences analysis further demonstrates that this type of mechanism is unlikely attributed to NAHR, but rather may be due to a recombination-coupled DNA replicative repair process.

%B Hum Mol Genet %V 24 %P 4061-77 %8 2015 Jul 15 %G eng %N 14 %1 https://www.ncbi.nlm.nih.gov/pubmed/25908615?dopt=Abstract %R 10.1093/hmg/ddv146 %0 Journal Article %J BMC Genomics %D 2015 %T Assessing structural variation in a personal genome-towards a human reference diploid genome. %A English, Adam C %A Salerno, William J %A Hampton, Oliver A %A Gonzaga-Jauregui, Claudia %A Ambreth, Shruthi %A Ritter, Deborah I %A Beck, Christine R %A Davis, Caleb F %A Dahdouli, Mahmoud %A Ma, Singer %A Carroll, Andrew %A Veeraraghavan, Narayanan %A Bruestle, Jeremy %A Drees, Becky %A Hastie, Alex %A Lam, Ernest T %A White, Simon %A Mishra, Pamela %A Wang, Min %A Han, Yi %A Zhang, Feng %A Stankiewicz, Pawel %A Wheeler, David A %A Reid, Jeffrey G %A Muzny, Donna M %A Rogers, Jeffrey %A Sabo, Aniko %A Worley, Kim C %A Lupski, James R %A Boerwinkle, Eric %A Gibbs, Richard A %K Computational Biology %K Databases, Genetic %K Diploidy %K Genome, Human %K Genomic Structural Variation %K Humans %K Sequence Analysis, DNA %K Software %X

BACKGROUND: Characterizing large genomic variants is essential to expanding the research and clinical applications of genome sequencing. While multiple data types and methods are available to detect these structural variants (SVs), they remain less characterized than smaller variants because of SV diversity, complexity, and size. These challenges are exacerbated by the experimental and computational demands of SV analysis. Here, we characterize the SV content of a personal genome with Parliament, a publicly available consensus SV-calling infrastructure that merges multiple data types and SV detection methods.

RESULTS: We demonstrate Parliament's efficacy via integrated analyses of data from whole-genome array comparative genomic hybridization, short-read next-generation sequencing, long-read (Pacific BioSciences RSII), long-insert (Illumina Nextera), and whole-genome architecture (BioNano Irys) data from the personal genome of a single subject (HS1011). From this genome, Parliament identified 31,007 genomic loci between 100 bp and 1 Mbp that are inconsistent with the hg19 reference assembly. Of these loci, 9,777 are supported as putative SVs by hybrid local assembly, long-read PacBio data, or multi-source heuristics. These SVs span 59 Mbp of the reference genome (1.8%) and include 3,801 events identified only with long-read data. The HS1011 data and complete Parliament infrastructure, including a BAM-to-SV workflow, are available on the cloud-based service DNAnexus.

CONCLUSIONS: HS1011 SV analysis reveals the limits and advantages of multiple sequencing technologies, specifically the impact of long-read SV discovery. With the full Parliament infrastructure, the HS1011 data constitute a public resource for novel SV discovery, software calibration, and personal genome structural variation analysis.

%B BMC Genomics %V 16 %P 286 %8 2015 Apr 11 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/25886820?dopt=Abstract %R 10.1186/s12864-015-1479-3 %0 Journal Article %J Eur J Hum Genet %D 2015 %T Cerebral visual impairment and intellectual disability caused by PGAP1 variants. %A Bosch, Daniëlle G M %A Boonstra, F Nienke %A Kinoshita, Taroh %A Jhangiani, Shalini %A de Ligt, Joep %A Cremers, Frans P M %A Lupski, James R %A Murakami, Yoshiko %A de Vries, Bert B A %K Animals %K Cell Line, Tumor %K Child %K CHO Cells %K Cricetinae %K Cricetulus %K Humans %K Intellectual Disability %K Male %K Membrane Proteins %K Mutation %K Phosphoinositide Phospholipase C %K Phosphoric Monoester Hydrolases %K Syndrome %K Vision Disorders %K Visual Perception %X

Homozygous variants in PGAP1 (post-GPI attachment to proteins 1) have recently been identified in two families with developmental delay, seizures and/or spasticity. PGAP1 is a member of the glycosylphosphatidylinositol anchor biosynthesis and remodeling pathway and defects in this pathway are a subclass of congenital disorders of glycosylation. Here we performed whole-exome sequencing in an individual with cerebral visual impairment (CVI), intellectual disability (ID), and factor XII deficiency and revealed compound heterozygous variants in PGAP1, c.274_276del (p.(Pro92del)) and c.921_925del (p.(Lys308Asnfs*25)). Subsequently, PGAP1-deficient Chinese hamster ovary (CHO)-cell lines were transfected with either mutant or wild-type constructs and their sensitivity to phosphatidylinositol-specific phospholipase C (PI-PLC) treatment was measured. The mutant constructs could not rescue the PGAP1-deficient CHO cell lines resistance to PI-PLC treatment. In addition, lymphoblastoid cell lines (LCLs) of the affected individual showed no sensitivity to PI-PLC treatment, whereas the LCLs of the heterozygous carrier parents were partially resistant. In conclusion, we report novel PGAP1 variants in a boy with CVI and ID and a proven functional loss of PGAP1 and show, to our knowledge, for the first time this genetic association with CVI.

%B Eur J Hum Genet %V 23 %P 1689-93 %8 2015 Dec %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/25804403?dopt=Abstract %R 10.1038/ejhg.2015.42 %0 Journal Article %J NPJ Schizophr %D 2015 %T Characterization of molecular and cellular phenotypes associated with a heterozygous deletion using patient-derived hiPSC neural cells. %A Lee, Inkyu S %A Carvalho, Claudia M B %A Douvaras, Panagiotis %A Ho, Seok-Man %A Hartley, Brigham J %A Zuccherato, Luciana W %A Ladran, Ian G %A Siegel, Arthur J %A McCarthy, Shane %A Malhotra, Dheeraj %A Sebat, Jonathan %A Rapoport, Judith %A Fossati, Valentina %A Lupski, James R %A Levy, Deborah L %A Brennand, Kristen J %X

Neurodevelopmental disorders, such as autism spectrum disorders (ASD) and schizophrenia (SZ), are complex disorders with a high degree of heritability. Genetic studies have identified several candidate genes associated with these disorders, including contactin-associated protein-like 2 (). Traditionally, in animal models or , the function of has been studied by genetic deletion or transcriptional knockdown, which reduce the expression of the entire gene; however, it remains unclear whether the mutations identified in clinical settings are sufficient to alter expression in human neurons. Here, using human induced pluripotent stem cells (hiPSCs) derived from two individuals with a large (289kb) and heterozygous deletion in (affecting exons 14-15) and discordant clinical outcomes, we have characterized expression patterns in hiPSC neural progenitor cells (NPCs), two independent populations of hiPSC-derived neurons and hiPSC-derived oligodendrocyte precursor cells (OPCs). First, we observed exon-specific changes in expression in both carriers; although the expression of exons 14-15 is significantly decreased, the expression of other exons is upregulated. Second, we observed significant differences in patterns of allele-specific expression in carriers that were consistent with clinical outcome. Third, we observed a robust neural migration phenotype that correlated with diagnosis and exon- and allele-specific expression patterns, but not with genotype. In all, our data highlight the importance of considering the nature, location and regulation of mutated alleles when attempting to connect GWAS studies to gene function.

%B NPJ Schizophr %V 1 %P 15019- %8 2015 Jun 24 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/26985448?dopt=Abstract %R 10.1038/npjschz.2015.19 %0 Journal Article %J JAMA %D 2015 %T Cognitive phenotypes and genomic copy number variations. %A Lupski, James R %K DNA Copy Number Variations %K Female %K Heterozygote %K Humans %K Intellectual Disability %K Male %K Mental Disorders %B JAMA %V 313 %P 2029-30 %8 2015 May 26 %G eng %N 20 %1 https://www.ncbi.nlm.nih.gov/pubmed/26010630?dopt=Abstract %R 10.1001/jama.2015.4846 %0 Journal Article %J PLoS Genet %D 2015 %T Comparative Genomic Analyses of the Human NPHP1 Locus Reveal Complex Genomic Architecture and Its Regional Evolution in Primates. %A Yuan, Bo %A Liu, Pengfei %A Gupta, Aditya %A Beck, Christine R %A Tejomurtula, Anusha %A Campbell, Ian M %A Gambin, Tomasz %A Simmons, Alexandra D %A Withers, Marjorie A %A Harris, R Alan %A Rogers, Jeffrey %A Schwartz, David C %A Lupski, James R %K Adaptor Proteins, Signal Transducing %K Alleles %K Animals %K Comparative Genomic Hybridization %K Cytoskeletal Proteins %K Evolution, Molecular %K Gene Dosage %K Gene Rearrangement %K Genome, Human %K Genomic Structural Variation %K Haplotypes %K Humans %K Kidney Diseases, Cystic %K Membrane Proteins %K Primates %X

Many loci in the human genome harbor complex genomic structures that can result in susceptibility to genomic rearrangements leading to various genomic disorders. Nephronophthisis 1 (NPHP1, MIM# 256100) is an autosomal recessive disorder that can be caused by defects of NPHP1; the gene maps within the human 2q13 region where low copy repeats (LCRs) are abundant. Loss of function of NPHP1 is responsible for approximately 85% of the NPHP1 cases-about 80% of such individuals carry a large recurrent homozygous NPHP1 deletion that occurs via nonallelic homologous recombination (NAHR) between two flanking directly oriented ~45 kb LCRs. Published data revealed a non-pathogenic inversion polymorphism involving the NPHP1 gene flanked by two inverted ~358 kb LCRs. Using optical mapping and array-comparative genomic hybridization, we identified three potential novel structural variant (SV) haplotypes at the NPHP1 locus that may protect a haploid genome from the NPHP1 deletion. Inter-species comparative genomic analyses among primate genomes revealed massive genomic changes during evolution. The aggregated data suggest that dynamic genomic rearrangements occurred historically within the NPHP1 locus and generated SV haplotypes observed in the human population today, which may confer differential susceptibility to genomic instability and the NPHP1 deletion within a personal genome. Our study documents diverse SV haplotypes at a complex LCR-laden human genomic region. Comparative analyses provide a model for how this complex region arose during primate evolution, and studies among humans suggest that intra-species polymorphism may potentially modulate an individual's susceptibility to acquiring disease-associated alleles.

%B PLoS Genet %V 11 %P e1005686 %8 2015 Dec %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/26641089?dopt=Abstract %R 10.1371/journal.pgen.1005686 %0 Journal Article %J PLoS Genet %D 2015 %T Complex genomic rearrangements at the PLP1 locus include triplication and quadruplication. %A Beck, Christine R %A Carvalho, Claudia M B %A Banser, Linda %A Gambin, Tomasz %A Stubbolo, Danielle %A Yuan, Bo %A Sperle, Karen %A McCahan, Suzanne M %A Henneke, Marco %A Seeman, Pavel %A Garbern, James Y %A Hobson, Grace M %A Lupski, James R %K Chromosome Breakpoints %K Chromosome Inversion %K Gene Dosage %K Gene Duplication %K Humans %K Myelin Proteolipid Protein %K Pelizaeus-Merzbacher Disease %X

Inverted repeats (IRs) can facilitate structural variation as crucibles of genomic rearrangement. Complex duplication-inverted triplication-duplication (DUP-TRP/INV-DUP) rearrangements that contain breakpoint junctions within IRs have been recently associated with both MECP2 duplication syndrome (MIM#300260) and Pelizaeus-Merzbacher disease (PMD, MIM#312080). We investigated 17 unrelated PMD subjects with copy number gains at the PLP1 locus including triplication and quadruplication of specific genomic intervals-16/17 were found to have a DUP-TRP/INV-DUP rearrangement product. An IR distal to PLP1 facilitates DUP-TRP/INV-DUP formation as well as an inversion structural variation found frequently amongst normal individuals. We show that a homology-or homeology-driven replicative mechanism of DNA repair can apparently mediate template switches within stretches of microhomology. Moreover, we provide evidence that quadruplication and potentially higher order amplification of a genomic interval can occur in a manner consistent with rolling circle amplification as predicted by the microhomology-mediated break induced replication (MMBIR) model.

%B PLoS Genet %V 11 %P e1005050 %8 2015 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/25749076?dopt=Abstract %R 10.1371/journal.pgen.1005050 %0 Journal Article %J Nat Genet %D 2015 %T COPA mutations impair ER-Golgi transport and cause hereditary autoimmune-mediated lung disease and arthritis. %A Watkin, Levi B %A Jessen, Birthe %A Wiszniewski, Wojciech %A Vece, Timothy J %A Jan, Max %A Sha, Youbao %A Thamsen, Maike %A Santos-Cortez, Regie L P %A Lee, Kwanghyuk %A Gambin, Tomasz %A Forbes, Lisa R %A Law, Christopher S %A Stray-Pedersen, Asbjørg %A Cheng, Mickie H %A Mace, Emily M %A Anderson, Mark S %A Liu, Dongfang %A Tang, Ling Fung %A Nicholas, Sarah K %A Nahmod, Karen %A Makedonas, George %A Canter, Debra L %A Kwok, Pui-Yan %A Hicks, John %A Jones, Kirk D %A Penney, Samantha %A Jhangiani, Shalini N %A Rosenblum, Michael D %A Dell, Sharon D %A Waterfield, Michael R %A Papa, Feroz R %A Muzny, Donna M %A Zaitlen, Noah %A Leal, Suzanne M %A Gonzaga-Jauregui, Claudia %A Boerwinkle, Eric %A Eissa, N Tony %A Gibbs, Richard A %A Lupski, James R %A Orange, Jordan S %A Shum, Anthony K %K Amino Acid Sequence %K Arthritis %K Autoimmune Diseases %K Child, Preschool %K Coatomer Protein %K Endoplasmic Reticulum %K Endoplasmic Reticulum Stress %K Female %K Genetic Association Studies %K Genetic Predisposition to Disease %K Golgi Apparatus %K HEK293 Cells %K Humans %K Infant %K Lod Score %K Lung Diseases, Interstitial %K Male %K Molecular Sequence Data %K Pedigree %K Protein Transport %X

Unbiased genetic studies have uncovered surprising molecular mechanisms in human cellular immunity and autoimmunity. We performed whole-exome sequencing and targeted sequencing in five families with an apparent mendelian syndrome of autoimmunity characterized by high-titer autoantibodies, inflammatory arthritis and interstitial lung disease. We identified four unique deleterious variants in the COPA gene (encoding coatomer subunit α) affecting the same functional domain. Hypothesizing that mutant COPA leads to defective intracellular transport via coat protein complex I (COPI), we show that COPA variants impair binding to proteins targeted for retrograde Golgi-to-ER transport. Additionally, expression of mutant COPA results in ER stress and the upregulation of cytokines priming for a T helper type 17 (TH17) response. Patient-derived CD4(+) T cells also demonstrate significant skewing toward a TH17 phenotype that is implicated in autoimmunity. Our findings uncover an unexpected molecular link between a vesicular transport protein and a syndrome of autoimmunity manifested by lung and joint disease.

%B Nat Genet %V 47 %P 654-60 %8 2015 Jun %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/25894502?dopt=Abstract %R 10.1038/ng.3279 %0 Journal Article %J Am J Hum Genet %D 2015 %T De Novo GMNN Mutations Cause Autosomal-Dominant Primordial Dwarfism Associated with Meier-Gorlin Syndrome. %A Burrage, Lindsay C %A Charng, Wu-Lin %A Eldomery, Mohammad K %A Willer, Jason R %A Davis, Erica E %A Lugtenberg, Dorien %A Zhu, Wenmiao %A Leduc, Magalie S %A Akdemir, Zeynep C %A Azamian, Mahshid %A Zapata, Gladys %A Hernandez, Patricia P %A Schoots, Jeroen %A de Munnik, Sonja A %A Roepman, Ronald %A Pearring, Jillian N %A Jhangiani, Shalini %A Katsanis, Nicholas %A Vissers, Lisenka E L M %A Brunner, Han G %A Beaudet, Arthur L %A Rosenfeld, Jill A %A Muzny, Donna M %A Gibbs, Richard A %A Eng, Christine M %A Xia, Fan %A Lalani, Seema R %A Lupski, James R %A Bongers, Ernie M H F %A Yang, Yaping %K Adolescent %K Amino Acid Sequence %K Base Sequence %K Cell Cycle %K Child, Preschool %K Congenital Microtia %K Dwarfism %K Exons %K Female %K Geminin %K Gene Expression %K Genes, Dominant %K Growth Disorders %K Heterozygote %K High-Throughput Nucleotide Sequencing %K Humans %K Inheritance Patterns %K Male %K Micrognathism %K Molecular Sequence Data %K Mutation %K Patella %K Pedigree %K Protein Stability %K Proteolysis %K RNA Splicing %K Sequence Alignment %X

Meier-Gorlin syndrome (MGS) is a genetically heterogeneous primordial dwarfism syndrome known to be caused by biallelic loss-of-function mutations in one of five genes encoding pre-replication complex proteins: ORC1, ORC4, ORC6, CDT1, and CDC6. Mutations in these genes cause disruption of the origin of DNA replication initiation. To date, only an autosomal-recessive inheritance pattern has been described in individuals with this disorder, with a molecular etiology established in about three-fourths of cases. Here, we report three subjects with MGS and de novo heterozygous mutations in the 5' end of GMNN, encoding the DNA replication inhibitor geminin. We identified two truncating mutations in exon 2 (the 1(st) coding exon), c.16A>T (p.Lys6(∗)) and c.35_38delTCAA (p.Ile12Lysfs(∗)4), and one missense mutation, c.50A>G (p.Lys17Arg), affecting the second-to-last nucleotide of exon 2 and possibly RNA splicing. Geminin is present during the S, G2, and M phases of the cell cycle and is degraded during the metaphase-anaphase transition by the anaphase-promoting complex (APC), which recognizes the destruction box sequence near the 5' end of the geminin protein. All three GMNN mutations identified alter sites 5' to residue Met28 of the protein, which is located within the destruction box. We present data supporting a gain-of-function mechanism, in which the GMNN mutations result in proteins lacking the destruction box and hence increased protein stability and prolonged inhibition of replication leading to autosomal-dominant MGS.

%B Am J Hum Genet %V 97 %P 904-13 %8 2015 Dec 03 %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/26637980?dopt=Abstract %R 10.1016/j.ajhg.2015.11.006 %0 Journal Article %J Science %D 2015 %T DNA REPAIR. Mus81 and converging forks limit the mutagenicity of replication fork breakage. %A Mayle, Ryan %A Campbell, Ian M %A Beck, Christine R %A Yu, Yang %A Wilson, Marenda %A Shaw, Chad A %A Bjergbaek, Lotte %A Lupski, James R %A Ira, Grzegorz %K Alu Elements %K Base Sequence %K DNA Breaks, Double-Stranded %K DNA Repair %K DNA Replication %K DNA-Binding Proteins %K DNA-Directed DNA Polymerase %K Endonucleases %K Genomic Instability %K Humans %K Molecular Sequence Data %K Neoplasms %K Saccharomyces cerevisiae %K Saccharomyces cerevisiae Proteins %X

Most spontaneous DNA double-strand breaks (DSBs) result from replication-fork breakage. Break-induced replication (BIR), a genome rearrangement-prone repair mechanism that requires the Pol32/POLD3 subunit of eukaryotic DNA Polδ, was proposed to repair broken forks, but how genome destabilization is avoided was unknown. We show that broken fork repair initially uses error-prone Pol32-dependent synthesis, but that mutagenic synthesis is limited to within a few kilobases from the break by Mus81 endonuclease and a converging fork. Mus81 suppresses template switches between both homologous sequences and diverged human Alu repetitive elements, highlighting its importance for stability of highly repetitive genomes. We propose that lack of a timely converging fork or Mus81 may propel genome instability observed in cancer.

%B Science %V 349 %P 742-7 %8 2015 Aug 14 %G eng %N 6249 %1 https://www.ncbi.nlm.nih.gov/pubmed/26273056?dopt=Abstract %R 10.1126/science.aaa8391 %0 Journal Article %J Am J Hum Genet %D 2015 %T DVL1 frameshift mutations clustering in the penultimate exon cause autosomal-dominant Robinow syndrome. %A White, Janson %A Mazzeu, Juliana F %A Hoischen, Alexander %A Jhangiani, Shalini N %A Gambin, Tomasz %A Alcino, Michele Calijorne %A Penney, Samantha %A Saraiva, Jorge M %A Hove, Hanne %A Skovby, Flemming %A Kayserili, Hulya %A Estrella, Elicia %A Vulto-van Silfhout, Anneke T %A Steehouwer, Marloes %A Muzny, Donna M %A Sutton, V Reid %A Gibbs, Richard A %A Lupski, James R %A Brunner, Han G %A van Bon, Bregje W M %A Carvalho, Claudia M B %K Adaptor Proteins, Signal Transducing %K Amino Acid Sequence %K Base Sequence %K Craniofacial Abnormalities %K Dishevelled Proteins %K DNA Primers %K Dwarfism %K Exome %K Exons %K Frameshift Mutation %K Gene Components %K Humans %K Limb Deformities, Congenital %K Molecular Sequence Data %K Phosphoproteins %K Sequence Analysis, DNA %K Urogenital Abnormalities %X

Robinow syndrome is a genetically heterogeneous disorder characterized by mesomelic limb shortening, genital hypoplasia, and distinctive facial features and for which both autosomal-recessive and autosomal-dominant inheritance patterns have been described. Causative variants in the non-canonical signaling gene WNT5A underlie a subset of autosomal-dominant Robinow syndrome (DRS) cases, but most individuals with DRS remain without a molecular diagnosis. We performed whole-exome sequencing in four unrelated DRS-affected individuals without coding mutations in WNT5A and found heterozygous DVL1 exon 14 mutations in three of them. Targeted Sanger sequencing in additional subjects with DRS uncovered DVL1 exon 14 mutations in five individuals, including a pair of monozygotic twins. In total, six distinct frameshift mutations were found in eight subjects, and all were heterozygous truncating variants within the penultimate exon of DVL1. In five families in which samples from unaffected parents were available, the variants were demonstrated to represent de novo mutations. All variant alleles are predicted to result in a premature termination codon within the last exon, escape nonsense-mediated decay (NMD), and most likely generate a C-terminally truncated protein with a distinct -1 reading-frame terminus. Study of the transcripts extracted from affected subjects' leukocytes confirmed expression of both wild-type and variant alleles, supporting the hypothesis that mutant mRNA escapes NMD. Genomic variants identified in our study suggest that truncation of the C-terminal domain of DVL1, a protein hypothesized to have a downstream role in the Wnt-5a non-canonical pathway, is a common cause of DRS.

%B Am J Hum Genet %V 96 %P 612-22 %8 2015 Apr 02 %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/25817016?dopt=Abstract %R 10.1016/j.ajhg.2015.02.015 %0 Journal Article %J Cell Rep %D 2015 %T Exome Sequence Analysis Suggests that Genetic Burden Contributes to Phenotypic Variability and Complex Neuropathy. %A Gonzaga-Jauregui, Claudia %A Harel, Tamar %A Gambin, Tomasz %A Kousi, Maria %A Griffin, Laurie B %A Francescatto, Ludmila %A Ozes, Burcak %A Karaca, Ender %A Jhangiani, Shalini N %A Bainbridge, Matthew N %A Lawson, Kim S %A Pehlivan, Davut %A Okamoto, Yuji %A Withers, Marjorie %A Mancias, Pedro %A Slavotinek, Anne %A Reitnauer, Pamela J %A Goksungur, Meryem T %A Shy, Michael %A Crawford, Thomas O %A Koenig, Michel %A Willer, Jason %A Flores, Brittany N %A Pediaditrakis, Igor %A Us, Onder %A Wiszniewski, Wojciech %A Parman, Yesim %A Antonellis, Anthony %A Muzny, Donna M %A Katsanis, Nicholas %A Battaloglu, Esra %A Boerwinkle, Eric %A Gibbs, Richard A %A Lupski, James R %K Animals %K Charcot-Marie-Tooth Disease %K Exome %K Female %K Genetic Load %K Genetic Variation %K HSP40 Heat-Shock Proteins %K Humans %K Male %K Mutation %K Myelin P2 Protein %K Pedigree %K Penetrance %K Peripheral Nervous System Diseases %K Phenotype %K Serine C-Palmitoyltransferase %K Suppression, Genetic %K Zebrafish %X

Charcot-Marie-Tooth (CMT) disease is a clinically and genetically heterogeneous distal symmetric polyneuropathy. Whole-exome sequencing (WES) of 40 individuals from 37 unrelated families with CMT-like peripheral neuropathy refractory to molecular diagnosis identified apparent causal mutations in ∼ 45% (17/37) of families. Three candidate disease genes are proposed, supported by a combination of genetic and in vivo studies. Aggregate analysis of mutation data revealed a significantly increased number of rare variants across 58 neuropathy-associated genes in subjects versus controls, confirmed in a second ethnically discrete neuropathy cohort, suggesting that mutation burden potentially contributes to phenotypic variability. Neuropathy genes shown to have highly penetrant Mendelizing variants (HPMVs) and implicated by burden in families were shown to interact genetically in a zebrafish assay exacerbating the phenotype established by the suppression of single genes. Our findings suggest that the combinatorial effect of rare variants contributes to disease burden and variable expressivity.

%B Cell Rep %V 12 %P 1169-83 %8 2015 Aug 18 %G eng %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/26257172?dopt=Abstract %R 10.1016/j.celrep.2015.07.023 %0 Journal Article %J Am J Med Genet A %D 2015 %T Exome sequencing identifies a homozygous C5orf42 variant in a Turkish kindred with oral-facial-digital syndrome type VI. %A Bayram, Yavuz %A Aydin, Hatip %A Gambin, Tomasz %A Akdemir, Zeynep Coban %A Atik, Mehmed M %A Karaca, Ender %A Karaman, Ali %A Pehlivan, Davut %A Jhangiani, Shalini N %A Gibbs, Richard A %A Lupski, James R %K Abnormalities, Multiple %K Cerebellar Diseases %K Cerebellum %K Child %K Cleft Palate %K Exome %K Eye Abnormalities %K Female %K Genetic Predisposition to Disease %K Hamartoma %K Homozygote %K Humans %K Kidney Diseases, Cystic %K Magnetic Resonance Imaging %K Male %K Membrane Proteins %K Middle Aged %K Mutation %K Orofaciodigital Syndromes %K Phenotype %K Retina %K Turkey %X

Oral-facial-digital syndrome type VI (OFDVI) is a rare ciliopathy in the spectrum of Joubert syndrome (JS) and distinguished from other oral-facial-digital syndromes by metacarpal abnormalities with central polydactyly and by a molar tooth sign on cranial MRI. Additional characteristic features include short stature, micrognathia, posteriorly rotated low-set ears, hypertelorism, epicanthal folds, broad nasal tip, tongue hamartoma, upper lip notch, intraoral frenula, cleft lip/palate, and renal anomalies. Recently, novel mutations in C5orf42 were identified in 9 out of 11 OFDVI families. In a subsequent study C5orf42 was found to be mutated in only 2 out of 17 OFDVI probands while 28 patients with a pure JS phenotype also had pathogenic mutations of C5orf42. We report on two affected cousins diagnosed with OFDVI who were born from first degree cousin marriages. Whole exome sequencing (WES) identified a homozygous predicted damaging missense mutation (c.4034A > G; p.Gln1345Arg) in the C5orf42 gene. Our data contribute to the evidence that C5orf42 is one of the causative genes for OFDVI.

%B Am J Med Genet A %V 167A %P 2132-7 %8 2015 Sep %G eng %N 9 %1 https://www.ncbi.nlm.nih.gov/pubmed/25846457?dopt=Abstract %R 10.1002/ajmg.a.37092 %0 Journal Article %J Hum Genet %D 2015 %T Exome sequencing reveals homozygous TRIM2 mutation in a patient with early onset CMT and bilateral vocal cord paralysis. %A Pehlivan, Davut %A Coban Akdemir, Zeynep %A Karaca, Ender %A Bayram, Yavuz %A Jhangiani, Shalini %A Yildiz, Edibe Pembegul %A Muzny, Donna %A Uluc, Kayihan %A Gibbs, Richard A %A Elcioglu, Nursel %A Lupski, James R %A Harel, Tamar %K Adult %K Charcot-Marie-Tooth Disease %K Exome %K Female %K High-Throughput Nucleotide Sequencing %K Homozygote %K Humans %K Infant, Newborn %K Male %K Mutation, Missense %K Nuclear Proteins %K Vocal Cord Paralysis %X

Charcot-Marie-Tooth disease is a heterogeneous group of inherited distal symmetric polyneuropathies associated with mutations in genes encoding components essential for normal functioning of the Schwann cell and axon. TRIM2, encoding a ligase that ubiquitinates the neurofilament light chain, was recently associated with early-onset neuropathy in a single patient. We report a TRIM2 homozygous missense mutation (c.2000A>C; p.D667A) in a patient with peripheral neuropathy and bilateral vocal cord paralysis, allowing for further delineation of the associated phenotypic spectrum.

%B Hum Genet %V 134 %P 671-3 %8 2015 Jun %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/25893792?dopt=Abstract %R 10.1007/s00439-015-1548-3 %0 Journal Article %J Am J Med Genet A %D 2015 %T FBN1 contributing to familial congenital diaphragmatic hernia. %A Beck, Tyler F %A Campeau, Philippe M %A Jhangiani, Shalini N %A Gambin, Tomasz %A Li, Alexander H %A Abo-Zahrah, Reem %A Jordan, Valerie K %A Hernandez-Garcia, Andres %A Wiszniewski, Wojciech K %A Muzny, Donna %A Gibbs, Richard A %A Boerwinkle, Eric %A Lupski, James R %A Lee, Brendan %A Reardon, Willie %A Scott, Daryl A %K Adult %K Child, Preschool %K DNA Mutational Analysis %K Exome %K Female %K Fibrillin-1 %K Fibrillins %K Frameshift Mutation %K Genetic Association Studies %K Hernias, Diaphragmatic, Congenital %K Humans %K Male %K Marfan Syndrome %K Microfilament Proteins %K Pedigree %X

Congenital diaphragmatic hernia (CDH) is a relatively common, life--threatening birth defect. We present a family with recurrent CDH--paraesophageal and central--for whom exome sequencing (ES) revealed a frameshift mutation (c.4969_4970insA, p.Ile1657Asnfs*30) in the fibrillin 1 gene (FBN1) that causes Marfan syndrome. A diagnosis of Marfan syndrome had not been considered previously in this family. However, a review of the literature demonstrated that FBN1 mutations have an unusual pattern of CDH in which paraesophageal hernias are particularly common. Subsequent clinical evaluations revealed evidence for ectopia lentis in affected family members supporting a clinical diagnosis of Marfan syndrome. Since only two other cases of familial CDH have been described in association with FBN1 mutations, we investigated an oligogenic hypothesis by examining ES data for deleterious sequence changes in other CDH-related genes. This search revealed putatively deleterious sequence changes in four other genes that have been shown to cause diaphragm defects in humans and/or mice--FREM1, DES, PAX3 and MET. It is unclear whether these changes, alone or in aggregate, are contributing to the development of CDH in this family. However, their individual contribution is likely to be small compared to that of the frameshift mutation in FBN1. We conclude that ES can be used to identify both major and minor genetic factors that may contribute to CDH. These results also suggest that ES should be considered in the diagnostic evaluation of individuals and families with CDH, particularly when other diagnostic modalities have failed to reveal a molecular etiology.

%B Am J Med Genet A %V 167A %P 831-6 %8 2015 Apr %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/25736269?dopt=Abstract %R 10.1002/ajmg.a.36960 %0 Journal Article %J Genome Med %D 2015 %T From genes to genomes in the clinic. %A Veltman, Joris A %A Lupski, James R %X

Next-generation sequencing is revolutionizing medical genetics and in the near future will pervade all medical fields. To maximize the potential clinical utility of this approach, global data sharing and phenotyping are needed, and the role of the geneticist in the interpretation of variation is vital.

%B Genome Med %V 7 %P 78 %8 2015 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/26221187?dopt=Abstract %R 10.1186/s13073-015-0200-0 %0 Journal Article %J Neuron %D 2015 %T Genes that Affect Brain Structure and Function Identified by Rare Variant Analyses of Mendelian Neurologic Disease. %A Karaca, Ender %A Harel, Tamar %A Pehlivan, Davut %A Jhangiani, Shalini N %A Gambin, Tomasz %A Coban Akdemir, Zeynep %A Gonzaga-Jauregui, Claudia %A Erdin, Serkan %A Bayram, Yavuz %A Campbell, Ian M %A Hunter, Jill V %A Atik, Mehmed M %A Van Esch, Hilde %A Yuan, Bo %A Wiszniewski, Wojciech %A Isikay, Sedat %A Yesil, Gozde %A Yuregir, Ozge O %A Tug Bozdogan, Sevcan %A Aslan, Huseyin %A Aydin, Hatip %A Tos, Tulay %A Aksoy, Ayse %A De Vivo, Darryl C %A Jain, Preti %A Geckinli, B Bilge %A Sezer, Ozlem %A Gul, Davut %A Durmaz, Burak %A Cogulu, Ozgur %A Ozkinay, Ferda %A Topcu, Vehap %A Candan, Sukru %A Cebi, Alper Han %A Ikbal, Mevlit %A Yilmaz Gulec, Elif %A Gezdirici, Alper %A Koparir, Erkan %A Ekici, Fatma %A Coskun, Salih %A Cicek, Salih %A Karaer, Kadri %A Koparir, Asuman %A Duz, Mehmet Bugrahan %A Kirat, Emre %A Fenercioglu, Elif %A Ulucan, Hakan %A Seven, Mehmet %A Guran, Tulay %A Elcioglu, Nursel %A Yildirim, Mahmut Selman %A Aktas, Dilek %A Alikaşifoğlu, Mehmet %A Ture, Mehmet %A Yakut, Tahsin %A Overton, John D %A Yuksel, Adnan %A Ozen, Mustafa %A Muzny, Donna M %A Adams, David R %A Boerwinkle, Eric %A Chung, Wendy K %A Gibbs, Richard A %A Lupski, James R %K Brain %K Cohort Studies %K Databases, Genetic %K Female %K Gene Regulatory Networks %K Genetic Association Studies %K Genetic Variation %K Humans %K Male %K Mendelian Randomization Analysis %K Nervous System Diseases %K Pedigree %X

Development of the human nervous system involves complex interactions among fundamental cellular processes and requires a multitude of genes, many of which remain to be associated with human disease. We applied whole exome sequencing to 128 mostly consanguineous families with neurogenetic disorders that often included brain malformations. Rare variant analyses for both single nucleotide variant (SNV) and copy number variant (CNV) alleles allowed for identification of 45 novel variants in 43 known disease genes, 41 candidate genes, and CNVs in 10 families, with an overall potential molecular cause identified in >85% of families studied. Among the candidate genes identified, we found PRUNE, VARS, and DHX37 in multiple families and homozygous loss-of-function variants in AGBL2, SLC18A2, SMARCA1, UBQLN1, and CPLX1. Neuroimaging and in silico analysis of functional and expression proximity between candidate and known disease genes allowed for further understanding of genetic networks underlying specific types of brain malformations.

%B Neuron %V 88 %P 499-513 %8 2015 Nov 04 %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/26539891?dopt=Abstract %R 10.1016/j.neuron.2015.09.048 %0 Journal Article %J Am J Hum Genet %D 2015 %T The Genetic Basis of Mendelian Phenotypes: Discoveries, Challenges, and Opportunities. %A Chong, Jessica X %A Buckingham, Kati J %A Jhangiani, Shalini N %A Boehm, Corinne %A Sobreira, Nara %A Smith, Joshua D %A Harrell, Tanya M %A McMillin, Margaret J %A Wiszniewski, Wojciech %A Gambin, Tomasz %A Coban Akdemir, Zeynep H %A Doheny, Kimberly %A Scott, Alan F %A Avramopoulos, Dimitri %A Chakravarti, Aravinda %A Hoover-Fong, Julie %A Mathews, Debra %A Witmer, P Dane %A Ling, Hua %A Hetrick, Kurt %A Watkins, Lee %A Patterson, Karynne E %A Reinier, Frederic %A Blue, Elizabeth %A Muzny, Donna %A Kircher, Martin %A Bilguvar, Kaya %A López-Giráldez, Francesc %A Sutton, V Reid %A Tabor, Holly K %A Leal, Suzanne M %A Gunel, Murat %A Mane, Shrikant %A Gibbs, Richard A %A Boerwinkle, Eric %A Hamosh, Ada %A Shendure, Jay %A Lupski, James R %A Lifton, Richard P %A Valle, David %A Nickerson, Deborah A %A Bamshad, Michael J %K Genetic Diseases, Inborn %K Genetics, Medical %K Humans %K Phenotype %K Proteins %X

Discovering the genetic basis of a Mendelian phenotype establishes a causal link between genotype and phenotype, making possible carrier and population screening and direct diagnosis. Such discoveries also contribute to our knowledge of gene function, gene regulation, development, and biological mechanisms that can be used for developing new therapeutics. As of February 2015, 2,937 genes underlying 4,163 Mendelian phenotypes have been discovered, but the genes underlying ∼50% (i.e., 3,152) of all known Mendelian phenotypes are still unknown, and many more Mendelian conditions have yet to be recognized. This is a formidable gap in biomedical knowledge. Accordingly, in December 2011, the NIH established the Centers for Mendelian Genomics (CMGs) to provide the collaborative framework and infrastructure necessary for undertaking large-scale whole-exome sequencing and discovery of the genetic variants responsible for Mendelian phenotypes. In partnership with 529 investigators from 261 institutions in 36 countries, the CMGs assessed 18,863 samples from 8,838 families representing 579 known and 470 novel Mendelian phenotypes as of January 2015. This collaborative effort has identified 956 genes, including 375 not previously associated with human health, that underlie a Mendelian phenotype. These results provide insight into study design and analytical strategies, identify novel mechanisms of disease, and reveal the extensive clinical variability of Mendelian phenotypes. Discovering the gene underlying every Mendelian phenotype will require tackling challenges such as worldwide ascertainment and phenotypic characterization of families affected by Mendelian conditions, improvement in sequencing and analytical techniques, and pervasive sharing of phenotypic and genomic data among researchers, clinicians, and families.

%B Am J Hum Genet %V 97 %P 199-215 %8 2015 Aug 06 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/26166479?dopt=Abstract %R 10.1016/j.ajhg.2015.06.009 %0 Journal Article %J Eur J Endocrinol %D 2015 %T Germline PRKACA amplification causes variable phenotypes that may depend on the extent of the genomic defect: molecular mechanisms and clinical presentations. %A Lodish, Maya B %A Bo Yuan %A Levy, Isaac %A Braunstein, Glenn D %A Lyssikatos, Charalampos %A Salpea, Paraskevi %A Szarek, Eva %A Karageorgiadis, Alexander S %A Belyavskaya, Elena %A Raygada, Margarita %A Faucz, Fabio Rueda %A Izzat, Louise %A Brain, Caroline %A Gardner, James %A Quezado, Martha %A Carney, J Aidan %A James R Lupski %A Stratakis, Constantine A %K Adrenal Glands %K Adrenalectomy %K Adult %K Child %K Child, Preschool %K Cushing Syndrome %K Cyclic AMP-Dependent Protein Kinase Catalytic Subunits %K DNA Copy Number Variations %K Female %K Gene Amplification %K Humans %K Hyperplasia %K Male %K Phenotype %K Young Adult %X

OBJECTIVE: We have recently reported five patients with bilateral adrenocortical hyperplasia (BAH) and Cushing's syndrome (CS) caused by constitutive activation of the catalytic subunit of protein kinase A (PRKACA). By doing new in-depth analysis of their cytogenetic abnormality, we attempted a better genotype-phenotype correlation of their PRKACA amplification.

DESIGN: This study is a case series.

METHODS: Molecular cytogenetic, genomic, clinical, and histopathological analyses were performed in five patients with CS.

RESULTS: Reinvestigation of the defects of previously described patients by state-of-the-art molecular cytogenetics showed complex genomic rearrangements in the chromosome 19p13.2p13.12 locus, resulting in copy number gains encompassing the entire PRKACA gene; three patients (one sporadic case and two related cases) were observed with gains consistent with duplications, while two sporadic patients were observed with gains consistent with triplications. Although all five patients presented with ACTH-independent CS, the three sporadic patients had micronodular BAH and underwent bilateral adrenalectomy in early childhood, whereas the two related patients, a mother and a son, presented with macronodular BAH as adults. In at least one patient, PRKACA triplication was associated with a more severe phenotype.

CONCLUSIONS: Constitutional chromosomal PRKACA gene amplification is a recently identified genetic defect associated with CS, a trait that may be inherited in an autosomal dominant manner or occur de novo. Genomic rearrangements can be complex and can result in different copy number states of dosage-sensitive genes, e.g., duplication and triplication. PRKACA amplification can lead to variable phenotypes clinically and pathologically, both micro- and macro-nodular BAH, the latter of which we speculate may depend on the extent of amplification.

%B Eur J Endocrinol %V 172 %P 803-11 %8 2015 06 %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/25924874?dopt=Abstract %R 10.1530/EJE-14-1154 %0 Journal Article %J J Clin Invest %D 2015 %T Global transcriptional disturbances underlie Cornelia de Lange syndrome and related phenotypes. %A Yuan, Bo %A Pehlivan, Davut %A Karaca, Ender %A Patel, Nisha %A Charng, Wu-Lin %A Gambin, Tomasz %A Gonzaga-Jauregui, Claudia %A Sutton, V Reid %A Yesil, Gozde %A Bozdogan, Sevcan Tug %A Tos, Tulay %A Koparir, Asuman %A Koparir, Erkan %A Beck, Christine R %A Gu, Shen %A Aslan, Huseyin %A Yuregir, Ozge Ozalp %A Al Rubeaan, Khalid %A Alnaqeb, Dhekra %A Alshammari, Muneera J %A Bayram, Yavuz %A Atik, Mehmed M %A Aydin, Hatip %A Geckinli, B Bilge %A Seven, Mehmet %A Ulucan, Hakan %A Fenercioglu, Elif %A Ozen, Mustafa %A Jhangiani, Shalini %A Muzny, Donna M %A Boerwinkle, Eric %A Tuysuz, Beyhan %A Alkuraya, Fowzan S %A Gibbs, Richard A %A Lupski, James R %K Adolescent %K Adult %K Cell Cycle Proteins %K Child %K Child, Preschool %K Chondroitin Sulfate Proteoglycans %K Chromosomal Proteins, Non-Histone %K Codon, Nonsense %K De Lange Syndrome %K Exome %K Exonucleases %K Gene Expression Profiling %K Gene Expression Regulation %K Genome-Wide Association Study %K Heterozygote %K Histone Deacetylases %K Histone-Lysine N-Methyltransferase %K Humans %K Infant %K Male %K Myeloid-Lymphoid Leukemia Protein %K Phenotype %K Proteins %K Repressor Proteins %K Transcriptome %X

Cornelia de Lange syndrome (CdLS) is a genetically heterogeneous disorder that presents with extensive phenotypic variability, including facial dysmorphism, developmental delay/intellectual disability (DD/ID), abnormal extremities, and hirsutism. About 65% of patients harbor mutations in genes that encode subunits or regulators of the cohesin complex, including NIPBL, SMC1A, SMC3, RAD21, and HDAC8. Wiedemann-Steiner syndrome (WDSTS), which shares CdLS phenotypic features, is caused by mutations in lysine-specific methyltransferase 2A (KMT2A). Here, we performed whole-exome sequencing (WES) of 2 male siblings clinically diagnosed with WDSTS; this revealed a hemizygous, missense mutation in SMC1A that was predicted to be deleterious. Extensive clinical evaluation and WES of 32 Turkish patients clinically diagnosed with CdLS revealed the presence of a de novo heterozygous nonsense KMT2A mutation in 1 patient without characteristic WDSTS features. We also identified de novo heterozygous mutations in SMC3 or SMC1A that affected RNA splicing in 2 independent patients with combined CdLS and WDSTS features. Furthermore, in families from 2 separate world populations segregating an autosomal-recessive disorder with CdLS-like features, we identified homozygous mutations in TAF6, which encodes a core transcriptional regulatory pathway component. Together, our data, along with recent transcriptome studies, suggest that CdLS and related phenotypes may be "transcriptomopathies" rather than cohesinopathies.

%B J Clin Invest %V 125 %P 636-51 %8 2015 Feb %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/25574841?dopt=Abstract %R 10.1172/JCI77435 %0 Journal Article %J J Clin Endocrinol Metab %D 2015 %T Homozygous loss-of-function mutations in SOHLH1 in patients with nonsyndromic hypergonadotropic hypogonadism. %A Bayram, Yavuz %A Gulsuner, Suleyman %A Guran, Tulay %A Abaci, Ayhan %A Yesil, Gozde %A Gulsuner, Hilal Unal %A Atay, Zeynep %A Pierce, Sarah B %A Gambin, Tomasz %A Lee, Ming %A Turan, Serap %A Bober, Ece %A Atik, Mehmed M %A Walsh, Tom %A Karaca, Ender %A Pehlivan, Davut %A Jhangiani, Shalini N %A Muzny, Donna %A Bereket, Abdullah %A Buyukgebiz, Atilla %A Boerwinkle, Eric %A Gibbs, Richard A %A King, Mary-Claire %A Lupski, James R %K Adolescent %K Basic Helix-Loop-Helix Transcription Factors %K Child %K Exome %K Female %K Homozygote %K Humans %K Hypogonadism %K Mutation %X

CONTEXT: Hypergonadotropic hypogonadism presents in females with delayed or arrested puberty, primary or secondary amenorrhea due to gonadal dysfunction, and is further characterized by elevated gonadotropins and low sex steroids. Chromosomal aberrations and various specific gene defects can lead to hypergonadotropic hypogonadism. Responsible genes include those with roles in gonadal development or maintenance, sex steroid synthesis, or end-organ resistance to gonadotropins. Identification of novel causative genes in this disorder will contribute to our understanding of the regulation of human reproductive function.

OBJECTIVES: The aim of this study was to identify and report the gene responsible for autosomal-recessive hypergonadotropic hypogonadism in two unrelated families.

DESIGN AND PARTICIPANTS: Clinical evaluation and whole-exome sequencing were performed in two pairs of sisters with nonsyndromic hypergonadotropic hypogonadism from two unrelated families.

RESULTS: Exome sequencing analysis revealed two different truncating mutations in the same gene: SOHLH1 c.705delT (p.Pro235fs*4) and SOHLH1 c.27C>G (p.Tyr9stop). Both mutations were unique to the families and segregation was consistent with Mendelian expectations for an autosomal-recessive mode of inheritance.

CONCLUSIONS: Sohlh1 was known from previous mouse studies to be a transcriptional regulator that functions in the maintenance and survival of primordial ovarian follicles, but loss-of-function mutations in human females have not been reported. Our results provide evidence that homozygous-truncating mutations in SOHLH1 cause female nonsyndromic hypergonadotropic hypogonadism.

%B J Clin Endocrinol Metab %V 100 %P E808-14 %8 2015 May %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/25774885?dopt=Abstract %R 10.1210/jc.2015-1150 %0 Journal Article %J Eur J Hum Genet %D 2015 %T Mutations in COL27A1 cause Steel syndrome and suggest a founder mutation effect in the Puerto Rican population. %A Gonzaga-Jauregui, Claudia %A Gamble, Candace N %A Yuan, Bo %A Penney, Samantha %A Jhangiani, Shalini %A Muzny, Donna M %A Gibbs, Richard A %A Lupski, James R %A Hecht, Jacqueline T %K Amino Acid Sequence %K Child, Preschool %K Comparative Genomic Hybridization %K Exome %K Female %K Fibrillar Collagens %K Follow-Up Studies %K Founder Effect %K Genotype %K Hispanic or Latino %K Humans %K Infant %K Male %K Molecular Sequence Data %K Mutation %K Osteochondrodysplasias %K Pedigree %K Polymorphism, Single Nucleotide %K Prostaglandins F %K Puerto Rico %K Sequence Alignment %X

Osteochondrodysplasias represent a large group of developmental structural disorders that can be caused by mutations in a variety of genes responsible for chondrocyte development, differentiation, mineralization and early ossification. The application of whole-exome sequencing to disorders apparently segregating as Mendelian traits has proven to be an effective approach to disease gene identification for conditions with unknown molecular etiology. We identified a homozygous missense variant p.(Gly697Arg) in COL27A1, in a family with Steel syndrome and no consanguinity. Interestingly, the identified variant seems to have arisen as a founder mutation in the Puerto Rican population.

%B Eur J Hum Genet %V 23 %P 342-6 %8 2015 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/24986830?dopt=Abstract %R 10.1038/ejhg.2014.107 %0 Journal Article %J JAMA Ophthalmol %D 2015 %T New mutations in the RAB28 gene in 2 Spanish families with cone-rod dystrophy. %A Riveiro-Álvarez, Rosa %A Xie, Yajing Angela %A López-Martínez, Miguel-Ángel %A Gambin, Tomasz %A Pérez-Carro, Raquel %A Ávila-Fernández, Almudena %A López-Molina, María-Isabel %A Zernant, Jana %A Jhangiani, Shalini %A Muzny, Donna %A Yuan, Bo %A Boerwinkle, Eric %A Gibbs, Richard %A Lupski, James R %A Ayuso, Carmen %A Allikmets, Rando %K Adolescent %K Adult %K Child %K Diagnosis, Differential %K DNA Mutational Analysis %K Female %K Follow-Up Studies %K Genetic Predisposition to Disease %K Hispanic or Latino %K Humans %K Male %K Microscopy, Acoustic %K Mutation %K Pedigree %K Phenotype %K rab GTP-Binding Proteins %K Retinitis Pigmentosa %K Retrospective Studies %K Young Adult %X

IMPORTANCE: The families evaluated in this study represent the second report of cone-rod dystrophy (CRD) cases caused by mutations in RAB28, a recently discovered gene associated with CRD.

OBJECTIVE: To determine the disease-causing gene in 2 families of Spanish descent presenting with CRD who do not have ABCA4 mutations.

DESIGN, SETTING, AND PARTICIPANTS: Molecular genetics and observational case studies of 2 families, each with 1 affected proband with CRD and 3 or 5 unaffected family members. The affected individual from each family received a complete ophthalmic examination including assessment of refractive errors and best-corrected visual acuity, biomicroscopy, color fundus photography, electroretinography analysis, and visual-evoked potential analysis. After complete sequencing of the ABCA4 gene with negative results, the screening for disease-causing mutations was performed by whole-exome sequencing. Possible disease-associated variants were determined by filtering based on minor allele frequency, predicted pathogenicity, and segregation analysis in all family members.

MAIN OUTCOMES AND MEASURES: The appearance of the macula was evaluated by clinical examination, fundus photography, and fundus autofluorescence imaging, and visual function was assessed by electroretinography. Disease-causing mutations were assessed by sequence analyses.

RESULTS: Ophthalmologic findings included markedly reduced visual acuity, bull's eye maculopathy, foveal hyperpigmentation, peripapillary atrophy, dyschromatopsia, extinguished photopic responses, and reduced scotopic responses observed on electroretinography consistent with the CRD phenotype often associated with ABCA4 mutations. Although no ABCA4 mutations were detected in either patient, whole-exome sequencing analysis identified 2 new homozygous mutations in the recently described RAB28 gene, the c.172 + 1G>C splice site variant in IVS2 and the missense c.T651G:p.C217W substitution. Both variants were determined as deleterious by predictive programs and were segregated with the disease in both families. Sequencing of 107 additional patients of Spanish descent with CRD did not reveal other cases with RAB28 mutations.

CONCLUSIONS AND RELEVANCE: Deleterious mutations in RAB28 result in a classic CRD phenotype and are an infrequent cause of CRD in the Spanish population.

%B JAMA Ophthalmol %V 133 %P 133-9 %8 2015 Feb %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/25356532?dopt=Abstract %R 10.1001/jamaophthalmol.2014.4266 %0 Journal Article %J Hum Mol Genet %D 2015 %T Non-coding genetic variants in human disease. %A Zhang, Feng %A Lupski, James R %K Animals %K Disease %K DNA Copy Number Variations %K Genetic Variation %K Genome-Wide Association Study %K Humans %K Polymorphism, Single Nucleotide %K Regulatory Sequences, Nucleic Acid %X

Genetic variants, including single-nucleotide variants (SNVs) and copy number variants (CNVs), in the non-coding regions of the human genome can play an important role in human traits and complex diseases. Most of the genome-wide association study (GWAS) signals map to non-coding regions and potentially point to non-coding variants, whereas their functional interpretation is challenging. In this review, we discuss the human non-coding variants and their contributions to human diseases in the following four parts. (i) Functional annotations of non-coding SNPs mapped by GWAS: we discuss recent progress revealing some of the molecular mechanisms for GWAS signals affecting gene function. (ii) Technical progress in interpretation of non-coding variants: we briefly describe some of the technologies for functional annotations of non-coding variants, including the methods for genome-wide mapping of chromatin interaction, computational tools for functional predictions and the new genome editing technologies useful for dissecting potential functional consequences of non-coding variants. (iii) Non-coding CNVs in human diseases: we review our emerging understanding the role of non-coding CNVs in human disease. (iv) Compound inheritance of large genomic deletions and non-coding variants: compound inheritance at a locus consisting of coding variants plus non-coding ones is described.

%B Hum Mol Genet %V 24 %P R102-10 %8 2015 Oct 15 %G eng %N R1 %1 https://www.ncbi.nlm.nih.gov/pubmed/26152199?dopt=Abstract %R 10.1093/hmg/ddv259 %0 Journal Article %J Am J Hum Genet %D 2015 %T Nonrecurrent 17p11.2p12 Rearrangement Events that Result in Two Concomitant Genomic Disorders: The PMP22-RAI1 Contiguous Gene Duplication Syndrome. %A Yuan, Bo %A Harel, Tamar %A Gu, Shen %A Liu, Pengfei %A Burglen, Lydie %A Chantot-Bastaraud, Sandra %A Gelowani, Violet %A Beck, Christine R %A Carvalho, Claudia M B %A Cheung, Sau Wai %A Coe, Andrew %A Malan, Valérie %A Munnich, Arnold %A Magoulas, Pilar L %A Potocki, Lorraine %A Lupski, James R %K Abnormalities, Multiple %K Charcot-Marie-Tooth Disease %K Child %K Child, Preschool %K Chromosome Disorders %K Chromosome Duplication %K Chromosomes, Human, Pair 17 %K Comparative Genomic Hybridization %K Female %K Follow-Up Studies %K Gene Duplication %K Gene Rearrangement %K Genome, Human %K Genomics %K Humans %K Infant %K Male %K Models, Genetic %K Myelin Proteins %K Phenotype %K Prognosis %K Recombination, Genetic %K Trans-Activators %K Transcription Factors %X

The genomic duplication associated with Potocki-Lupski syndrome (PTLS) maps in close proximity to the duplication associated with Charcot-Marie-Tooth disease type 1A (CMT1A). PTLS is characterized by hypotonia, failure to thrive, reduced body weight, intellectual disability, and autistic features. CMT1A is a common autosomal dominant distal symmetric peripheral polyneuropathy. The key dosage-sensitive genes RAI1 and PMP22 are respectively associated with PTLS and CMT1A. Recurrent duplications accounting for the majority of subjects with these conditions are mediated by nonallelic homologous recombination between distinct low-copy repeat (LCR) substrates. The LCRs flanking a contiguous genomic interval encompassing both RAI1 and PMP22 do not share extensive homology; thus, duplications encompassing both loci are rare and potentially generated by a different mutational mechanism. We characterized genomic rearrangements that simultaneously duplicate PMP22 and RAI1, including nine potential complex genomic rearrangements, in 23 subjects by high-resolution array comparative genomic hybridization and breakpoint junction sequencing. Insertions and microhomologies were found at the breakpoint junctions, suggesting potential replicative mechanisms for rearrangement formation. At the breakpoint junctions of these nonrecurrent rearrangements, enrichment of repetitive DNA sequences was observed, indicating that they might predispose to genomic instability and rearrangement. Clinical evaluation revealed blended PTLS and CMT1A phenotypes with a potential earlier onset of neuropathy. Moreover, additional clinical findings might be observed due to the extra duplicated material included in the rearrangements. Our genomic analysis suggests replicative mechanisms as a predominant mechanism underlying PMP22-RAI1 contiguous gene duplications and provides further evidence supporting the role of complex genomic architecture in genomic instability.

%B Am J Hum Genet %V 97 %P 691-707 %8 2015 Nov 05 %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/26544804?dopt=Abstract %R 10.1016/j.ajhg.2015.10.003 %0 Journal Article %J BMC Genomics %D 2015 %T PacBio-LITS: a large-insert targeted sequencing method for characterization of human disease-associated chromosomal structural variations. %A Wang, Min %A Beck, Christine R %A English, Adam C %A Meng, Qingchang %A Buhay, Christian %A Han, Yi %A Doddapaneni, Harsha V %A Yu, Fuli %A Boerwinkle, Eric %A Lupski, James R %A Muzny, Donna M %A Gibbs, Richard A %K Chromosome Aberrations %K Gene Library %K Gene Rearrangement %K Genetic Association Studies %K Genomics %K High-Throughput Nucleotide Sequencing %K Humans %K Workflow %X

BACKGROUND: Generation of long (>5 Kb) DNA sequencing reads provides an approach for interrogation of complex regions in the human genome. Currently, large-insert whole genome sequencing (WGS) technologies from Pacific Biosciences (PacBio) enable analysis of chromosomal structural variations (SVs), but the cost to achieve the required sequence coverage across the entire human genome is high.

RESULTS: We developed a method (termed PacBio-LITS) that combines oligonucleotide-based DNA target-capture enrichment technologies with PacBio large-insert library preparation to facilitate SV studies at specific chromosomal regions. PacBio-LITS provides deep sequence coverage at the specified sites at substantially reduced cost compared with PacBio WGS. The efficacy of PacBio-LITS is illustrated by delineating the breakpoint junctions of low copy repeat (LCR)-associated complex structural rearrangements on chr17p11.2 in patients diagnosed with Potocki-Lupski syndrome (PTLS; MIM#610883). We successfully identified previously determined breakpoint junctions in three PTLS cases, and also were able to discover novel junctions in repetitive sequences, including LCR-mediated breakpoints. The new information has enabled us to propose mechanisms for formation of these structural variants.

CONCLUSIONS: The new method leverages the cost efficiency of targeted capture-sequencing as well as the mappability and scaffolding capabilities of long sequencing reads generated by the PacBio platform. It is therefore suitable for studying complex SVs, especially those involving LCRs, inversions, and the generation of chimeric Alu elements at the breakpoints. Other genomic research applications, such as haplotype phasing and small insertion and deletion validation could also benefit from this technology.

%B BMC Genomics %V 16 %P 214 %8 2015 Mar 19 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/25887218?dopt=Abstract %R 10.1186/s12864-015-1370-2 %0 Journal Article %J Am J Med Genet A %D 2015 %T Rare variants in the notch signaling pathway describe a novel type of autosomal recessive Klippel-Feil syndrome. %A Karaca, Ender %A Yuregir, Ozge O %A Bozdogan, Sevcan T %A Aslan, Huseyin %A Pehlivan, Davut %A Jhangiani, Shalini N %A Akdemir, Zeynep C %A Gambin, Tomasz %A Bayram, Yavuz %A Atik, Mehmed M %A Erdin, Serkan %A Muzny, Donna %A Gibbs, Richard A %A Lupski, James R %K Adolescent %K Base Sequence %K Female %K Humans %K Klippel-Feil Syndrome %K Male %K Molecular Sequence Data %K Mutation %K Pedigree %K Radiography %K Receptors, Notch %K Signal Transduction %K Spine %X

Klippel-Feil syndrome is a rare disorder represented by a subgroup of segmentation defects of the vertebrae and characterized by fusion of the cervical vertebrae, low posterior hairline, and short neck with limited motion. Both autosomal dominant and recessive inheritance patterns were reported in families with Klippel-Feil. Mutated genes for both dominant (GDF6 and GDF3) and recessive (MEOX1) forms of Klippel-Feil syndrome have been shown to be involved in somite development via transcription regulation and signaling pathways. Heterotaxy arises from defects in proteins that function in the development of left-right asymmetry of the developing embryo. We describe a consanguineous family with a male proband who presents with classical Klippel-Feil syndrome together with heterotaxy (situs inversus totalis). The present patient also had Sprengel's deformity, deformity of the sternum, and a solitary kidney. Using exome sequencing, we identified a homozygous frameshift mutation (c.299delT; p.L100fs) in RIPPLY2, a gene shown to play a crucial role in somitogenesis and participate in the Notch signaling pathway via negatively regulating Tbx6. Our data confirm RIPPLY2 as a novel gene for autosomal recessive Klippel-Feil syndrome, and in addition-from a mechanistic standpoint-suggest the possibility that mutations in RIPPLY2 could also lead to heterotaxy. © 2015 Wiley Periodicals, Inc.

%B Am J Med Genet A %V 167A %P 2795-9 %8 2015 Nov %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/26238661?dopt=Abstract %R 10.1002/ajmg.a.37263 %0 Journal Article %J Genome Med %D 2015 %T Secondary findings and carrier test frequencies in a large multiethnic sample. %A Gambin, Tomasz %A Jhangiani, Shalini N %A Below, Jennifer E %A Campbell, Ian M %A Wiszniewski, Wojciech %A Muzny, Donna M %A Staples, Jeffrey %A Morrison, Alanna C %A Bainbridge, Matthew N %A Penney, Samantha %A McGuire, Amy L %A Gibbs, Richard A %A Lupski, James R %A Boerwinkle, Eric %X

BACKGROUND: Besides its growing importance in clinical diagnostics and understanding the genetic basis of Mendelian and complex diseases, whole exome sequencing (WES) is a rich source of additional information of potential clinical utility for physicians, patients and their families. We analyzed the frequency and nature of single nucleotide variants (SNVs) considered secondary findings and recessive disease allele carrier status in the exomes of 8554 individuals from a large, randomly sampled cohort study and 2514 patients from a study of presumed Mendelian disease having undergone WES.

METHODS: We used the same sequencing platform and data processing pipeline to analyze all samples and characterized the distributions of reported pathogenic (ClinVar, Human Gene Mutation Database (HGMD)) and predicted deleterious variants in the pre-specified American College of Medical Genetics and Genomics (ACMG) secondary findings and recessive disease genes in different ethnic groups.

RESULTS: In the 56 ACMG secondary findings genes, the average number of predicted deleterious variants per individual was 0.74, and the mean number of ClinVar reported pathogenic variants was 0.06. We observed an average of 10 deleterious and 0.78 ClinVar reported pathogenic variants per individual in 1423 autosomal recessive disease genes. By repeatedly sampling pairs of exomes, 0.5 % of the randomly generated couples were at 25 % risk of having an affected offspring for an autosomal recessive disorder based on the ClinVar variants.

CONCLUSIONS: By investigating reported pathogenic and novel, predicted deleterious variants we estimated the lower and upper limits of the population fraction for which exome sequencing may reveal additional medically relevant information. We suggest that the observed wide range for the lower and upper limits of these frequency numbers will be gradually reduced due to improvement in classification databases and prediction algorithms.

%B Genome Med %V 7 %P 54 %8 2015 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/26195989?dopt=Abstract %R 10.1186/s13073-015-0171-1 %0 Journal Article %J Trends Genet %D 2015 %T Somatic mosaicism: implications for disease and transmission genetics. %A Campbell, Ian M %A Shaw, Chad A %A Stankiewicz, Pawel %A Lupski, James R %K Animals %K Genetic Diseases, Inborn %K Genome, Human %K Humans %K Mosaicism %K Mutagenesis, Insertional %K Mutation %K Polymorphism, Single Nucleotide %K Risk %K Trinucleotide Repeat Expansion %X

Nearly all of the genetic material among cells within an organism is identical. However, single-nucleotide variants (SNVs), small insertions/deletions (indels), copy-number variants (CNVs), and other structural variants (SVs) continually accumulate as cells divide during development. This process results in an organism composed of countless cells, each with its own unique personal genome. Thus, every human is undoubtedly mosaic. Mosaic mutations can go unnoticed, underlie genetic disease or normal human variation, and may be transmitted to the next generation as constitutional variants. We review the influence of the developmental timing of mutations, the mechanisms by which they arise, methods for detecting mosaic variants, and the risk of passing these mutations on to the next generation.

%B Trends Genet %V 31 %P 382-92 %8 2015 Jul %G eng %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/25910407?dopt=Abstract %R 10.1016/j.tig.2015.03.013 %0 Journal Article %J Ophthalmic Genet %D 2015 %T Whole Exome Sequencing Identifies an Adult-Onset Case of Methylmalonic Aciduria and Homocystinuria Type C (cblC) with Non-Syndromic Bull's Eye Maculopathy. %A Collison, Frederick T %A Xie, Yajing Angela %A Gambin, Tomasz %A Jhangiani, Shalini %A Muzny, Donna %A Gibbs, Richard %A Lupski, James R %A Fishman, Gerald A %A Allikmets, Rando %K Adult %K Carrier Proteins %K Electroretinography %K Exome %K Female %K Genetic Testing %K Heterozygote %K Homocystinuria %K Humans %K Macular Degeneration %K Mutation %K Oxidoreductases %K Pedigree %K Scotoma %K Sequence Analysis, DNA %K Tomography, Optical Coherence %K Visual Acuity %K Visual Fields %K Vitamin B 12 %K Vitamin B 12 Deficiency %K Vitamin B Complex %X

BACKGROUND: Methylmalonic aciduria and homocystinuria type C (cblC), a disorder of vitamin B12 (cobalamin) metabolism caused by mutations in the MMACHC gene, presents with many systemic symptoms, including neurological, cognitive, psychiatric, and thromboembolic events. Retinal phenotypes, including maculopathy, pigmentary retinopathy, and optic atrophy are common in early onset form of the disease but are rare in adult onset forms.

MATERIALS AND METHODS: An adult Hispanic female presented with decreased central vision, bilateral pericentral ring scotomas and bull's eye-appearing macular lesions at 28 years of age. Her medical history was otherwise unremarkable except for iron deficiency anemia and both urinary tract and kidney infections. Screening of the ABCA4 gene, mutations in which frequently cause bull's eye maculopathy, was negative. Subsequently, analysis with whole exome sequencing was performed.

RESULTS: Whole exome sequencing discovered compound heterozygous mutations in MMACHC, c.G482A:p.Arg161Gln and c.270_271insA:p.Arg91Lysfs*14, which segregated with the disease in the family. The genetic diagnosis was confirmed by biochemical laboratory testing, showing highly elevated urine methylmalonic acid/creatinine and homocysteine levels, and suggesting disease management with hydroxycobalamin injections and carnitine supplementation.

CONCLUSIONS: In summary, a unique case of an adult patient with bull's eye macular lesions and no clinically relevant systemic symptoms was diagnosed with cblC by genetic screening and follow-up biochemical laboratory tests.

%B Ophthalmic Genet %V 36 %P 270-5 %8 2015 %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/25687216?dopt=Abstract %R 10.3109/13816810.2015.1010736 %0 Journal Article %J J Clin Endocrinol Metab %D 2015 %T Whole-exome sequencing identifies homozygous GPR161 mutation in a family with pituitary stalk interruption syndrome. %A Karaca, Ender %A Buyukkaya, Ramazan %A Pehlivan, Davut %A Charng, Wu-Lin %A Yaykasli, Kursat O %A Bayram, Yavuz %A Gambin, Tomasz %A Withers, Marjorie %A Atik, Mehmed M %A Arslanoglu, Ilknur %A Bolu, Semih %A Erdin, Serkan %A Buyukkaya, Ayla %A Yaykasli, Emine %A Jhangiani, Shalini N %A Muzny, Donna M %A Gibbs, Richard A %A Lupski, James R %K Adolescent %K Child, Preschool %K Exome %K Female %K Genome-Wide Association Study %K Humans %K Hypopituitarism %K Mutation %K Pituitary Gland %K Receptors, G-Protein-Coupled %X

CONTEXT: Pituitary stalk interruption syndrome (PSIS) is a rare, congenital anomaly of the pituitary gland characterized by pituitary gland insufficiency, thin or discontinuous pituitary stalk, anterior pituitary hypoplasia, and ectopic positioning of the posterior pituitary gland (neurohypophysis). The clinical presentation of patients with PSIS varies from isolated growth hormone (GH) deficiency to combined pituitary insufficiency and accompanying extrapituitary findings. Mutations in HESX1, LHX4, OTX2, SOX3, and PROKR2 have been associated with PSIS in less than 5% of cases; thus, the underlying genetic etiology for the vast majority of cases remains to be determined.

OBJECTIVE: We applied whole-exome sequencing (WES) to a consanguineous family with two affected siblings who have pituitary gland insufficiency and radiographic findings of hypoplastic (thin) pituitary gland, empty sella, ectopic neurohypophysis, and interrupted pitiutary stalk-characteristic clinical diagnostic findings of PSIS.

DESIGN AND PARTICIPANTS: WES was applied to two affected and one unaffected siblings.

RESULTS: WES of two affected and one unaffected sibling revealed a unique homozygous missense mutation in GPR161, which encodes the orphan G protein-coupled receptor 161, a protein responsible for transducing extracellular signals across the plasma membrane into the cell.

CONCLUSION: Mutations of GPR161 may be implicated as a potential novel cause of PSIS.

%B J Clin Endocrinol Metab %V 100 %P E140-7 %8 2015 Jan %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/25322266?dopt=Abstract %R 10.1210/jc.2014-1984 %0 Journal Article %J Fertil Steril %D 2015 %T Whole-exome sequencing identifies novel homozygous mutation in NPAS2 in family with nonobstructive azoospermia. %A Ramasamy, Ranjith %A Bakırcıoğlu, M Emre %A Cengiz, Cenk %A Karaca, Ender %A Scovell, Jason %A Jhangiani, Shalini N %A Akdemir, Zeynep C %A Bainbridge, Matthew %A Yu, Yao %A Huff, Chad %A Gibbs, Richard A %A Lupski, James R %A Lamb, Dolores J %K Adult %K Azoospermia %K Base Sequence %K Basic Helix-Loop-Helix Transcription Factors %K Exome %K Homozygote %K Humans %K Male %K Molecular Sequence Data %K Mutation %K Nerve Tissue Proteins %K Pedigree %X

OBJECTIVE: To investigate the genetic cause of nonobstructive azoospermia (NOA) in a consanguineous Turkish family through homozygosity mapping followed by targeted exon/whole-exome sequencing to identify genetic variations.

DESIGN: Whole-exome sequencing (WES).

SETTING: Research laboratory.

PATIENT(S): Two siblings in a consanguineous family with NOA.

INTERVENTION(S): Validating all variants passing filter criteria with Sanger sequencing to confirm familial segregation and absence in the control population.

MAIN OUTCOME MEASURE(S): Discovery of a mutation that could potentially cause NOA.

RESULT(S): A novel nonsynonymous mutation in the neuronal PAS-2 domain (NPAS2) was identified in a consanguineous family from Turkey. This mutation in exon 14 (chr2: 101592000 C>G) of NPAS2 is likely a disease-causing mutation as it is predicted to be damaging, it is a novel variant, and it segregates with the disease. Family segregation of the variants showed the presence of the homozygous mutation in the three brothers with NOA and a heterozygous mutation in the mother as well as one brother and one sister who were both fertile. The mutation is not found in the single-nucleotide polymorphism database, the 1000 Genomes Project, the Baylor College of Medicine cohort of 500 Turkish patients (not a population-specific polymorphism), or the matching 50 fertile controls.

CONCLUSION(S): With the use of WES we identified a novel homozygous mutation in NPAS2 as a likely disease-causing variant in a Turkish family diagnosed with NOA. Our data reinforce the clinical role of WES in the molecular diagnosis of highly heterogeneous genetic diseases for which conventional genetic approaches have previously failed to find a molecular diagnosis.

%B Fertil Steril %V 104 %P 286-91 %8 2015 Aug %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/25956372?dopt=Abstract %R 10.1016/j.fertnstert.2015.04.001 %0 Journal Article %J Endocr Relat Cancer %D 2015 %T X-linked acrogigantism syndrome: clinical profile and therapeutic responses. %A Beckers, Albert %A Lodish, Maya Beth %A Trivellin, Giampaolo %A Rostomyan, Liliya %A Lee, Misu %A Faucz, Fabio R %A Bo Yuan %A Choong, Catherine S %A Caberg, Jean-Hubert %A Verrua, Elisa %A Naves, Luciana Ansaneli %A Cheetham, Tim D %A Young, Jacques %A Lysy, Philippe A %A Petrossians, Patrick %A Cotterill, Andrew %A Shah, Nalini Samir %A Metzger, Daniel %A Castermans, Emilie %A Ambrosio, Maria Rosaria %A Villa, Chiara %A Strebkova, Natalia %A Mazerkina, Nadia %A Gaillard, Stéphan %A Barra, Gustavo Barcelos %A Casulari, Luis Augusto %A Neggers, Sebastian J %A Salvatori, Roberto %A Jaffrain-Rea, Marie-Lise %A Zacharin, Margaret %A Santamaria, Beatriz Lecumberri %A Zacharieva, Sabina %A Lim, Ee Mun %A Mantovani, Giovanna %A Zatelli, Maria Chaira %A Collins, Michael T %A Bonneville, Jean-François %A Quezado, Martha %A Chittiboina, Prashant %A Oldfield, Edward H %A Bours, Vincent %A Liu, Pengfei %A W de Herder, Wouter %A Pellegata, Natalia %A James R Lupski %A Daly, Adrian F %A Stratakis, Constantine A %K Acromegaly %K Adenoma %K Adolescent %K Child %K Child, Preschool %K Chromosomes, Human, X %K Female %K Gigantism %K Humans %K Infant %K Male %K Pituitary Neoplasms %K Young Adult %X

X-linked acrogigantism (X-LAG) is a new syndrome of pituitary gigantism, caused by microduplications on chromosome Xq26.3, encompassing the gene GPR101, which is highly upregulated in pituitary tumors. We conducted this study to explore the clinical, radiological, and hormonal phenotype and responses to therapy in patients with X-LAG syndrome. The study included 18 patients (13 sporadic) with X-LAG and microduplication of chromosome Xq26.3. All sporadic cases had unique duplications and the inheritance pattern in two families was dominant, with all Xq26.3 duplication carriers being affected. Patients began to grow rapidly as early as 2-3 months of age (median 12 months). At diagnosis (median delay 27 months), patients had a median height and weight standard deviation scores (SDS) of >+3.9 SDS. Apart from the increased overall body size, the children had acromegalic symptoms including acral enlargement and facial coarsening. More than a third of cases had increased appetite. Patients had marked hypersecretion of GH/IGF1 and usually prolactin, due to a pituitary macroadenoma or hyperplasia. Primary neurosurgical control was achieved with extensive anterior pituitary resection, but postoperative hypopituitarism was frequent. Control with somatostatin analogs was not readily achieved despite moderate to high levels of expression of somatostatin receptor subtype-2 in tumor tissue. Postoperative use of adjuvant pegvisomant resulted in control of IGF1 in all five cases where it was employed. X-LAG is a new infant-onset gigantism syndrome that has a severe clinical phenotype leading to challenging disease management.

%B Endocr Relat Cancer %V 22 %P 353-67 %8 2015 Jun %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/25712922?dopt=Abstract %R 10.1530/ERC-15-0038 %0 Journal Article %J Am J Hum Genet %D 2014 %T The Alu-rich genomic architecture of SPAST predisposes to diverse and functionally distinct disease-associated CNV alleles. %A Boone, Philip M %A Bo Yuan %A Campbell, Ian M %A Scull, Jennifer C %A Withers, Marjorie A %A Baggett, Brett C %A Beck, Christine R %A Shaw, Christine J %A Stankiewicz, Pawel %A Moretti, Paolo %A Goodwin, Wendy E %A Hein, Nichole %A Fink, John K %A Seong, Moon-Woo %A Seo, Soo Hyun %A Park, Sung Sup %A Karbassi, Izabela D %A Batish, Sat Dev %A Ordóñez-Ugalde, Andrés %A Quintáns, Beatriz %A Sobrido, María-Jesús %A Stemmler, Susanne %A James R Lupski %K Adenosine Triphosphatases %K Alu Elements %K Base Sequence %K Cation Transport Proteins %K Cell Line, Transformed %K DNA Copy Number Variations %K Genotype %K Humans %K Protein Isoforms %K Recombinant Fusion Proteins %K Sequence Analysis, DNA %K Sequence Deletion %K Spastic Paraplegia, Hereditary %K Spastin %X

Intragenic copy-number variants (CNVs) contribute to the allelic spectrum of both Mendelian and complex disorders. Although pathogenic deletions and duplications in SPAST (mutations in which cause autosomal-dominant spastic paraplegia 4 [SPG4]) have been described, their origins and molecular consequences remain obscure. We mapped breakpoint junctions of 54 SPAST CNVs at nucleotide resolution. Diverse combinations of exons are deleted or duplicated, highlighting the importance of particular exons for spastin function. Of the 54 CNVs, 38 (70%) appear to be mediated by an Alu-based mechanism, suggesting that the Alu-rich genomic architecture of SPAST renders this locus susceptible to various genome rearrangements. Analysis of breakpoint Alus further informs a model of Alu-mediated CNV formation characterized by small CNV size and potential involvement of mechanisms other than homologous recombination. Twelve deletions (22%) overlap part of SPAST and a portion of a nearby, directly oriented gene, predicting novel chimeric genes in these subjects' genomes. cDNA from a subject with a SPAST final exon deletion contained multiple SPAST:SLC30A6 fusion transcripts, indicating that SPAST CNVs can have transcriptional effects beyond the gene itself. SLC30A6 has been implicated in Alzheimer disease, so these fusion gene data could explain a report of spastic paraplegia and dementia cosegregating in a family with deletion of the final exon of SPAST. Our findings provide evidence that the Alu genomic architecture of SPAST predisposes to diverse CNV alleles with distinct transcriptional--and possibly phenotypic--consequences. Moreover, we provide further mechanistic insights into Alu-mediated copy-number change that are extendable to other loci.

%B Am J Hum Genet %V 95 %P 143-61 %8 2014 Aug 07 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/25065914?dopt=Abstract %R 10.1016/j.ajhg.2014.06.014 %0 Journal Article %J Hum Mol Genet %D 2014 %T Analysis of the ABCA4 genomic locus in Stargardt disease. %A Zernant, Jana %A Xie, Yajing Angela %A Ayuso, Carmen %A Riveiro-Álvarez, Rosa %A López-Martínez, Miguel-Ángel %A Simonelli, Francesca %A Testa, Francesco %A Gorin, Michael B %A Strom, Samuel P %A Bertelsen, Mette %A Rosenberg, Thomas %A Boone, Philip M %A Bo Yuan %A Ayyagari, Radha %A Nagy, Peter L %A Tsang, Stephen H %A Gouras, Peter %A Collison, Frederick T %A James R Lupski %A Fishman, Gerald A %A Allikmets, Rando %K Alleles %K ATP-Binding Cassette Transporters %K Blacks %K Case-Control Studies %K Comparative Genomic Hybridization %K Exons %K Female %K Gene Expression %K Genes, Recessive %K Genetic Loci %K Genetic Variation %K Heterozygote %K High-Throughput Nucleotide Sequencing %K Homozygote %K Humans %K Introns %K Macular Degeneration %K Male %K Mutation %K Pedigree %K Stargardt Disease %K Whites %X

Autosomal recessive Stargardt disease (STGD1, MIM 248200) is caused by mutations in the ABCA4 gene. Complete sequencing of ABCA4 in STGD patients identifies compound heterozygous or homozygous disease-associated alleles in 65-70% of patients and only one mutation in 15-20% of patients. This study was designed to find the missing disease-causing ABCA4 variation by a combination of next-generation sequencing (NGS), array-Comparative Genome Hybridization (aCGH) screening, familial segregation and in silico analyses. The entire 140 kb ABCA4 genomic locus was sequenced in 114 STGD patients with one known ABCA4 exonic mutation revealing, on average, 200 intronic variants per sample. Filtering of these data resulted in 141 candidates for new mutations. Two variants were detected in four samples, two in three samples, and 20 variants in two samples, the remaining 117 new variants were detected only once. Multimodal analysis suggested 12 new likely pathogenic intronic ABCA4 variants, some of which were specific to (isolated) ethnic groups. No copy number variation (large deletions and insertions) was detected in any patient suggesting that it is a very rare event in the ABCA4 locus. Many variants were excluded since they were not conserved in non-human primates, were frequent in African populations and, therefore, represented ancestral, and not disease-associated, variants. The sequence variability in the ABCA4 locus is extensive and the non-coding sequences do not harbor frequent mutations in STGD patients of European-American descent. Defining disease-associated alleles in the ABCA4 locus requires exceptionally well characterized large cohorts and extensive analyses by a combination of various approaches.

%B Hum Mol Genet %V 23 %P 6797-806 %8 2014 Dec 20 %G eng %N 25 %1 https://www.ncbi.nlm.nih.gov/pubmed/25082829?dopt=Abstract %R 10.1093/hmg/ddu396 %0 Journal Article %J Am J Hum Genet %D 2014 %T De novo truncating mutations in AHDC1 in individuals with syndromic expressive language delay, hypotonia, and sleep apnea. %A Xia, Fan %A Bainbridge, Matthew N %A Tan, Tiong Yang %A Wangler, Michael F %A Scheuerle, Angela E %A Zackai, Elaine H %A Harr, Margaret H %A Sutton, V Reid %A Nalam, Roopa L %A Zhu, Wenmiao %A Nash, Margot %A Ryan, Monique M %A Yaplito-Lee, Joy %A Hunter, Jill V %A Deardorff, Matthew A %A Penney, Samantha J %A Beaudet, Arthur L %A Plon, Sharon E %A Boerwinkle, Eric A %A Lupski, James R %A Eng, Christine M %A Muzny, Donna M %A Yang, Yaping %A Gibbs, Richard A %K Child %K Child, Preschool %K DNA-Binding Proteins %K Exome %K Female %K Humans %K Infant %K Intellectual Disability %K Language Development Disorders %K Male %K Muscle Hypotonia %K Mutation %K Sleep Apnea Syndromes %K Syndrome %X

Clinical whole-exome sequencing (WES) for identification of mutations leading to Mendelian disease has been offered to the medical community since 2011. Clinically undiagnosed neurological disorders are the most frequent basis for test referral, and currently, approximately 25% of such cases are diagnosed at the molecular level. To date, there are approximately 4,000 "known" disease-associated loci, and many are associated with striking dysmorphic features, making genotype-phenotype correlations relatively straightforward. A significant fraction of cases, however, lack characteristic dysmorphism or clinical pathognomonic traits and are dependent upon molecular tests for definitive diagnoses. Further, many molecular diagnoses are guided by recent gene-disease association discoveries. Hence, there is a critical interplay between clinical testing and research leading to gene-disease association discovery. Here, we describe four probands, all of whom presented with hypotonia, intellectual disability, global developmental delay, and mildly dysmorphic facial features. Three of the four also had sleep apnea. Each was a simplex case without a remarkable family history. Using WES, we identified AHDC1 de novo truncating mutations that most likely cause this genetic syndrome.

%B Am J Hum Genet %V 94 %P 784-9 %8 2014 May 01 %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/24791903?dopt=Abstract %R 10.1016/j.ajhg.2014.04.006 %0 Journal Article %J Cell %D 2014 %T A drosophila genetic resource of mutants to study mechanisms underlying human genetic diseases. %A Yamamoto, Shinya %A Jaiswal, Manish %A Charng, Wu-Lin %A Gambin, Tomasz %A Karaca, Ender %A Mirzaa, Ghayda %A Wiszniewski, Wojciech %A Sandoval, Hector %A Haelterman, Nele A %A Xiong, Bo %A Zhang, Ke %A Bayat, Vafa %A David, Gabriela %A Li, Tongchao %A Chen, Kuchuan %A Gala, Upasana %A Harel, Tamar %A Pehlivan, Davut %A Penney, Samantha %A Vissers, Lisenka E L M %A de Ligt, Joep %A Jhangiani, Shalini N %A Xie, Yajing %A Tsang, Stephen H %A Parman, Yesim %A Sivaci, Merve %A Battaloglu, Esra %A Muzny, Donna %A Wan, Ying-Wooi %A Liu, Zhandong %A Lin-Moore, Alexander T %A Clark, Robin D %A Curry, Cynthia J %A Link, Nichole %A Schulze, Karen L %A Boerwinkle, Eric %A Dobyns, William B %A Allikmets, Rando %A Gibbs, Richard A %A Chen, Rui %A Lupski, James R %A Wangler, Michael F %A Bellen, Hugo J %K Animals %K Disease %K Disease Models, Animal %K Drosophila melanogaster %K Genetic Testing %K Humans %K Inheritance Patterns %K RNA Interference %K X Chromosome %X

Invertebrate model systems are powerful tools for studying human disease owing to their genetic tractability and ease of screening. We conducted a mosaic genetic screen of lethal mutations on the Drosophila X chromosome to identify genes required for the development, function, and maintenance of the nervous system. We identified 165 genes, most of whose function has not been studied in vivo. In parallel, we investigated rare variant alleles in 1,929 human exomes from families with unsolved Mendelian disease. Genes that are essential in flies and have multiple human homologs were found to be likely to be associated with human diseases. Merging the human data sets with the fly genes allowed us to identify disease-associated mutations in six families and to provide insights into microcephaly associated with brain dysgenesis. This bidirectional synergism between fly genetics and human genomics facilitates the functional annotation of evolutionarily conserved genes involved in human health.

%B Cell %V 159 %P 200-214 %8 2014 Sep 25 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/25259927?dopt=Abstract %R 10.1016/j.cell.2014.09.002 %0 Journal Article %J Genet Med %D 2014 %T Exonic duplication CNV of NDRG1 associated with autosomal-recessive HMSN-Lom/CMT4D. %A Okamoto, Yuji %A Goksungur, Meryem Tuba %A Pehlivan, Davut %A Beck, Christine R %A Gonzaga-Jauregui, Claudia %A Muzny, Donna M %A Atik, Mehmed M %A Carvalho, Claudia M B %A Matur, Zeliha %A Bayraktar, Serife %A Boone, Philip M %A Akyuz, Kaya %A Gibbs, Richard A %A Battaloglu, Esra %A Parman, Yesim %A Lupski, James R %K Adult %K Base Sequence %K Cell Cycle Proteins %K Charcot-Marie-Tooth Disease %K Comparative Genomic Hybridization %K DNA Copy Number Variations %K Female %K Gene Duplication %K Gene Expression %K Genes, Recessive %K Humans %K Intracellular Signaling Peptides and Proteins %K Male %K Mutation %K Refsum Disease %K Sequence Analysis, DNA %K Turkey %K Young Adult %X

PURPOSE: Copy-number variations as a mutational mechanism contribute significantly to human disease. Approximately one-half of the patients with Charcot-Marie-Tooth (CMT) disease have a 1.4 Mb duplication copy-number variation as the cause of their neuropathy. However, non-CMT1A neuropathy patients rarely have causative copy-number variations, and to date, autosomal-recessive disease has not been associated with copy-number variation as a mutational mechanism.

METHODS: We performed Agilent 8 × 60 K array comparative genomic hybridization on DNA from 12 recessive Turkish families with CMT disease. Additional molecular studies were conducted to detect breakpoint junctions and to evaluate gene expression levels in a family in which we detected an intragenic duplication copy-number variation.

RESULTS: We detected an ~6.25 kb homozygous intragenic duplication in NDRG1, a gene known to be causative for recessive HMSNL/CMT4D, in three individuals from a Turkish family with CMT neuropathy. Further studies showed that this intragenic copy-number variation resulted in a homozygous duplication of exons 6-8 that caused decreased mRNA expression of NDRG1.

CONCLUSION: Exon-focused high-resolution array comparative genomic hybridization enables the detection of copy-number variation carrier states in recessive genes, particularly small copy-number variations encompassing or disrupting single genes. In families for whom a molecular diagnosis has not been elucidated by conventional clinical assays, an assessment for copy-number variations in known CMT genes might be considered.

%B Genet Med %V 16 %P 386-394 %8 2014 May %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/24136616?dopt=Abstract %R 10.1038/gim.2013.155 %0 Journal Article %J Hum Mutat %D 2014 %T Genetic and clinical analysis of ABCA4-associated disease in African American patients. %A Zernant, Jana %A Collison, Frederick T %A Lee, Winston %A Fishman, Gerald A %A Nõupuu, Kalev %A Bo Yuan %A Cai, Carolyn %A James R Lupski %A Yannuzzi, Lawrence A %A Tsang, Stephen H %A Allikmets, Rando %K Adult %K African Americans %K ATP-Binding Cassette Transporters %K Comparative Genomic Hybridization %K DNA Mutational Analysis %K Electroretinography %K Female %K Genetic Predisposition to Disease %K Humans %K Macular Degeneration %K Male %K Middle Aged %K Mutation %K Stargardt Disease %K United States %K Whites %X

Autosomal recessive Stargardt disease (STGD1) is caused by hundreds of mutations in the ABCA4 gene, which are often specific to racial and ethnic groups. Here, we investigated the ABCA4 variation and their phenotypic expression in a cohort of 44 patients of African American descent, a previously under-characterized racial group. Patients were screened for mutations in ABCA4 by next-generation sequencing and array-comparative genomic hybridization (aCGH), followed by analyses for pathogenicity by in silico programs. Thorough ophthalmic examination was performed on all patients. At least two (expected) disease-causing alleles in the ABCA4 gene were identified in 27 (61.4%) patients, one allele in 11 (25%) patients, and no ABCA4 mutations were found in six (13.6%) patients. Altogether, 39 different disease-causing ABCA4 variants, including seven new, were identified on 65 (74%) chromosomes, most of which were unique for this racial group. The most frequent ABCA4 mutation in this cohort was c.6320G>A (p.(R2107H)), representing 19.3% of all disease-associated alleles. No large copy number variants were identified in any patient. Most patients reported later onset of symptoms. In summary, the ABCA4 mutation spectrum in patients of West African descent differs significantly from that in patients of European descent, resulting in a later onset and "milder" disease.

%B Hum Mutat %V 35 %P 1187-94 %8 2014 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/25066811?dopt=Abstract %R 10.1002/humu.22626 %0 Journal Article %J N Engl J Med %D 2014 %T Gigantism and acromegaly due to Xq26 microduplications and GPR101 mutation. %A Trivellin, Giampaolo %A Daly, Adrian F %A Faucz, Fabio R %A Bo Yuan %A Rostomyan, Liliya %A Larco, Darwin O %A Schernthaner-Reiter, Marie Helene %A Szarek, Eva %A Leal, Letícia F %A Caberg, Jean-Hubert %A Castermans, Emilie %A Villa, Chiara %A Dimopoulos, Aggeliki %A Chittiboina, Prashant %A Xekouki, Paraskevi %A Shah, Nalini %A Metzger, Daniel %A Lysy, Philippe A %A Ferrante, Emanuele %A Strebkova, Natalia %A Mazerkina, Nadia %A Zatelli, Maria Chiara %A Lodish, Maya %A Horvath, Anelia %A de Alexandre, Rodrigo Bertollo %A Manning, Allison D %A Levy, Isaac %A Keil, Margaret F %A Sierra, Maria de la Luz %A Palmeira, Leonor %A Coppieters, Wouter %A Georges, Michel %A Naves, Luciana A %A Jamar, Mauricette %A Bours, Vincent %A Wu, T John %A Choong, Catherine S %A Bertherat, Jérôme %A Chanson, Philippe %A Kamenický, Peter %A Farrell, William E %A Barlier, Anne %A Quezado, Martha %A Bjelobaba, Ivana %A Stojilkovic, Stanko S %A Wess, Jurgen %A Costanzi, Stefano %A Liu, Pengfei %A James R Lupski %A Beckers, Albert %A Stratakis, Constantine A %K Acromegaly %K Adolescent %K Adult %K Age of Onset %K Child %K Child, Preschool %K Chromosome Duplication %K Chromosomes, Human, X %K Female %K Gigantism %K Human Growth Hormone %K Humans %K Infant %K Male %K Mutation %K Phenotype %K Protein Conformation %K Receptors, G-Protein-Coupled %X

BACKGROUND: Increased secretion of growth hormone leads to gigantism in children and acromegaly in adults; the genetic causes of gigantism and acromegaly are poorly understood.

METHODS: We performed clinical and genetic studies of samples obtained from 43 patients with gigantism and then sequenced an implicated gene in samples from 248 patients with acromegaly.

RESULTS: We observed microduplication on chromosome Xq26.3 in samples from 13 patients with gigantism; of these samples, 4 were obtained from members of two unrelated kindreds, and 9 were from patients with sporadic cases. All the patients had disease onset during early childhood. Of the patients with gigantism who did not carry an Xq26.3 microduplication, none presented before the age of 5 years. Genomic characterization of the Xq26.3 region suggests that the microduplications are generated during chromosome replication and that they contain four protein-coding genes. Only one of these genes, GPR101, which encodes a G-protein-coupled receptor, was overexpressed in patients' pituitary lesions. We identified a recurrent GPR101 mutation (p.E308D) in 11 of 248 patients with acromegaly, with the mutation found mostly in tumors. When the mutation was transfected into rat GH3 cells, it led to increased release of growth hormone and proliferation of growth hormone-producing cells.

CONCLUSIONS: We describe a pediatric disorder (which we have termed X-linked acrogigantism [X-LAG]) that is caused by an Xq26.3 genomic duplication and is characterized by early-onset gigantism resulting from an excess of growth hormone. Duplication of GPR101 probably causes X-LAG. We also found a recurrent mutation in GPR101 in some adults with acromegaly. (Funded by the Eunice Kennedy Shriver National Institute of Child Health and Human Development and others.).

%B N Engl J Med %V 371 %P 2363-74 %8 2014 Dec 18 %G eng %N 25 %1 https://www.ncbi.nlm.nih.gov/pubmed/25470569?dopt=Abstract %R 10.1056/NEJMoa1408028 %0 Journal Article %J PLoS Genet %D 2014 %T Heterozygous de novo and inherited mutations in the smooth muscle actin (ACTG2) gene underlie megacystis-microcolon-intestinal hypoperistalsis syndrome. %A Wangler, Michael F %A Gonzaga-Jauregui, Claudia %A Gambin, Tomasz %A Penney, Samantha %A Moss, Timothy %A Chopra, Atul %A Probst, Frank J %A Xia, Fan %A Yang, Yaping %A Werlin, Steven %A Eglite, Ieva %A Kornejeva, Liene %A Bacino, Carlos A %A Baldridge, Dustin %A Neul, Jeff %A Lehman, Efrat Lev %A Larson, Austin %A Beuten, Joke %A Muzny, Donna M %A Jhangiani, Shalini %A Gibbs, Richard A %A Lupski, James R %A Beaudet, Arthur %K Abnormalities, Multiple %K Actins %K Adolescent %K Adult %K Child %K Child, Preschool %K Colon %K Exome %K Female %K Heterozygote %K Humans %K Intestinal Pseudo-Obstruction %K Male %K Muscle, Smooth %K Mutation %K Urinary Bladder %X

Megacystis-microcolon-intestinal hypoperistalsis syndrome (MMIHS) is a rare disorder of enteric smooth muscle function affecting the intestine and bladder. Patients with this severe phenotype are dependent on total parenteral nutrition and urinary catheterization. The cause of this syndrome has remained a mystery since Berdon's initial description in 1976. No genes have been clearly linked to MMIHS. We used whole-exome sequencing for gene discovery followed by targeted Sanger sequencing in a cohort of patients with MMIHS and intestinal pseudo-obstruction. We identified heterozygous ACTG2 missense variants in 15 unrelated subjects, ten being apparent de novo mutations. Ten unique variants were detected, of which six affected CpG dinucleotides and resulted in missense mutations at arginine residues, perhaps related to biased usage of CpG containing codons within actin genes. We also found some of the same heterozygous mutations that we observed as apparent de novo mutations in MMIHS segregating in families with intestinal pseudo-obstruction, suggesting that ACTG2 is responsible for a spectrum of smooth muscle disease. ACTG2 encodes γ2 enteric actin and is the first gene to be clearly associated with MMIHS, suggesting an important role for contractile proteins in enteric smooth muscle disease.

%B PLoS Genet %V 10 %P e1004258 %8 2014 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/24676022?dopt=Abstract %R 10.1371/journal.pgen.1004258 %0 Journal Article %J Cell %D 2014 %T Human CLP1 mutations alter tRNA biogenesis, affecting both peripheral and central nervous system function. %A Karaca, Ender %A Weitzer, Stefan %A Pehlivan, Davut %A Shiraishi, Hiroshi %A Gogakos, Tasos %A Hanada, Toshikatsu %A Jhangiani, Shalini N %A Wiszniewski, Wojciech %A Withers, Marjorie %A Campbell, Ian M %A Erdin, Serkan %A Isikay, Sedat %A Franco, Luis M %A Gonzaga-Jauregui, Claudia %A Gambin, Tomasz %A Gelowani, Violet %A Hunter, Jill V %A Yesil, Gozde %A Koparir, Erkan %A Yilmaz, Sarenur %A Brown, Miguel %A Briskin, Daniel %A Hafner, Markus %A Morozov, Pavel %A Farazi, Thalia A %A Bernreuther, Christian %A Glatzel, Markus %A Trattnig, Siegfried %A Friske, Joachim %A Kronnerwetter, Claudia %A Bainbridge, Matthew N %A Gezdirici, Alper %A Seven, Mehmet %A Muzny, Donna M %A Boerwinkle, Eric %A Ozen, Mustafa %A Clausen, Tim %A Tuschl, Thomas %A Yuksel, Adnan %A Hess, Andreas %A Gibbs, Richard A %A Martinez, Javier %A Penninger, Josef M %A Lupski, James R %K Abnormalities, Multiple %K Animals %K Central Nervous System Diseases %K Cerebrum %K Child, Preschool %K Endoribonucleases %K Female %K Fibroblasts %K Humans %K Infant %K Male %K Mice %K Mice, Inbred CBA %K Microcephaly %K Mutation, Missense %K Nuclear Proteins %K Peripheral Nervous System Diseases %K Phosphotransferases %K RNA, Transfer %K RNA-Binding Proteins %K Transcription Factors %X

CLP1 is a RNA kinase involved in tRNA splicing. Recently, CLP1 kinase-dead mice were shown to display a neuromuscular disorder with loss of motor neurons and muscle paralysis. Human genome analyses now identified a CLP1 homozygous missense mutation (p.R140H) in five unrelated families, leading to a loss of CLP1 interaction with the tRNA splicing endonuclease (TSEN) complex, largely reduced pre-tRNA cleavage activity, and accumulation of linear tRNA introns. The affected individuals develop severe motor-sensory defects, cortical dysgenesis, and microcephaly. Mice carrying kinase-dead CLP1 also displayed microcephaly and reduced cortical brain volume due to the enhanced cell death of neuronal progenitors that is associated with reduced numbers of cortical neurons. Our data elucidate a neurological syndrome defined by CLP1 mutations that impair tRNA splicing. Reduction of a founder mutation to homozygosity illustrates the importance of rare variations in disease and supports the clan genomics hypothesis.

%B Cell %V 157 %P 636-50 %8 2014 Apr 24 %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/24766809?dopt=Abstract %R 10.1016/j.cell.2014.02.058 %0 Journal Article %J Am J Hum Genet %D 2014 %T Mechanism, prevalence, and more severe neuropathy phenotype of the Charcot-Marie-Tooth type 1A triplication. %A Liu, Pengfei %A Gelowani, Violet %A Zhang, Feng %A Drory, Vivian E %A Ben-Shachar, Shay %A Roney, Erin %A Medeiros, Adam C %A Moore, Rebecca J %A DiVincenzo, Christina %A Burnette, William B %A Higgins, Joseph J %A Li, Jun %A Orr-Urtreger, Avi %A Lupski, James R %K Alleles %K Charcot-Marie-Tooth Disease %K DNA Copy Number Variations %K Female %K Gene Dosage %K Gene Duplication %K Humans %K Male %K Microsatellite Repeats %K Muscular Atrophy %K Nucleic Acid Hybridization %K Pedigree %K Phenotype %K Polyneuropathies %K Recombination, Genetic %X

Copy-number variations cause genomic disorders. Triplications, unlike deletions and duplications, are poorly understood because of challenges in molecular identification, the choice of a proper model system for study, and awareness of their phenotypic consequences. We investigated the genomic disorder Charcot-Marie-Tooth disease type 1A (CMT1A), a dominant peripheral neuropathy caused by a 1.4 Mb recurrent duplication occurring by nonallelic homologous recombination. We identified CMT1A triplications in families in which the duplication segregates. The triplications arose de novo from maternally transmitted duplications and caused a more severe distal symmetric polyneuropathy phenotype. The recombination that generated the triplication occurred between sister chromatids on the duplication-bearing chromosome and could accompany gene conversions with the homologous chromosome. Diagnostic testing for CMT1A (n = 20,661 individuals) identified 13% (n = 2,752 individuals) with duplication and 0.024% (n = 5 individuals) with segmental tetrasomy, suggesting that triplications emerge from duplications at a rate as high as ~1:550, which is more frequent than the rate of de novo duplication. We propose that individuals with duplications are predisposed to acquiring triplications and that the population prevalence of triplication is underascertained.

%B Am J Hum Genet %V 94 %P 462-9 %8 2014 Mar 06 %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/24530202?dopt=Abstract %R 10.1016/j.ajhg.2014.01.017 %0 Journal Article %J JAMA %D 2014 %T Molecular findings among patients referred for clinical whole-exome sequencing. %A Yang, Yaping %A Muzny, Donna M %A Xia, Fan %A Niu, Zhiyv %A Person, Richard %A Ding, Yan %A Ward, Patricia %A Braxton, Alicia %A Wang, Min %A Buhay, Christian %A Veeraraghavan, Narayanan %A Hawes, Alicia %A Chiang, Theodore %A Leduc, Magalie %A Beuten, Joke %A Zhang, Jing %A He, Weimin %A Scull, Jennifer %A Willis, Alecia %A Landsverk, Megan %A Craigen, William J %A Bekheirnia, Mir Reza %A Stray-Pedersen, Asbjorg %A Liu, Pengfei %A Wen, Shu %A Alcaraz, Wendy %A Cui, Hong %A Walkiewicz, Magdalena %A Reid, Jeffrey %A Bainbridge, Matthew %A Patel, Ankita %A Boerwinkle, Eric %A Beaudet, Arthur L %A Lupski, James R %A Plon, Sharon E %A Gibbs, Richard A %A Eng, Christine M %K Adolescent %K Adult %K Child %K Child, Preschool %K Exome %K Female %K Fetus %K Genetic Diseases, Inborn %K Genetic Testing %K Genomics %K Humans %K Incidental Findings %K Infant %K Infant, Newborn %K Male %K Molecular Diagnostic Techniques %K Mutation %K Phenotype %K Referral and Consultation %K Sequence Analysis, DNA %X

IMPORTANCE: Clinical whole-exome sequencing is increasingly used for diagnostic evaluation of patients with suspected genetic disorders.

OBJECTIVE: To perform clinical whole-exome sequencing and report (1) the rate of molecular diagnosis among phenotypic groups, (2) the spectrum of genetic alterations contributing to disease, and (3) the prevalence of medically actionable incidental findings such as FBN1 mutations causing Marfan syndrome.

DESIGN, SETTING, AND PATIENTS: Observational study of 2000 consecutive patients with clinical whole-exome sequencing analyzed between June 2012 and August 2014. Whole-exome sequencing tests were performed at a clinical genetics laboratory in the United States. Results were reported by clinical molecular geneticists certified by the American Board of Medical Genetics and Genomics. Tests were ordered by the patient's physician. The patients were primarily pediatric (1756 [88%]; mean age, 6 years; 888 females [44%], 1101 males [55%], and 11 fetuses [1% gender unknown]), demonstrating diverse clinical manifestations most often including nervous system dysfunction such as developmental delay.

MAIN OUTCOMES AND MEASURES: Whole-exome sequencing diagnosis rate overall and by phenotypic category, mode of inheritance, spectrum of genetic events, and reporting of incidental findings.

RESULTS: A molecular diagnosis was reported for 504 patients (25.2%) with 58% of the diagnostic mutations not previously reported. Molecular diagnosis rates for each phenotypic category were 143/526 (27.2%; 95% CI, 23.5%-31.2%) for the neurological group, 282/1147 (24.6%; 95% CI, 22.1%-27.2%) for the neurological plus other organ systems group, 30/83 (36.1%; 95% CI, 26.1%-47.5%) for the specific neurological group, and 49/244 (20.1%; 95% CI, 15.6%-25.8%) for the nonneurological group. The Mendelian disease patterns of the 527 molecular diagnoses included 280 (53.1%) autosomal dominant, 181 (34.3%) autosomal recessive (including 5 with uniparental disomy), 65 (12.3%) X-linked, and 1 (0.2%) mitochondrial. Of 504 patients with a molecular diagnosis, 23 (4.6%) had blended phenotypes resulting from 2 single gene defects. About 30% of the positive cases harbored mutations in disease genes reported since 2011. There were 95 medically actionable incidental findings in genes unrelated to the phenotype but with immediate implications for management in 92 patients (4.6%), including 59 patients (3%) with mutations in genes recommended for reporting by the American College of Medical Genetics and Genomics.

CONCLUSIONS AND RELEVANCE: Whole-exome sequencing provided a potential molecular diagnosis for 25% of a large cohort of patients referred for evaluation of suspected genetic conditions, including detection of rare genetic events and new mutations contributing to disease. The yield of whole-exome sequencing may offer advantages over traditional molecular diagnostic approaches in certain patients.

%B JAMA %V 312 %P 1870-9 %8 2014 Nov 12 %G eng %N 18 %1 https://www.ncbi.nlm.nih.gov/pubmed/25326635?dopt=Abstract %R 10.1001/jama.2014.14601 %0 Journal Article %J Am J Hum Genet %D 2014 %T Monoallelic and biallelic mutations in MAB21L2 cause a spectrum of major eye malformations. %A Rainger, Joe %A Pehlivan, Davut %A Johansson, Stefan %A Bengani, Hemant %A Sanchez-Pulido, Luis %A Williamson, Kathleen A %A Ture, Mehmet %A Barker, Heather %A Rosendahl, Karen %A Spranger, Jürgen %A Horn, Denise %A Meynert, Alison %A Floyd, James A B %A Prescott, Trine %A Anderson, Carl A %A Rainger, Jacqueline K %A Karaca, Ender %A Gonzaga-Jauregui, Claudia %A Jhangiani, Shalini %A Muzny, Donna M %A Seawright, Anne %A Soares, Dinesh C %A Kharbanda, Mira %A Murday, Victoria %A Finch, Andrew %A Gibbs, Richard A %A van Heyningen, Veronica %A Taylor, Martin S %A Yakut, Tahsin %A Knappskog, Per M %A Hurles, Matthew E %A Ponting, Chris P %A Lupski, James R %A Houge, Gunnar %A FitzPatrick, David R %K Adult %K Alleles %K Animals %K Anophthalmos %K Brain Diseases, Metabolic, Inborn %K Coloboma %K Corneal Opacity %K Exome %K Eye Proteins %K Female %K Gene Expression %K HEK293 Cells %K Heterozygote %K Homozygote %K Humans %K Intellectual Disability %K Intracellular Signaling Peptides and Proteins %K Male %K Mice %K Microcephaly %K Microphthalmos %K Mutation, Missense %K Pedigree %K Phenotype %K Protein Conformation %K Signal Transduction %X

We identified four different missense mutations in the single-exon gene MAB21L2 in eight individuals with bilateral eye malformations from five unrelated families via three independent exome sequencing projects. Three mutational events altered the same amino acid (Arg51), and two were identical de novo mutations (c.151C>T [p.Arg51Cys]) in unrelated children with bilateral anophthalmia, intellectual disability, and rhizomelic skeletal dysplasia. c.152G>A (p.Arg51His) segregated with autosomal-dominant bilateral colobomatous microphthalmia in a large multiplex family. The fourth heterozygous mutation (c.145G>A [p.Glu49Lys]) affected an amino acid within two residues of Arg51 in an adult male with bilateral colobomata. In a fifth family, a homozygous mutation (c.740G>A [p.Arg247Gln]) altering a different region of the protein was identified in two male siblings with bilateral retinal colobomata. In mouse embryos, Mab21l2 showed strong expression in the developing eye, pharyngeal arches, and limb bud. As predicted by structural homology, wild-type MAB21L2 bound single-stranded RNA, whereas this activity was lost in all altered forms of the protein. MAB21L2 had no detectable nucleotidyltransferase activity in vitro, and its function remains unknown. Induced expression of wild-type MAB21L2 in human embryonic kidney 293 cells increased phospho-ERK (pERK1/2) signaling. Compared to the wild-type and p.Arg247Gln proteins, the proteins with the Glu49 and Arg51 variants had increased stability. Abnormal persistence of pERK1/2 signaling in MAB21L2-expressing cells during development is a plausible pathogenic mechanism for the heterozygous mutations. The phenotype associated with the homozygous mutation might be a consequence of complete loss of MAB21L2 RNA binding, although the cellular function of this interaction remains unknown.

%B Am J Hum Genet %V 94 %P 915-23 %8 2014 Jun 05 %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/24906020?dopt=Abstract %R 10.1016/j.ajhg.2014.05.005 %0 Journal Article %J Am J Hum Genet %D 2014 %T Mutations in PURA cause profound neonatal hypotonia, seizures, and encephalopathy in 5q31.3 microdeletion syndrome. %A Lalani, Seema R %A Zhang, Jing %A Schaaf, Christian P %A Brown, Chester W %A Magoulas, Pilar %A Tsai, Anne Chun-Hui %A El-Gharbawy, Areeg %A Wierenga, Klaas J %A Bartholomew, Dennis %A Fong, Chin-To %A Barbaro-Dieber, Tina %A Kukolich, Mary K %A Burrage, Lindsay C %A Austin, Elise %A Keller, Kory %A Pastore, Matthew %A Fernandez, Fabio %A Lotze, Timothy %A Wilfong, Angus %A Purcarin, Gabriela %A Zhu, Wenmiao %A Craigen, William J %A McGuire, Marianne %A Jain, Mahim %A Cooney, Erin %A Azamian, Mahshid %A Bainbridge, Matthew N %A Muzny, Donna M %A Boerwinkle, Eric %A Person, Richard E %A Niu, Zhiyv %A Eng, Christine M %A Lupski, James R %A Gibbs, Richard A %A Beaudet, Arthur L %A Yang, Yaping %A Wang, Meng C %A Xia, Fan %K Abnormalities, Multiple %K Amino Acid Sequence %K Animals %K Base Sequence %K Caenorhabditis elegans %K Chromosome Deletion %K Chromosome Mapping %K Chromosomes, Human, Pair 5 %K DNA-Binding Proteins %K Humans %K Molecular Sequence Data %K Muscle Hypotonia %K Mutation %K Seizures %K Sequence Analysis, DNA %K Syndrome %K Transcription Factors %X

5q31.3 microdeletion syndrome is characterized by neonatal hypotonia, encephalopathy with or without epilepsy, and severe developmental delay, and the minimal critical deletion interval harbors three genes. We describe 11 individuals with clinical features of 5q31.3 microdeletion syndrome and de novo mutations in PURA, encoding transcriptional activator protein Pur-α, within the critical region. These data implicate causative PURA mutations responsible for the severe neurological phenotypes observed in this syndrome.

%B Am J Hum Genet %V 95 %P 579-83 %8 2014 Nov 06 %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/25439098?dopt=Abstract %R 10.1016/j.ajhg.2014.09.014 %0 Journal Article %J Hum Mol Genet %D 2014 %T New syndrome with retinitis pigmentosa is caused by nonsense mutations in retinol dehydrogenase RDH11. %A Xie, Yajing Angela %A Lee, Winston %A Cai, Carolyn %A Gambin, Tomasz %A Nõupuu, Kalev %A Sujirakul, Tharikarn %A Ayuso, Carmen %A Jhangiani, Shalini %A Muzny, Donna %A Boerwinkle, Eric %A Gibbs, Richard %A Greenstein, Vivienne C %A Lupski, James R %A Tsang, Stephen H %A Allikmets, Rando %K Adolescent %K Child %K Codon, Nonsense %K Female %K Humans %K Male %K Oxidoreductases %K Pedigree %K Phenotype %K Retinitis Pigmentosa %K Syndrome %K Vision Tests %K Visual Acuity %K Young Adult %X

Retinitis pigmentosa (RP), a genetically heterogeneous group of retinopathies that occur in both non-syndromic and syndromic forms, is caused by mutations in ∼100 genes. Although recent advances in next-generation sequencing have aided in the discovery of novel RP genes, a number of the underlying contributing genes and loci remain to be identified. We investigated three siblings, born to asymptomatic parents of Italian-American descent, who each presented with atypical RP with systemic features, including facial dysmorphologies, psychomotor developmental delays recognized since early childhood, learning disabilities and short stature. RP-associated ophthalmological findings included salt-and-pepper retinopathy, attenuation of the arterioles and generalized rod-cone dysfunction as determined by almost extinguished electroretinogram in 2 of 3 siblings. Atypical for RP features included mottled macula at an early age and peripapillary sparing of the retinal pigment epithelium. Whole-exome sequencing data, queried under a recessive model of inheritance, identified compound heterozygous stop mutations, c.C199T:p.R67* and c.C322T:p.R108*, in the retinol dehydrogenase 11 (RDH11) gene, resulting in a non-functional protein, in all affected children. In summary, deleterious mutations in RDH11, an important enzyme for vision-related and systemic retinoic acid metabolism, cause a new syndrome with RP.

%B Hum Mol Genet %V 23 %P 5774-80 %8 2014 Nov 01 %G eng %N 21 %1 https://www.ncbi.nlm.nih.gov/pubmed/24916380?dopt=Abstract %R 10.1093/hmg/ddu291 %0 Journal Article %J Am J Hum Genet %D 2014 %T NR2F1 mutations cause optic atrophy with intellectual disability. %A Bosch, Daniëlle G M %A Boonstra, F Nienke %A Gonzaga-Jauregui, Claudia %A Xu, Mafei %A de Ligt, Joep %A Jhangiani, Shalini %A Wiszniewski, Wojciech %A Muzny, Donna M %A Yntema, Helger G %A Pfundt, Rolph %A Vissers, Lisenka E L M %A Spruijt, Liesbeth %A Blokland, Ellen A W %A Chen, Chun-An %A Lewis, Richard A %A Tsai, Sophia Y %A Gibbs, Richard A %A Tsai, Ming-Jer %A Lupski, James R %A Zoghbi, Huda Y %A Cremers, Frans P M %A de Vries, Bert B A %A Schaaf, Christian P %K Adolescent %K Adult %K Amino Acid Sequence %K Child %K Child, Preschool %K COUP Transcription Factor I %K DNA-Binding Proteins %K Female %K Genotype %K Humans %K Intellectual Disability %K Male %K Molecular Sequence Data %K Mutation, Missense %K Optic Atrophy %K Phenotype %K Young Adult %K Zinc Fingers %X

Optic nerve atrophy and hypoplasia can be primary disorders or can result from trans-synaptic degeneration arising from cerebral visual impairment (CVI). Here we report six individuals with CVI and/or optic nerve abnormalities, born after an uneventful pregnancy and delivery, who have either de novo heterozygous missense mutations in NR2F1, also known as COUP-TFI, or deletions encompassing NR2F1. All affected individuals show mild to moderate intellectual impairment. NR2F1 encodes a nuclear receptor protein that regulates transcription. A reporter assay showed that missense mutations in the zinc-finger DNA-binding domain and the putative ligand-binding domain decrease NR2F1 transcriptional activity. These findings indicate that NR2F1 plays an important role in the neurodevelopment of the visual system and that its disruption can lead to optic atrophy with intellectual disability.

%B Am J Hum Genet %V 94 %P 303-9 %8 2014 Feb 06 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/24462372?dopt=Abstract %R 10.1016/j.ajhg.2014.01.002 %0 Journal Article %J Am J Hum Genet %D 2014 %T Parent of origin, mosaicism, and recurrence risk: probabilistic modeling explains the broken symmetry of transmission genetics. %A Campbell, Ian M %A Stewart, Jonathan R %A James, Regis A %A Lupski, James R %A Stankiewicz, Paweł %A Olofsson, Peter %A Shaw, Chad A %K Adult %K Aged %K Aged, 80 and over %K Chromosome Aberrations %K DNA Copy Number Variations %K Fathers %K Female %K Gametogenesis %K Genetic Diseases, Inborn %K Genomics %K Germ Cells %K Germ-Line Mutation %K Humans %K Inheritance Patterns %K Male %K Middle Aged %K Models, Theoretical %K Mosaicism %K Mothers %K Pregnancy %K Recurrence %K Risk Factors %K Young Adult %X

Most new mutations are observed to arise in fathers, and increasing paternal age positively correlates with the risk of new variants. Interestingly, new mutations in X-linked recessive disease show elevated familial recurrence rates. In male offspring, these mutations must be inherited from mothers. We previously developed a simulation model to consider parental mosaicism as a source of transmitted mutations. In this paper, we extend and formalize the model to provide analytical results and flexible formulas. The results implicate parent of origin and parental mosaicism as central variables in recurrence risk. Consistent with empirical data, our model predicts that more transmitted mutations arise in fathers and that this tendency increases as fathers age. Notably, the lack of expansion later in the male germline determines relatively lower variance in the proportion of mutants, which decreases with paternal age. Subsequently, observation of a transmitted mutation has less impact on the expected risk for future offspring. Conversely, for the female germline, which arrests after clonal expansion in early development, variance in the mutant proportion is higher, and observation of a transmitted mutation dramatically increases the expected risk of recurrence in another pregnancy. Parental somatic mosaicism considerably elevates risk for both parents. These findings have important implications for genetic counseling and for understanding patterns of recurrence in transmission genetics. We provide a convenient online tool and source code implementing our analytical results. These tools permit varying the underlying parameters that influence recurrence risk and could be useful for analyzing risk in diverse family structures.

%B Am J Hum Genet %V 95 %P 345-59 %8 2014 Oct 02 %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/25242496?dopt=Abstract %R 10.1016/j.ajhg.2014.08.010 %0 Journal Article %J Am J Hum Genet %D 2014 %T Parental somatic mosaicism is underrecognized and influences recurrence risk of genomic disorders. %A Campbell, Ian M %A Yuan, Bo %A Robberecht, Caroline %A Pfundt, Rolph %A Szafranski, Przemyslaw %A McEntagart, Meriel E %A Nagamani, Sandesh C S %A Erez, Ayelet %A Bartnik, Magdalena %A Wiśniowiecka-Kowalnik, Barbara %A Plunkett, Katie S %A Pursley, Amber N %A Kang, Sung-Hae L %A Bi, Weimin %A Lalani, Seema R %A Bacino, Carlos A %A Vast, Mala %A Marks, Karen %A Patton, Michael %A Olofsson, Peter %A Patel, Ankita %A Veltman, Joris A %A Cheung, Sau Wai %A Shaw, Chad A %A Vissers, Lisenka E L M %A Vermeesch, Joris R %A Lupski, James R %A Stankiewicz, Paweł %K Cell Division %K DNA Copy Number Variations %K Female %K Gametogenesis %K Genetic Diseases, Inborn %K Genomics %K Germ Cells %K Germ-Line Mutation %K Humans %K Male %K Models, Genetic %K Mosaicism %K Mutation %K Pedigree %K Prospective Studies %K Recurrence %K Risk %K Sex Characteristics %K Smith-Magenis Syndrome %X

New human mutations are thought to originate in germ cells, thus making a recurrence of the same mutation in a sibling exceedingly rare. However, increasing sensitivity of genomic technologies has anecdotally revealed mosaicism for mutations in somatic tissues of apparently healthy parents. Such somatically mosaic parents might also have germline mosaicism that can potentially cause unexpected intergenerational recurrences. Here, we show that somatic mosaicism for transmitted mutations among parents of children with simplex genetic disease is more common than currently appreciated. Using the sensitivity of individual-specific breakpoint PCR, we prospectively screened 100 families with children affected by genomic disorders due to rare deletion copy-number variants (CNVs) determined to be de novo by clinical analysis of parental DNA. Surprisingly, we identified four cases of low-level somatic mosaicism for the transmitted CNV in DNA isolated from parental blood. Integrated probabilistic modeling of gametogenesis developed in response to our observations predicts that mutations in parental blood increase recurrence risk substantially more than parental mutations confined to the germline. Moreover, despite the fact that maternally transmitted mutations are the minority of alleles, our model suggests that sexual dimorphisms in gametogenesis result in a greater proportion of somatically mosaic transmitting mothers who are thus at increased risk of recurrence. Therefore, somatic mosaicism together with sexual differences in gametogenesis might explain a considerable fraction of unexpected recurrences of X-linked recessive disease. Overall, our results underscore an important role for somatic mosaicism and mitotic replicative mutational mechanisms in transmission genetics.

%B Am J Hum Genet %V 95 %P 173-82 %8 2014 Aug 07 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/25087610?dopt=Abstract %R 10.1016/j.ajhg.2014.07.003 %0 Journal Article %J Stem Cells %D 2014 %T Passage number is a major contributor to genomic structural variations in mouse iPSCs. %A Liu, Pengfei %A Kaplan, Anna %A Bo Yuan %A Hanna, Jacob H %A James R Lupski %A Reiner, Orly %K Aneuploidy %K Animals %K Base Sequence %K Cell Proliferation %K Chromosome Breakage %K Clone Cells %K Comparative Genomic Hybridization %K DNA Copy Number Variations %K Genetic Loci %K Genomic Instability %K Genomic Structural Variation %K Induced Pluripotent Stem Cells %K Mice %K Molecular Sequence Data %K Neural Stem Cells %K Spheroids, Cellular %X

Emergence of genomic instability is a practical issue in preparing neural stem cells (NSCs) and induced pluripotent stem cells (iPSCs). However, it is still not fully understood what the origins and mechanisms for formation are for the genomic alternations observed. Here, we studied the extent of genomic variation on the scale of individual cells originating from the same animal. We used mouse NSCs grown from embryonic cells and iPSCs generated from embryonic brain cells, B cells or fibroblasts, and performed comparative analysis with cultures of fibroblasts from the same mouse. In the first passage of these cell lines, aneuploidies were only observed for chromosomes 6, 11, 12, 19, and Y, which is overall at a rate lower than previously reported; de novo copy number variations (CNVs) were observed in 4.3% of neural iPSCs, 29% of B cell iPSCs, 10% of fibroblast iPSCs, and 1.3% of neurospheres. In contrast, propagation of these first passage cells to a later passage induced additional aneuploidies and CNVs. Breakpoint sequencing analysis suggested that the majority of the detected CNVs arose by replicative mechanisms. Interestingly, we detected identical de novo CNVs in different single cell colonies that appeared to have arisen independently from each other, which suggests a novel CNV formation mechanism in these cells. Our findings provide insights into mechanisms of CNV formation during reprogramming and suggest that replicative mechanisms for CNV formation accompany mitotic divisions.

%B Stem Cells %V 32 %P 2657-67 %8 2014 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/24965231?dopt=Abstract %R 10.1002/stem.1779 %0 Journal Article %J Am J Hum Genet %D 2014 %T PGM3 mutations cause a congenital disorder of glycosylation with severe immunodeficiency and skeletal dysplasia. %A Stray-Pedersen, Asbjørg %A Backe, Paul H %A Sorte, Hanne S %A Mørkrid, Lars %A Chokshi, Niti Y %A Erichsen, Hans Christian %A Gambin, Tomasz %A Elgstøen, Katja B P %A Bjørås, Magnar %A Wlodarski, Marcin W %A Krüger, Marcus %A Jhangiani, Shalini N %A Muzny, Donna M %A Patel, Ankita %A Raymond, Kimiyo M %A Sasa, Ghadir S %A Krance, Robert A %A Martinez, Caridad A %A Abraham, Shirley M %A Speckmann, Carsten %A Ehl, Stephan %A Hall, Patricia %A Forbes, Lisa R %A Merckoll, Else %A Westvik, Jostein %A Nishimura, Gen %A Rustad, Cecilie F %A Abrahamsen, Tore G %A Rønnestad, Arild %A Osnes, Liv T %A Egeland, Torstein %A Rødningen, Olaug K %A Beck, Christine R %A Boerwinkle, Eric A %A Gibbs, Richard A %A Lupski, James R %A Orange, Jordan S %A Lausch, Ekkehart %A Hanson, I Celine %K Bone Diseases, Developmental %K Congenital Disorders of Glycosylation %K Female %K Humans %K Immunologic Deficiency Syndromes %K Male %K Mutation %K Pedigree %K Phosphoglucomutase %X

Human phosphoglucomutase 3 (PGM3) catalyzes the conversion of N-acetyl-glucosamine (GlcNAc)-6-phosphate into GlcNAc-1-phosphate during the synthesis of uridine diphosphate (UDP)-GlcNAc, a sugar nucleotide critical to multiple glycosylation pathways. We identified three unrelated children with recurrent infections, congenital leukopenia including neutropenia, B and T cell lymphopenia, and progression to bone marrow failure. Whole-exome sequencing demonstrated deleterious mutations in PGM3 in all three subjects, delineating their disease to be due to an unsuspected congenital disorder of glycosylation (CDG). Functional studies of the disease-associated PGM3 variants in E. coli cells demonstrated reduced PGM3 activity for all mutants tested. Two of the three children had skeletal anomalies resembling Desbuquois dysplasia: short stature, brachydactyly, dysmorphic facial features, and intellectual disability. However, these additional features were absent in the third child, showing the clinical variability of the disease. Two children received hematopoietic stem cell transplantation of cord blood and bone marrow from matched related donors; both had successful engraftment and correction of neutropenia and lymphopenia. We define PGM3-CDG as a treatable immunodeficiency, document the power of whole-exome sequencing in gene discoveries for rare disorders, and illustrate the utility of genomic analyses in studying combined and variable phenotypes.

%B Am J Hum Genet %V 95 %P 96-107 %8 2014 Jul 03 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/24931394?dopt=Abstract %R 10.1016/j.ajhg.2014.05.007 %0 Journal Article %J Am J Hum Genet %D 2014 %T Recurrent CNVs and SNVs at the NPHP1 locus contribute pathogenic alleles to Bardet-Biedl syndrome. %A Lindstrand, Anna %A Davis, Erica E %A Carvalho, Claudia M B %A Pehlivan, Davut %A Willer, Jason R %A Tsai, I-Chun %A Ramanathan, Subhadra %A Zuppan, Craig %A Sabo, Aniko %A Muzny, Donna %A Gibbs, Richard %A Liu, Pengfei %A Lewis, Richard A %A Banin, Eyal %A Lupski, James R %A Clark, Robin %A Katsanis, Nicholas %K Adaptor Proteins, Signal Transducing %K Alleles %K Animals %K Bardet-Biedl Syndrome %K Cytoskeletal Proteins %K DNA Copy Number Variations %K Gastrulation %K Genetic Loci %K Heterozygote %K Homozygote %K Humans %K Kidney %K Membrane Proteins %K Mice %K Pedigree %K Sequence Deletion %K Zebrafish %X

Homozygosity for a recurrent 290 kb deletion of NPHP1 is the most frequent cause of isolated nephronophthisis (NPHP) in humans. A deletion of the same genomic interval has also been detected in individuals with Joubert syndrome (JBTS), and in the mouse, Nphp1 interacts genetically with Ahi1, a known JBTS locus. Given these observations, we investigated the contribution of NPHP1 in Bardet-Biedl syndrome (BBS), a ciliopathy of intermediate severity. By using a combination of array-comparative genomic hybridization, TaqMan copy number assays, and sequencing, we studied 200 families affected by BBS. We report a homozygous NPHP1 deletion CNV in a family with classical BBS that is transmitted with autosomal-recessive inheritance. Further, we identified heterozygous NPHP1 deletions in two more unrelated persons with BBS who bear primary mutations at another BBS locus. In parallel, we identified five families harboring an SNV in NPHP1 resulting in a conserved missense change, c.14G>T (p.Arg5Leu), that is enriched in our Hispanic pedigrees; in each case, affected individuals carried additional bona fide pathogenic alleles in another BBS gene. In vivo functional modeling in zebrafish embryos demonstrated that c.14G>T is a loss-of-function variant, and suppression of nphp1 in concert with each of the primary BBS loci found in our NPHP1-positive pedigrees exacerbated the severity of the phenotype. These results suggest that NPHP1 mutations are probably rare primary causes of BBS that contribute to the mutational burden of the disorder.

%B Am J Hum Genet %V 94 %P 745-54 %8 2014 May 01 %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/24746959?dopt=Abstract %R 10.1016/j.ajhg.2014.03.017 %0 Journal Article %J Am J Med Genet A %D 2014 %T Whole exome sequencing identifies three novel mutations in ANTXR1 in families with GAPO syndrome. %A Bayram, Yavuz %A Pehlivan, Davut %A Karaca, Ender %A Gambin, Tomasz %A Jhangiani, Shalini N %A Erdin, Serkan %A Gonzaga-Jauregui, Claudia %A Wiszniewski, Wojciech %A Muzny, Donna %A Elcioglu, Nursel H %A Yildirim, M Selman %A Bozkurt, Banu %A Zamani, Ayse Gul %A Boerwinkle, Eric %A Gibbs, Richard A %A Lupski, James R %K Adolescent %K Adult %K Alopecia %K Anodontia %K Base Sequence %K Child %K Chromosome Segregation %K DNA Mutational Analysis %K Exome %K Facies %K Family %K Female %K Growth Disorders %K Humans %K Male %K Microfilament Proteins %K Molecular Sequence Data %K Mutation %K Neoplasm Proteins %K Optic Atrophies, Hereditary %K Pedigree %K Protein Structure, Tertiary %K Receptors, Cell Surface %X

GAPO syndrome (OMIM#230740) is the acronym for growth retardation, alopecia, pseudoanodontia, and optic atrophy. About 35 cases have been reported, making it among one of the rarest recessive conditions. Distinctive craniofacial features including alopecia, rarefaction of eyebrows and eyelashes, frontal bossing, high forehead, mid-facial hypoplasia, hypertelorism, and thickened eyelids and lips make GAPO syndrome a clinically recognizable phenotype. While this genomic study was in progress mutations in ANTXR1 were reported to cause GAPO syndrome. In our study we performed whole exome sequencing (WES) for five affected individuals from three Turkish kindreds segregating the GAPO trait. Exome sequencing analysis identified three novel homozygous mutations including; one frame-shift (c.1220_1221insT; p.Ala408Cysfs*2), one splice site (c.411A>G; p.Gln137Gln), and one non-synonymous (c.1150G>A; p.Gly384Ser) mutation in the ANTXR1 gene. Our studies expand the allelic spectrum in this rare condition and potentially provide insight into the role of ANTXR1 in the regulation of the extracellular matrix.

%B Am J Med Genet A %V 164A %P 2328-34 %8 2014 Sep %G eng %N 9 %1 https://www.ncbi.nlm.nih.gov/pubmed/25045128?dopt=Abstract %R 10.1002/ajmg.a.36678 %0 Journal Article %J Eur J Hum Genet %D 2014 %T Whole-exome sequencing links TMCO1 defect syndrome with cerebro-facio-thoracic dysplasia. %A Pehlivan, Davut %A Karaca, Ender %A Aydin, Hatip %A Beck, Christine R %A Gambin, Tomasz %A Muzny, Donna M %A Bilge Geckinli, B %A Karaman, Ali %A Jhangiani, Shalini N %A Gibbs, Richard A %A Lupski, James R %K Abnormalities, Multiple %K Calcium Channels %K Exome %K Humans %K Infant %K Intellectual Disability %K Male %K Membrane Proteins %K Mutation %K Protein Isoforms %X

Whole-exome sequencing (WES) is a type of disruptive technology that has tremendous influence on human and clinical genetics research. An efficient and cost-effective method, WES is now widely used as a diagnostic tool for identifying the molecular basis of genetic syndromes that are often challenging to diagnose. Here we report a patient with a clinical diagnosis of cerebro-facio-thoracic dysplasia (CFTD; MIM#213980) in whom we identified a homozygous splice-site mutation in the transmembrane and coiled-coil domains 1 (TMCO1) gene using WES. TMCO1 mutations cause craniofacial dysmorphism, skeletal anomalies characterized by multiple malformations of the vertebrae and ribs, and intellectual disability (MIM#614132). A retrospective review revealed that clinical manifestations of both syndromes are very similar and overlap remarkably. We propose that mutations of TMCO1 are not only responsible for craniofacial dysmorphism, skeletal anomalies and mental retardation syndrome but also for CFTD.

%B Eur J Hum Genet %V 22 %P 1145-8 %8 2014 Sep %G eng %N 9 %1 https://www.ncbi.nlm.nih.gov/pubmed/24424126?dopt=Abstract %R 10.1038/ejhg.2013.291 %0 Journal Article %J Am J Hum Genet %D 2013 %T ARMC4 mutations cause primary ciliary dyskinesia with randomization of left/right body asymmetry. %A Hjeij, Rim %A Lindstrand, Anna %A Francis, Richard %A Zariwala, Maimoona A %A Liu, Xiaoqin %A Li, You %A Damerla, Rama %A Dougherty, Gerard W %A Abouhamed, Marouan %A Olbrich, Heike %A Loges, Niki T %A Pennekamp, Petra %A Davis, Erica E %A Carvalho, Claudia M B %A Pehlivan, Davut %A Werner, Claudius %A Raidt, Johanna %A Köhler, Gabriele %A Häffner, Karsten %A Reyes-Mugica, Miguel %A Lupski, James R %A Leigh, Margaret W %A Rosenfeld, Margaret %A Morgan, Lucy C %A Knowles, Michael R %A Lo, Cecilia W %A Katsanis, Nicholas %A Omran, Heymut %K Amino Acid Sequence %K Animals %K Armadillo Domain Proteins %K Axoneme %K Body Patterning %K Cilia %K DNA Copy Number Variations %K DNA Mutational Analysis %K Dyneins %K Gene Expression Regulation %K Humans %K Kartagener Syndrome %K Mice %K Microtubule-Associated Proteins %K Molecular Sequence Data %K Mutation %K Respiratory System %K Zebrafish %X

The motive forces for ciliary movement are generated by large multiprotein complexes referred to as outer dynein arms (ODAs), which are preassembled in the cytoplasm prior to transport to the ciliary axonemal compartment. In humans, defects in structural components, docking complexes, or cytoplasmic assembly factors can cause primary ciliary dyskinesia (PCD), a disorder characterized by chronic airway disease and defects in laterality. By using combined high resolution copy-number variant and mutation analysis, we identified ARMC4 mutations in twelve PCD individuals whose cells showed reduced numbers of ODAs and severely impaired ciliary beating. Transient suppression in zebrafish and analysis of an ENU mouse mutant confirmed in both model organisms that ARMC4 is critical for left-right patterning. We demonstrate that ARMC4 is an axonemal protein that is necessary for proper targeting and anchoring of ODAs.

%B Am J Hum Genet %V 93 %P 357-67 %8 2013 Aug 08 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/23849778?dopt=Abstract %R 10.1016/j.ajhg.2013.06.009 %0 Journal Article %J Genome Med %D 2013 %T De novo truncating mutations in ASXL3 are associated with a novel clinical phenotype with similarities to Bohring-Opitz syndrome. %A Bainbridge, Matthew N %A Hu, Hao %A Muzny, Donna M %A Musante, Luciana %A Lupski, James R %A Graham, Brett H %A Chen, Wei %A Gripp, Karen W %A Jenny, Kim %A Wienker, Thomas F %A Yang, Yaping %A Sutton, V Reid %A Gibbs, Richard A %A Ropers, H Hilger %X

BACKGROUND: Molecular diagnostics can resolve locus heterogeneity underlying clinical phenotypes that may otherwise be co-assigned as a specific syndrome based on shared clinical features, and can associate phenotypically diverse diseases to a single locus through allelic affinity. Here we describe an apparently novel syndrome, likely caused by de novo truncating mutations in ASXL3, which shares characteristics with Bohring-Opitz syndrome, a disease associated with de novo truncating mutations in ASXL1.

METHODS: We used whole-genome and whole-exome sequencing to interrogate the genomes of four subjects with an undiagnosed syndrome.

RESULTS: Using genome-wide sequencing, we identified heterozygous, de novo truncating mutations in ASXL3, a transcriptional repressor related to ASXL1, in four unrelated probands. We found that these probands shared similar phenotypes, including severe feeding difficulties, failure to thrive, and neurologic abnormalities with significant developmental delay. Further, they showed less phenotypic overlap with patients who had de novo truncating mutations in ASXL1.

CONCLUSION: We have identified truncating mutations in ASXL3 as the likely cause of a novel syndrome with phenotypic overlap with Bohring-Opitz syndrome.

%B Genome Med %V 5 %P 11 %8 2013 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/23383720?dopt=Abstract %R 10.1186/gm415 %0 Journal Article %J Genome Res %D 2013 %T Deletions of recessive disease genes: CNV contribution to carrier states and disease-causing alleles. %A Boone, Philip M %A Campbell, Ian M %A Baggett, Brett C %A Soens, Zachry T %A Rao, Mitchell M %A Hixson, Patricia M %A Patel, Ankita %A Bi, Weimin %A Cheung, Sau Wai %A Lalani, Seema R %A Beaudet, Arthur L %A Stankiewicz, Pawel %A Shaw, Chad A %A Lupski, James R %K Alleles %K Comparative Genomic Hybridization %K Databases, Genetic %K DNA Copy Number Variations %K Gene Deletion %K Gene Frequency %K Genes, Dominant %K Genes, Recessive %K Genetic Diseases, Inborn %K Homozygote %K Humans %X

Over 1200 recessive disease genes have been described in humans. The prevalence, allelic architecture, and per-genome load of pathogenic alleles in these genes remain to be fully elucidated, as does the contribution of DNA copy-number variants (CNVs) to carrier status and recessive disease. We mined CNV data from 21,470 individuals obtained by array-comparative genomic hybridization in a clinical diagnostic setting to identify deletions encompassing or disrupting recessive disease genes. We identified 3212 heterozygous potential carrier deletions affecting 419 unique recessive disease genes. Deletion frequency of these genes ranged from one occurrence to 1.5%. When compared with recessive disease genes never deleted in our cohort, the 419 recessive disease genes affected by at least one carrier deletion were longer and located farther from known dominant disease genes, suggesting that the formation and/or prevalence of carrier CNVs may be affected by both local and adjacent genomic features and by selection. Some subjects had multiple carrier CNVs (307 subjects) and/or carrier deletions encompassing more than one recessive disease gene (206 deletions). Heterozygous deletions spanning multiple recessive disease genes may confer carrier status for multiple single-gene disorders, for complex syndromes resulting from the combination of two or more recessive conditions, or may potentially cause clinical phenotypes due to a multiply heterozygous state. In addition to carrier mutations, we identified homozygous and hemizygous deletions potentially causative for recessive disease. We provide further evidence that CNVs contribute to the allelic architecture of both carrier and recessive disease-causing mutations. Thus, a complete recessive carrier screening method or diagnostic test should detect CNV alleles.

%B Genome Res %V 23 %P 1383-94 %8 2013 Sep %G eng %N 9 %1 https://www.ncbi.nlm.nih.gov/pubmed/23685542?dopt=Abstract %R 10.1101/gr.156075.113 %0 Journal Article %J Hum Mutat %D 2013 %T Detection of clinically relevant copy number variants with whole-exome sequencing. %A de Ligt, Joep %A Boone, Philip M %A Pfundt, Rolph %A Vissers, Lisenka E L M %A Richmond, Todd %A Geoghegan, Joel %A O'Moore, Kathleen %A de Leeuw, Nicole %A Shaw, Christine %A Brunner, Han G %A Lupski, James R %A Veltman, Joris A %A Hehir-Kwa, Jayne Y %K Algorithms %K DNA Copy Number Variations %K Exome %K Genetic Testing %K Genome-Wide Association Study %K High-Throughput Nucleotide Sequencing %K Humans %K Intellectual Disability %K Reproducibility of Results %X

Copy number variation (CNV) is a common source of genetic variation that has been implicated in many genomic disorders. This has resulted in the widespread application of genomic microarrays as a first-tier diagnostic tool for CNV detection. More recently, whole-exome sequencing (WES) has been proven successful for the detection of clinically relevant point mutations and small insertion-deletions exome wide. We evaluate the utility of short-read WES (SOLiD 5500xl) to detect clinically relevant CNVs in DNA from 10 patients with intellectual disability and compare these results to data from two independent high-resolution microarrays. Eleven of the 12 clinically relevant CNVs were detected via read-depth analysis of WES data; a heterozygous single-exon deletion remained undetected by all algorithms evaluated. Although the detection power of WES for small CNVs currently does not match that of high-resolution microarray platforms, we show that the majority (88%) of rare coding CNVs containing three or more exons are successfully identified by WES. These results show that the CNV detection resolution of WES is comparable to that of medium-resolution genomic microarrays commonly used as clinical assays. The combined detection of point mutations, indels, and CNVs makes WES a very attractive first-tier diagnostic test for genetically heterogeneous disorders.

%B Hum Mutat %V 34 %P 1439-48 %8 2013 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/23893877?dopt=Abstract %R 10.1002/humu.22387 %0 Journal Article %J Am J Med Genet A %D 2013 %T Evidence for replicative mechanism in a CHD7 rearrangement in a patient with CHARGE syndrome. %A Vatta, Matteo %A Niu, Zhiyv %A Lupski, James R %A Putnam, Philip %A Spoonamore, Katherine G %A Fang, Ping %A Eng, Christine M %A Willis, Alecia S %K Abnormalities, Multiple %K CHARGE Syndrome %K Child %K DNA Helicases %K DNA Replication %K DNA-Binding Proteins %K Exons %K Female %K Gene Deletion %K Haploinsufficiency %K Humans %K Mutation %X

Haploinsufficiency of CHD7 (OMIM# 608892) is known to cause CHARGE syndrome (OMIM# 214800). Molecular testing supports a definitive diagnosis in approximately 65-70% of cases. Most CHD7 mutations arise de novo, and no mutations affecting exon-7 have been reported to date. We report on an 8-year-old girl diagnosed with CHARGE syndrome that was referred to our laboratory for comprehensive CHD7 gene screening. Genomic DNA from the subject with a suspected diagnosis of CHARGE was isolated from peripheral blood lymphocytes and comprehensive Sanger sequencing, along with deletion/duplication analysis of the CHD7 gene using multiplex ligation-dependent probe amplification (MLPA), was performed. MLPA analysis identified a reduced single probe signal for exon-7 of the CHD7 gene consistent with potential heterozygous deletion. Long-range PCR breakpoint analysis identified a complex genomic rearrangement (CGR) leading to the deletion of exon-7 and breakpoints consistent with a replicative mechanism such as fork stalling and template switching (FoSTeS) or microhomology-mediated break-induced replication (MMBIR). Taken together this represents the first evidence for a CHD7 intragenic CGR in a patient with CHARGE syndrome leading to what appears to be also the first report of a mutation specifically disrupting exon-7. Although likely rare, CGR may represent an overlooked mechanism in subjects with CHARGE syndrome that can be missed by current sequencing and dosage assays.

%B Am J Med Genet A %V 161A %P 3182-6 %8 2013 Dec %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/23956205?dopt=Abstract %R 10.1002/ajmg.a.36178 %0 Journal Article %J Genome Med %D 2013 %T Exome sequencing resolves apparent incidental findings and reveals further complexity of SH3TC2 variant alleles causing Charcot-Marie-Tooth neuropathy. %A Lupski, James R %A Gonzaga-Jauregui, Claudia %A Yang, Yaping %A Bainbridge, Matthew N %A Jhangiani, Shalini %A Buhay, Christian J %A Kovar, Christie L %A Wang, Min %A Hawes, Alicia C %A Reid, Jeffrey G %A Eng, Christine %A Muzny, Donna M %A Gibbs, Richard A %X

BACKGROUND: The debate regarding the relative merits of whole genome sequencing (WGS) versus exome sequencing (ES) centers around comparative cost, average depth of coverage for each interrogated base, and their relative efficiency in the identification of medically actionable variants from the myriad of variants identified by each approach. Nevertheless, few genomes have been subjected to both WGS and ES, using multiple next generation sequencing platforms. In addition, no personal genome has been so extensively analyzed using DNA derived from peripheral blood as opposed to DNA from transformed cell lines that may either accumulate mutations during propagation or clonally expand mosaic variants during cell transformation and propagation.

METHODS: We investigated a genome that was studied previously by SOLiD chemistry using both ES and WGS, and now perform six independent ES assays (Illumina GAII (x2), Illumina HiSeq (x2), Life Technologies' Personal Genome Machine (PGM) and Proton), and one additional WGS (Illumina HiSeq).

RESULTS: We compared the variants identified by the different methods and provide insights into the differences among variants identified between ES runs in the same technology platform and among different sequencing technologies. We resolved the true genotypes of medically actionable variants identified in the proband through orthogonal experimental approaches. Furthermore, ES identified an additional SH3TC2 variant (p.M1?) that likely contributes to the phenotype in the proband.

CONCLUSIONS: ES identified additional medically actionable variant calls and helped resolve ambiguous single nucleotide variants (SNV) documenting the power of increased depth of coverage of the captured targeted regions. Comparative analyses of WGS and ES reveal that pseudogenes and segmental duplications may explain some instances of apparent disease mutations in unaffected individuals.

%B Genome Med %V 5 %P 57 %8 2013 %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/23806086?dopt=Abstract %R 10.1186/gm461 %0 Journal Article %J Clin Genet %D 2013 %T Exploring the utility of whole-exome sequencing as a diagnostic tool in a child with atypical episodic muscle weakness. %A Hanchard, Neil A %A David R Murdock %A Magoulas, Pilar L %A Matthew N Bainbridge %A Donna M Muzny %A Wu, Yuanqing %A Wang, Min %A James R Lupski %A Richard A Gibbs %A Brown, Chester W %K Base Sequence %K Calcium Channels %K Child, Preschool %K Exome %K Exons %K Female %K Genotype %K High-Throughput Nucleotide Sequencing %K Humans %K Male %K Muscle Weakness %K Mutation %K NAV1.4 Voltage-Gated Sodium Channel %K Pedigree %K Phenotype %X

The advent of whole-exome next-generation sequencing (WES) has been pivotal for the molecular characterization of Mendelian disease; however, the clinical applicability of WES has remained relatively unexplored. We describe our exploration of WES as a diagnostic tool in a 3½-year old female patient with a 2-year history of episodic muscle weakness and paroxysmal dystonia who presented following a previous extensive but unrevealing diagnostic work-up. WES was performed on the proband and her two parents. Parental exome data was used to filter potential de novo genomic events in the proband and suspected variants were confirmed using di-deoxy sequencing. WES revealed a de novo non-synonymous mutation in exon 21 of the calcium channel gene CACNA1S that has been previously reported in a single patient as a rare cause of atypical hypokalemic periodic paralysis. This was unexpected, as the proband's original differential diagnosis had included hypokalemic periodic paralysis, but clinical and laboratory features were equivocal, and standard clinical molecular testing for hypokalemic periodic paralysis and related disorders was negative. This report highlights the potential diagnostic utility of WES in clinical practice, with implications for the approach to similar diagnostic dilemmas in the future.

%B Clin Genet %V 83 %P 457-461 %8 2013 May %G eng %N 5 %R 10.1111/j.1399-0004.2012.01951.x %0 Journal Article %J Genet Med %D 2013 %T Incidental copy-number variants identified by routine genome testing in a clinical population. %A Boone, Philip M %A Soens, Zachry T %A Campbell, Ian M %A Stankiewicz, Pawel %A Cheung, Sau Wai %A Patel, Ankita %A Beaudet, Arthur L %A Plon, Sharon E %A Shaw, Chad A %A McGuire, Amy L %A Lupski, James R %K Age of Onset %K Base Sequence %K Chromosome Mapping %K Comparative Genomic Hybridization %K DNA Copy Number Variations %K Female %K Gene Order %K Genetic Predisposition to Disease %K Humans %K Inheritance Patterns %K Male %K Reproducibility of Results %X

PURPOSE: Mutational load of susceptibility variants has not been studied on a genomic scale in a clinical population, nor has the potential to identify these mutations as incidental findings during clinical testing been systematically ascertained.

METHODS: Array comparative genomic hybridization, a method for genome-wide detection of DNA copy-number variants, was performed clinically on DNA from 9,005 individuals. Copy-number variants encompassing or disrupting single genes were identified and analyzed for their potential to confer predisposition to dominant, adult-onset disease. Multigene copy-number variants affecting dominant, adult-onset cancer syndrome genes were also assessed.

RESULTS: In our cohort, 83 single-gene copy-number variants affected 40 unique genes associated with dominant, adult-onset disorders and unrelated to the patients' referring diagnoses (i.e., incidental) were found. Fourteen of these copy-number variants are likely disease-predisposing, 25 are likely benign, and 44 are of unknown clinical consequence. When incidental copy-number variants spanning up to 20 genes were considered, 27 copy-number variants affected 17 unique genes associated with dominant, adult-onset cancer predisposition.

CONCLUSION: Copy-number variants potentially conferring susceptibility to adult-onset disease can be identified as incidental findings during routine genome-wide testing. Some of these mutations may be medically actionable, enabling disease surveillance or prevention; however, most incidentally observed single-gene copy-number variants are currently of unclear significance to the patient.

%B Genet Med %V 15 %P 45-54 %8 2013 Jan %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/22878507?dopt=Abstract %R 10.1038/gim.2012.95 %0 Journal Article %J JAMA Neurol %D 2013 %T Mutations in VRK1 associated with complex motor and sensory axonal neuropathy plus microcephaly. %A Gonzaga-Jauregui, Claudia %A Lotze, Timothy %A Jamal, Leila %A Penney, Samantha %A Campbell, Ian M %A Pehlivan, Davut %A Hunter, Jill V %A Woodbury, Suzanne L %A Raymond, Gerald %A Adesina, Adekunle M %A Jhangiani, Shalini N %A Reid, Jeffrey G %A Muzny, Donna M %A Boerwinkle, Eric %A Lupski, James R %A Gibbs, Richard A %A Wiszniewski, Wojciech %K Child %K Child, Preschool %K DNA Mutational Analysis %K Female %K Genotype %K Hereditary Sensory and Motor Neuropathy %K Humans %K Infant %K Intracellular Signaling Peptides and Proteins %K Magnetic Resonance Imaging %K Male %K Microcephaly %K Mutation %K Neural Conduction %K Polymorphism, Single Nucleotide %K Protein Serine-Threonine Kinases %X

IMPORTANCE: Patients with rare diseases and complex clinical presentations represent a challenge for clinical diagnostics. Genomic approaches are allowing the identification of novel variants in genes for very rare disorders, enabling a molecular diagnosis. Genomics is also revealing a phenotypic expansion whereby the full spectrum of clinical expression conveyed by mutant alleles at a locus can be better appreciated.

OBJECTIVE: To elucidate the molecular cause of a complex neuropathy phenotype in 3 patients by applying genomic sequencing strategies.

DESIGN, SETTING, AND PARTICIPANTS: Three affected individuals from 2 unrelated families presented with a complex neuropathy phenotype characterized by axonal sensorimotor neuropathy and microcephaly. They were recruited into the Centers for Mendelian Genomics research program to identify the molecular cause of their phenotype. Whole-genome, targeted whole-exome sequencing, and high-resolution single-nucleotide polymorphism arrays were performed in genetics clinics of tertiary care pediatric hospitals and biomedical research institutions.

MAIN OUTCOMES AND MEASURES: Whole-genome and whole-exome sequencing identified the variants responsible for the patients' clinical phenotype.

RESULTS: We identified compound heterozygous alleles in 2 affected siblings from 1 family and a homozygous nonsense variant in the third unrelated patient in the vaccinia-related kinase 1 gene (VRK1). In the latter subject, we found a common haplotype on which the nonsense mutation occurred and that segregates in the Ashkenazi Jewish population.

CONCLUSIONS AND RELEVANCE: We report the identification of disease-causing alleles in 3 children from 2 unrelated families with a previously uncharacterized complex axonal motor and sensory neuropathy accompanied by severe nonprogressive microcephaly and cerebral dysgenesis. Our data raise the question of whether VRK1 mutations disturb cell cycle progression and may result in apoptosis of cells in the nervous system. The application of unbiased genomic approaches allows the identification of potentially pathogenic mutations in unsuspected genes in highly genetically heterogeneous and uncharacterized neurological diseases.

%B JAMA Neurol %V 70 %P 1491-8 %8 2013 Dec %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/24126608?dopt=Abstract %R 10.1001/jamaneurol.2013.4598 %0 Journal Article %J Nat Genet %D 2013 %T Replicative mechanisms for CNV formation are error prone. %A Carvalho, Claudia M B %A Pehlivan, Davut %A Ramocki, Melissa B %A Fang, Ping %A Alleva, Benjamin %A Franco, Luis M %A Belmont, John W %A Hastings, P J %A Lupski, James R %K Base Sequence %K DNA Breaks %K DNA Copy Number Variations %K DNA Repair %K DNA Replication %K Frameshift Mutation %K Gene Rearrangement %K Genetic Variation %K Genotype %K Humans %K Sequence Analysis, DNA %K Sequence Deletion %X

We investigated 67 breakpoint junctions of gene copy number gains in 31 unrelated subjects. We observed a strikingly high frequency of small deletions and insertions (29%) apparently originating from polymerase slippage events, in addition to frameshifts and point mutations in homonucleotide runs (13%), at or flanking the breakpoint junctions of complex copy number variants. These single-nucleotide variants were generated concomitantly with the de novo complex genomic rearrangement (CGR) event. Our findings implicate low-fidelity, error-prone DNA polymerase activity in synthesis associated with DNA repair mechanisms as the cause of local increase in point mutation burden associated with human CGR.

%B Nat Genet %V 45 %P 1319-26 %8 2013 Nov %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/24056715?dopt=Abstract %R 10.1038/ng.2768 %0 Journal Article %J JAMA %D 2013 %T Reporting genomic sequencing results to ordering clinicians: incidental, but not exceptional. %A Green, Robert C %A Lupski, James R %A Biesecker, Leslie G %K Disclosure %K Genetic Predisposition to Disease %K Genetic Testing %K Humans %K Incidental Findings %K Mandatory Reporting %K Mutation %K Personal Autonomy %K Risk %K Sequence Analysis, DNA %B JAMA %V 310 %P 365-6 %8 2013 Jul 24 %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/23917280?dopt=Abstract %R 10.1001/jama.2013.41703 %0 Journal Article %J Am J Hum Genet %D 2013 %T TM4SF20 ancestral deletion and susceptibility to a pediatric disorder of early language delay and cerebral white matter hyperintensities. %A Wiszniewski, Wojciech %A Hunter, Jill V %A Hanchard, Neil A %A Willer, Jason R %A Shaw, Chad %A Tian, Qi %A Illner, Anna %A Wang, Xueqing %A Cheung, Sau W %A Patel, Ankita %A Campbell, Ian M %A Gelowani, Violet %A Hixson, Patricia %A Ester, Audrey R %A Azamian, Mahshid S %A Potocki, Lorraine %A Zapata, Gladys %A Hernandez, Patricia P %A Ramocki, Melissa B %A Santos-Cortez, Regie L P %A Wang, Gao %A York, Michele K %A Justice, Monica J %A Chu, Zili D %A Bader, Patricia I %A Omo-Griffith, Lisa %A Madduri, Nirupama S %A Scharer, Gunter %A Crawford, Heather P %A Yanatatsaneejit, Pattamawadee %A Eifert, Anna %A Kerr, Jeffery %A Bacino, Carlos A %A Franklin, Adiaha I A %A Goin-Kochel, Robin P %A Simpson, Gayle %A Immken, Ladonna %A Haque, Muhammad E %A Stosic, Marija %A Williams, Misti D %A Morgan, Thomas M %A Pruthi, Sumit %A Omary, Reed %A Boyadjiev, Simeon A %A Win, Kay K %A Thida, Aye %A Hurles, Matthew %A Hibberd, Martin Lloyd %A Khor, Chiea Chuen %A Van Vinh Chau, Nguyen %A Gallagher, Thomas E %A Mutirangura, Apiwat %A Stankiewicz, Pawel %A Beaudet, Arthur L %A Maletic-Savatic, Mirjana %A Rosenfeld, Jill A %A Shaffer, Lisa G %A Davis, Erica E %A Belmont, John W %A Dunstan, Sarah %A Simmons, Cameron P %A Bonnen, Penelope E %A Leal, Suzanne M %A Katsanis, Nicholas %A Lupski, James R %A Lalani, Seema R %K Age of Onset %K Aging, Premature %K Asian People %K Base Sequence %K Brain %K Child %K Child, Preschool %K Chromosomes, Human, Pair 2 %K Exons %K Female %K Genetic Predisposition to Disease %K Humans %K Language Development Disorders %K Leukoencephalopathies %K Magnetic Resonance Imaging %K Male %K Molecular Sequence Data %K Pedigree %K Sequence Analysis, DNA %K Sequence Deletion %K Tetraspanins %X

White matter hyperintensities (WMHs) of the brain are important markers of aging and small-vessel disease. WMHs are rare in healthy children and, when observed, often occur with comorbid neuroinflammatory or vasculitic processes. Here, we describe a complex 4 kb deletion in 2q36.3 that segregates with early childhood communication disorders and WMH in 15 unrelated families predominantly from Southeast Asia. The premature brain aging phenotype with punctate and multifocal WMHs was observed in ~70% of young carrier parents who underwent brain MRI. The complex deletion removes the penultimate exon 3 of TM4SF20, a gene encoding a transmembrane protein of unknown function. Minigene analysis showed that the resultant net loss of an exon introduces a premature stop codon, which, in turn, leads to the generation of a stable protein that fails to target to the plasma membrane and accumulates in the cytoplasm. Finally, we report this deletion to be enriched in individuals of Vietnamese Kinh descent, with an allele frequency of about 1%, embedded in an ancestral haplotype. Our data point to a constellation of early language delay and WMH phenotypes, driven by a likely toxic mechanism of TM4SF20 truncation, and highlight the importance of understanding and managing population-specific low-frequency pathogenic alleles.

%B Am J Hum Genet %V 93 %P 197-210 %8 2013 Aug 08 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/23810381?dopt=Abstract %R 10.1016/j.ajhg.2013.05.027 %0 Journal Article %J Biol Psychiatry %D 2012 %T Brain copy number variants and neuropsychiatric traits. %A Lupski, James R %K Brain %K DNA Copy Number Variations %K Genetic Predisposition to Disease %K Humans %K Mental Disorders %K Nervous System Diseases %K Phenotype %B Biol Psychiatry %V 72 %P 617-9 %8 2012 Oct 15 %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/22999336?dopt=Abstract %R 10.1016/j.biopsych.2012.08.007 %0 Journal Article %J Am J Med Genet A %D 2012 %T The Centers for Mendelian Genomics: a new large-scale initiative to identify the genes underlying rare Mendelian conditions. %A Bamshad, Michael J %A Shendure, Jay A %A Valle, David %A Hamosh, Ada %A Lupski, James R %A Gibbs, Richard A %A Boerwinkle, Eric %A Lifton, Richard P %A Gerstein, Mark %A Gunel, Murat %A Mane, Shrikant %A Nickerson, Deborah A %K Academies and Institutes %K Genetic Diseases, Inborn %K Genetics, Medical %K Genome, Human %K Genome-Wide Association Study %K Genomics %K High-Throughput Nucleotide Sequencing %K Humans %X

Next generation exome sequencing (ES) and whole genome sequencing (WGS) are new powerful tools for discovering the gene(s) that underlie Mendelian disorders. To accelerate these discoveries, the National Institutes of Health has established three Centers for Mendelian Genomics (CMGs): the Center for Mendelian Genomics at the University of Washington; the Center for Mendelian Genomics at Yale University; and the Baylor-Johns Hopkins Center for Mendelian Genomics at Baylor College of Medicine and Johns Hopkins University. The CMGs will provide ES/WGS and extensive analysis expertise at no cost to collaborating investigators where the causal gene(s) for a Mendelian phenotype has yet to be uncovered. Over the next few years and in collaboration with the global human genetics community, the CMGs hope to facilitate the identification of the genes underlying a very large fraction of all Mendelian disorders; see http://mendelian.org.

%B Am J Med Genet A %V 158A %P 1523-5 %8 2012 Jul %G eng %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/22628075?dopt=Abstract %R 10.1002/ajmg.a.35470 %0 Journal Article %J Annu Rev Med %D 2012 %T Human genome sequencing in health and disease. %A Gonzaga-Jauregui, Claudia %A Lupski, James R %A Gibbs, Richard A %K Genetic Diseases, Inborn %K Genetic Privacy %K Genome, Human %K HapMap Project %K Human Genome Project %K Humans %X

Following the "finished," euchromatic, haploid human reference genome sequence, the rapid development of novel, faster, and cheaper sequencing technologies is making possible the era of personalized human genomics. Personal diploid human genome sequences have been generated, and each has contributed to our better understanding of variation in the human genome. We have consequently begun to appreciate the vastness of individual genetic variation from single nucleotide to structural variants. Translation of genome-scale variation into medically useful information is, however, in its infancy. This review summarizes the initial steps undertaken in clinical implementation of personal genome information, and describes the application of whole-genome and exome sequencing to identify the cause of genetic diseases and to suggest adjuvant therapies. Better analysis tools and a deeper understanding of the biology of our genome are necessary in order to decipher, interpret, and optimize clinical utility of what the variation in the human genome can teach us. Personal genome sequencing may eventually become an instrument of common medical practice, providing information that assists in the formulation of a differential diagnosis. We outline herein some of the remaining challenges.

%B Annu Rev Med %V 63 %P 35-61 %8 2012 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/22248320?dopt=Abstract %R 10.1146/annurev-med-051010-162644 %0 Journal Article %J Cell %D 2011 %T Clan genomics and the complex architecture of human disease. %A Lupski, James R %A Belmont, John W %A Boerwinkle, Eric %A Gibbs, Richard A %K Genetic Predisposition to Disease %K Genetic Variation %K Genetics, Population %K Genome, Human %K Genomics %K Humans %K Pedigree %K Pilot Projects %K Precision Medicine %X

Human diseases are caused by alleles that encompass the full range of variant types, from single-nucleotide changes to copy-number variants, and these variations span a broad frequency spectrum, from the very rare to the common. The picture emerging from analysis of whole-genome sequences, the 1000 Genomes Project pilot studies, and targeted genomic sequencing derived from very large sample sizes reveals an abundance of rare and private variants. One implication of this realization is that recent mutation may have a greater influence on disease susceptibility or protection than is conferred by variations that arose in distant ancestors.

%B Cell %V 147 %P 32-43 %8 2011 Sep 30 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/21962505?dopt=Abstract %R 10.1016/j.cell.2011.09.008 %0 Journal Article %J Mol Vis %D 2011 %T Exome capture sequencing identifies a novel mutation in BBS4. %A Wang, Hui %A Chen, Xianfeng %A Dudinsky, Lynn %A Patenia, Claire %A Chen, Yiyun %A Li, Yumei %A Wei, Yue %A Abboud, Emad B %A Al-Rajhi, Ali A %A Lewis, Richard Alan %A Lupski, James R %A Mardon, Graeme %A Gibbs, Richard A %A Perkins, Brian D %A Chen, Rui %K Alleles %K Animals %K Base Sequence %K Chromosome Mapping %K Consanguinity %K Exome %K Exons %K Female %K Genotype %K High-Throughput Nucleotide Sequencing %K Humans %K Infant %K Leber Congenital Amaurosis %K Male %K Microtubule-Associated Proteins %K Molecular Sequence Data %K Mutation, Missense %K Pedigree %K Polymorphism, Single Nucleotide %K Proteins %K Retina %K Rhodopsin %K Saudi Arabia %K Zebrafish %X

PURPOSE: Leber congenital amaurosis (LCA) is one of the most severe eye dystrophies characterized by severe vision loss at an early stage and accounts for approximately 5% of all retinal dystrophies. The purpose of this study was to identify a novel LCA disease allele or gene and to develop an approach combining genetic mapping with whole exome sequencing.

METHODS: Three patients from King Khaled Eye Specialist Hospital (KKESH205) underwent whole genome single nucleotide polymorphism genotyping, and a single candidate region was identified. Taking advantage of next-generation high-throughput DNA sequencing technologies, whole exome capture sequencing was performed on patient KKESH205#7. Sanger direct sequencing was used during the validation step. The zebrafish model was used to examine the function of the mutant allele.

RESULTS: A novel missense mutation in Bardet-Biedl syndrome 4 protein (BBS4) was identified in a consanguineous family from Saudi Arabia. This missense mutation in the fifth exon (c.253G>C;p.E85Q) of BBS4 is likely a disease-causing mutation as it segregates with the disease. The mutation is not found in the single nucleotide polymorphism (SNP) database, the 1000 Genomes Project, or matching normal controls. Functional analysis of this mutation in zebrafish indicates that the G253C allele is pathogenic. Coinjection of the G253C allele cannot rescue the mislocalization of rhodopsin in the retina when BBS4 is knocked down by morpholino injection. Immunofluorescence analysis in cell culture shows that this missense mutation in BBS4 does not cause obvious defects in protein expression or pericentriolar localization.

CONCLUSIONS: This mutation likely mainly reduces or abolishes BBS4 function in the retina. Further studies of this allele will provide important insights concerning the pleiotropic nature of BBS4 function.

%B Mol Vis %V 17 %P 3529-40 %8 2011 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/22219648?dopt=Abstract %0 Journal Article %J Hum Mutat %D 2011 %T Whole-exome sequencing identifies ALMS1, IQCB1, CNGA3, and MYO7A mutations in patients with Leber congenital amaurosis. %A Wang, Xia %A Wang, Hui %A Cao, Ming %A Li, Zhe %A Chen, Xianfeng %A Patenia, Claire %A Gore, Athurva %A Abboud, Emad B %A Al-Rajhi, Ali A %A Lewis, Richard A %A Lupski, James R %A Mardon, Graeme %A Zhang, Kun %A Muzny, Donna %A Gibbs, Richard A %A Chen, Rui %K Calmodulin-Binding Proteins %K Cell Cycle Proteins %K Child, Preschool %K Chromosome Mapping %K Consanguinity %K Cyclic Nucleotide-Gated Cation Channels %K DNA Mutational Analysis %K Exome %K Family %K Homozygote %K Humans %K Leber Congenital Amaurosis %K Mutation %K Myosin VIIa %K Myosins %K Pedigree %K Proteins %K Saudi Arabia %K Sequence Analysis, DNA %X

It has been well documented that mutations in the same retinal disease gene can result in different clinical phenotypes due to difference in the mutant allele and/or genetic background. To evaluate this, a set of consanguineous patient families with Leber congenital amaurosis (LCA) that do not carry mutations in known LCA disease genes was characterized through homozygosity mapping followed by targeted exon/whole-exome sequencing to identify genetic variations. Among these families, a total of five putative disease-causing mutations, including four novel alleles, were found for six families. These five mutations are located in four genes, ALMS1, IQCB1, CNGA3, and MYO7A. Therefore, in our LCA collection from Saudi Arabia, three of the 37 unassigned families carry mutations in retinal disease genes ALMS1, CNGA3, and MYO7A, which have not been previously associated with LCA, and 3 of the 37 carry novel mutations in IQCB1, which has been recently associated with LCA. Together with other reports, our results emphasize that the molecular heterogeneity underlying LCA, and likely other retinal diseases, may be highly complex. Thus, to obtain accurate diagnosis and gain a complete picture of the disease, it is essential to sequence a larger set of retinal disease genes and combine the clinical phenotype with molecular diagnosis.

%B Hum Mutat %V 32 %P 1450-9 %8 2011 Dec %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/21901789?dopt=Abstract %R 10.1002/humu.21587 %0 Journal Article %J Sci Transl Med %D 2011 %T Whole-genome sequencing for optimized patient management. %A Bainbridge, Matthew N %A Wiszniewski, Wojciech %A Murdock, David R %A Friedman, Jennifer %A Gonzaga-Jauregui, Claudia %A Newsham, Irene %A Reid, Jeffrey G %A Fink, John K %A Morgan, Margaret B %A Gingras, Marie-Claude %A Muzny, Donna M %A Hoang, Linh D %A Yousaf, Shahed %A Lupski, James R %A Gibbs, Richard A %K Adolescent %K Decision Making %K Dystonic Disorders %K Female %K Genome, Human %K Humans %K Levodopa %K Male %K Patient Care %K Pedigree %K Sequence Analysis, DNA %K Treatment Outcome %K Twins, Dizygotic %X

Whole-genome sequencing of patient DNA can facilitate diagnosis of a disease, but its potential for guiding treatment has been under-realized. We interrogated the complete genome sequences of a 14-year-old fraternal twin pair diagnosed with dopa (3,4-dihydroxyphenylalanine)-responsive dystonia (DRD; Mendelian Inheritance in Man #128230). DRD is a genetically heterogeneous and clinically complex movement disorder that is usually treated with l-dopa, a precursor of the neurotransmitter dopamine. Whole-genome sequencing identified compound heterozygous mutations in the SPR gene encoding sepiapterin reductase. Disruption of SPR causes a decrease in tetrahydrobiopterin, a cofactor required for the hydroxylase enzymes that synthesize the neurotransmitters dopamine and serotonin. Supplementation of l-dopa therapy with 5-hydroxytryptophan, a serotonin precursor, resulted in clinical improvements in both twins.

%B Sci Transl Med %V 3 %P 87re3 %8 2011 Jun 15 %G eng %N 87 %1 https://www.ncbi.nlm.nih.gov/pubmed/21677200?dopt=Abstract %R 10.1126/scitranslmed.3002243 %0 Journal Article %J Trends Genet %D 2010 %T Personal genome research : what should the participant be told? %A McGuire, Amy L %A Lupski, James R %K Data Interpretation, Statistical %K Genetic Variation %K Genome, Human %K Humans %K Sequence Analysis, DNA %K Truth Disclosure %X

Should the results of whole genome sequencing research be disclosed to participants, in particular when the results have uncertain or indeterminate phenotypic consequences? This controversial question is considered in light of one author's (J.L.) experience as a geneticist who recently had his own genome sequenced.

%B Trends Genet %V 26 %P 199-201 %8 2010 May %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/20381895?dopt=Abstract %R 10.1016/j.tig.2009.12.007 %0 Journal Article %J N Engl J Med %D 2010 %T Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. %A Lupski, James R %A Reid, Jeffrey G %A Gonzaga-Jauregui, Claudia %A Rio Deiros, David %A Chen, David C Y %A Nazareth, Lynne %A Bainbridge, Matthew %A Dinh, Huyen %A Jing, Chyn %A Wheeler, David A %A McGuire, Amy L %A Zhang, Feng %A Stankiewicz, Pawel %A Halperin, John J %A Yang, Chengyong %A Gehman, Curtis %A Guo, Danwei %A Irikat, Rola K %A Tom, Warren %A Fantin, Nick J %A Muzny, Donna M %A Gibbs, Richard A %K Adult %K Aged %K Aged, 80 and over %K Charcot-Marie-Tooth Disease %K Codon, Nonsense %K Female %K Genes, Recessive %K Genetic Association Studies %K Genome, Human %K Genotype %K Humans %K Male %K Middle Aged %K Mutation, Missense %K Pedigree %K Phenotype %K Polymorphism, Single Nucleotide %K Sequence Analysis, DNA %X

BACKGROUND: Whole-genome sequencing may revolutionize medical diagnostics through rapid identification of alleles that cause disease. However, even in cases with simple patterns of inheritance and unambiguous diagnoses, the relationship between disease phenotypes and their corresponding genetic changes can be complicated. Comprehensive diagnostic assays must therefore identify all possible DNA changes in each haplotype and determine which are responsible for the underlying disorder. The high number of rare, heterogeneous mutations present in all humans and the paucity of known functional variants in more than 90% of annotated genes make this challenge particularly difficult. Thus, the identification of the molecular basis of a genetic disease by means of whole-genome sequencing has remained elusive. We therefore aimed to assess the usefulness of human whole-genome sequencing for genetic diagnosis in a patient with Charcot-Marie-Tooth disease.

METHODS: We identified a family with a recessive form of Charcot-Marie-Tooth disease for which the genetic basis had not been identified. We sequenced the whole genome of the proband, identified all potential functional variants in genes likely to be related to the disease, and genotyped these variants in the affected family members.

RESULTS: We identified and validated compound, heterozygous, causative alleles in SH3TC2 (the SH3 domain and tetratricopeptide repeats 2 gene), involving two mutations, in the proband and in family members affected by Charcot-Marie-Tooth disease. Separate subclinical phenotypes segregated independently with each of the two mutations; heterozygous mutations confer susceptibility to neuropathy, including the carpal tunnel syndrome.

CONCLUSIONS: As shown in this study of a family with Charcot-Marie-Tooth disease, whole-genome sequencing can identify clinically relevant variants and provide diagnostic information to inform the care of patients.

%B N Engl J Med %V 362 %P 1181-91 %8 2010 Apr 01 %G eng %N 13 %1 https://www.ncbi.nlm.nih.gov/pubmed/20220177?dopt=Abstract %R 10.1056/NEJMoa0908094 %0 Journal Article %J Invest Ophthalmol Vis Sci %D 2009 %T Mutation survey of known LCA genes and loci in the Saudi Arabian population. %A Li, Yumei %A Wang, Hui %A Peng, Jianlan %A Gibbs, Richard A %A Lewis, Richard Alan %A Lupski, James R %A Mardon, Graeme %A Chen, Rui %K Blindness %K Carrier Proteins %K cis-trans-Isomerases %K Consanguinity %K DNA Mutational Analysis %K Eye Proteins %K Female %K Genes %K Genotype %K Guanylate Cyclase %K Humans %K Male %K Membrane Proteins %K Microsatellite Repeats %K Mutation %K Nerve Tissue Proteins %K Pedigree %K Phenotype %K Polymerase Chain Reaction %K Receptors, Cell Surface %K Retinal Degeneration %K Saudi Arabia %X

PURPOSE: The purpose of this study was to perform a comprehensive survey of all known Leber congenital amaurosis (LCA) genes and loci in a collection of 37 consanguineous LCA families from Saudi Arabia.

METHODS: Direct PCR and sequencing were used to screen 13 known LCA genes (GUCY2D, CRX, RPE65, TULP1, AIPL1, CRB1, RPGRIP1, LRAT, RDH12, IMPDH1, CEP290, RD3, LCA5). In addition, families without mutations identified were further screened with STR markers around these 13 known LCA genes and two loci.

RESULTS: Disease-causing mutations were identified in nine of the 37 families: five in TULP1, two in CRB1, one in RPE65, and one in GUCY2D. Mutations in known genes only accounted for 24% of the Saudi families--much less than what has been observed in the European population (65%). Phenotype-genotype analysis was carried out to investigate the LCA disease penetrance for all families whose mutations identified. All identified mutations were found to segregate perfectly with the disease phenotype. On the other hand, severity of the disease varies for different patients carrying the same mutation and even within the same family. Furthermore, based on homozygosity mapping with both STR and SNP markers, one family is likely to map to the LCA3 locus.

CONCLUSIONS: These results underscore the importance of studying LCA disease families from different ethnic backgrounds to identify additional novel LCA disease genes. Furthermore, perfect segregation between mutation and disease indicates that LCA is fully penetrant. However, phenotypic variations among patients carrying the same mutation suggest that at least some of the variations in the clinical phenotype is due to modification from the genetic background, environment, or other factors.

%B Invest Ophthalmol Vis Sci %V 50 %P 1336-43 %8 2009 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/18936139?dopt=Abstract %R 10.1167/iovs.08-2589 %0 Journal Article %J Am J Hum Genet %D 2009 %T Mutations in SPATA7 cause Leber congenital amaurosis and juvenile retinitis pigmentosa. %A Wang, Hui %A den Hollander, Anneke I %A Moayedi, Yalda %A Abulimiti, Abuduaini %A Li, Yumei %A Collin, Rob W J %A Hoyng, Carel B %A Lopez, Irma %A Abboud, Emad B %A Al-Rajhi, Ali A %A Bray, Molly %A Lewis, Richard Alan %A Lupski, James R %A Mardon, Graeme %A Koenekoop, Robert K %A Chen, Rui %K Animals %K Child %K Codon, Nonsense %K DNA-Binding Proteins %K Homozygote %K Humans %K Mice %K Middle Aged %K Pedigree %K Retina %K Retinal Diseases %K Retinitis Pigmentosa %X

Leber congenital amaurosis (LCA) and juvenile retinitis pigmentosa (RP) are the most common hereditary causes of visual impairment in infants and children. Using homozygosity mapping, we narrowed down the critical region of the LCA3 locus to 3.8 Mb between markers D14S1022 and D14S1005. By direct Sanger sequencing of all genes within this region, we found a homozygous nonsense mutation in the SPATA7 gene in Saudi Arabian family KKESH-060. Three other loss-of-function mutations were subsequently discovered in patients with LCA or juvenile RP from distinct populations. Furthermore, we determined that Spata7 is expressed in the mature mouse retina. Our findings reveal another human visual-disease gene that causes LCA and juvenile RP.

%B Am J Hum Genet %V 84 %P 380-7 %8 2009 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/19268277?dopt=Abstract %R 10.1016/j.ajhg.2009.02.005 %0 Journal Article %J Nature %D 2008 %T The complete genome of an individual by massively parallel DNA sequencing. %A Wheeler, David A %A Srinivasan, Maithreyan %A Egholm, Michael %A Shen, Yufeng %A Chen, Lei %A McGuire, Amy %A He, Wen %A Chen, Yi-Ju %A Makhijani, Vinod %A Roth, G Thomas %A Gomes, Xavier %A Tartaro, Karrie %A Niazi, Faheem %A Turcotte, Cynthia L %A Irzyk, Gerard P %A Lupski, James R %A Chinault, Craig %A Song, Xing-Zhi %A Liu, Yue %A Yuan, Ye %A Nazareth, Lynne %A Xiang Qin %A Donna M Muzny %A Margulies, Marcel %A Weinstock, George M %A Richard A Gibbs %A Rothberg, Jonathan M %K Alleles %K Computational Biology %K Genetic Predisposition to Disease %K Genetic Variation %K Genome, Human %K Genomics %K Genotype %K Humans %K Individuality %K Male %K Oligonucleotide Array Sequence Analysis %K Polymorphism, Single Nucleotide %K Reproducibility of Results %K Sensitivity and Specificity %K Sequence Alignment %K Sequence Analysis, DNA %K Software %X

The association of genetic variation with disease and drug response, and improvements in nucleic acid technologies, have given great optimism for the impact of 'genomic medicine'. However, the formidable size of the diploid human genome, approximately 6 gigabases, has prevented the routine application of sequencing methods to deciphering complete individual human genomes. To realize the full potential of genomics for human health, this limitation must be overcome. Here we report the DNA sequence of a diploid genome of a single individual, James D. Watson, sequenced to 7.4-fold redundancy in two months using massively parallel sequencing in picolitre-size reaction vessels. This sequence was completed in two months at approximately one-hundredth of the cost of traditional capillary electrophoresis methods. Comparison of the sequence to the reference genome led to the identification of 3.3 million single nucleotide polymorphisms, of which 10,654 cause amino-acid substitution within the coding sequence. In addition, we accurately identified small-scale (2-40,000 base pair (bp)) insertion and deletion polymorphism as well as copy number variation resulting in the large-scale gain and loss of chromosomal segments ranging from 26,000 to 1.5 million base pairs. Overall, these results agree well with recent results of sequencing of a single individual by traditional methods. However, in addition to being faster and significantly less expensive, this sequencing technology avoids the arbitrary loss of genomic sequences inherent in random shotgun sequencing by bacterial cloning because it amplifies DNA in a cell-free system. As a result, we further demonstrate the acquisition of novel human sequence, including novel genes not previously identified by traditional genomic sequencing. This is the first genome sequenced by next-generation technologies. Therefore it is a pilot for the future challenges of 'personalized genome sequencing'.

%B Nature %V 452 %P 872-6 %8 2008 Apr 17 %G eng %N 7189 %1 https://www.ncbi.nlm.nih.gov/pubmed/18421352?dopt=Abstract %R 10.1038/nature06884 %0 Journal Article %J Proc Natl Acad Sci U S A %D 2002 %T A computational/functional genomics approach for the enrichment of the retinal transcriptome and the identification of positional candidate retinopathy genes. %A Katsanis, Nicholas %A Worley, Kim C %A Gonzalez, Guillermo %A Ansley, Stephen J %A Lupski, James R %K Databases, Nucleic Acid %K Electronic Data Processing %K Expressed Sequence Tags %K Genome %K Humans %K Retina %K Retinal Diseases %K Transcription, Genetic %X

Grouping genes by virtue of their sequence similarity, functional association, or spatiotemporal distribution is an important first step in investigating function. Given the recent identification of >30,000 human genes either by analyses of genomic sequence or by derivation/assembly of ESTs, automated means of discerning gene function and association with disease are critical for the efficient processing of this large volume of data. We have designed a series of computational tools to manipulate the EST sequence database (dbEST) to predict EST clusters likely representing genes expressed exclusively or preferentially in a specific tissue. We implemented this tool by extracting 40,000 human retinal ESTs and performing in silico subtraction against 1.4 million human ESTs. This process yielded 925 ESTs likely to be specifically or preferentially expressed in the retina. We mapped all retinal-specific/predominant sequences in the human genome and produced a web-based searchable map of the retina transcriptome, onto which we overlaid the positions of all mapped but uncloned retinopathy genes. This resource has provided positional candidates for 42 of 51 uncloned retinopathies and may expedite substantially the identification of disease-associated genes. More importantly, the ability to systematically group ESTs according to their predicted expression profile is likely to be an important resource for studying gene function in a wide range of tissues and physiological systems and to identify positional candidate genes for human disorders whose phenotypic manifestations are restricted to specific tissues/organs/cell types.

%B Proc Natl Acad Sci U S A %V 99 %P 14326-31 %8 2002 Oct 29 %G eng %N 22 %1 https://www.ncbi.nlm.nih.gov/pubmed/12391299?dopt=Abstract %R 10.1073/pnas.222409099 %0 Journal Article %J Nat Genet %D 2001 %T An evaluation of the draft human genome sequence. %A Katsanis, N %A Kim C Worley %A James R Lupski %K Chromosome Mapping %K Chromosomes, Artificial, Bacterial %K Expressed Sequence Tags %K Genome, Human %K Humans %K Polymerase Chain Reaction %X

The completed draft version of the human genome, comprised of multiple short contigs encompassing 85% or more of euchromatin, was announced in June of 2000 (ref. 1). The detailed findings of the sequencing consortium were reported several months later. The draft sequence has provided insight into global characteristics, such as the total number of genes and a more accurate definition of gene families. Also of importance are genome positional details such as local genome architecture, regional gene density and the location of transcribed units that are critical for disease gene identification. We carried out a series of mapping and computational experiments using a nonredundant collection of 925 expressed sequence tags (ESTs) and sections of the public draft genome sequence that were available at different timepoints between April 2000 and April 2001. We found discrepancies in both the reported coverage of the human genome and the accuracy of mapping of genomic clones, suggesting some limitations of the draft genome sequence in providing accurate positional information and detailed characterization of chromosomal subregions.

%B Nat Genet %V 29 %P 88-91 %8 2001 Sep %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/11528399?dopt=Abstract %R 10.1038/ng0901-88 %0 Journal Article %J Hum Mol Genet %D 1997 %T The human COX10 gene is disrupted during homologous recombination between the 24 kb proximal and distal CMT1A-REPs. %A Reiter, L T %A Murakami, T %A Koeuth, T %A Richard A Gibbs %A James R Lupski %K Alkyl and Aryl Transferases %K Base Sequence %K Blotting, Southern %K Centromere %K Charcot-Marie-Tooth Disease %K Chromosomes, Human, Pair 17 %K Electron Transport Complex IV %K Exons %K Humans %K Membrane Proteins %K Molecular Sequence Data %K Nucleic Acid Hybridization %K Restriction Mapping %K Sequence Homology, Nucleic Acid %K Telomere %X

The CMT1A-REPs are two large directly repeating DNA sequences located on chromosome 17p11.2-p12 flanking the region duplicated in patients with Charcot-Marie-Tooth disease type 1A (CMT1A) and deleted in patients with hereditary neuropathy with liability to pressure palsies (HNPP). We have sequenced two cosmids, c74F4 and c15H12, which contain the entire proximal and distal CMT1A-REPs and determined that these repeats are approximately 99% identical across a 24,011 bp region. In addition, both contain an exon of the human heme A:farnesyltransferase gene (COX10). Hybridization studies revealed that COX10 spans the distal CMT1A-REP, while the proximal CMT1A-REP contains an isolated COX10 'pseudo-exon'. There is also a COX10 hybridization signal on chromosome 10 which appears to represent a processed pseudogene. We propose that the distal CMT1A-REP represents the progenitor copy of COX10 exon VI which was duplicated with surrounding intronic sequences during mammalian genome evolution and that the HNPP deletion results in a COX10 null allele.

%B Hum Mol Genet %V 6 %P 1595-603 %8 1997 Sep %G eng %N 9 %1 https://www.ncbi.nlm.nih.gov/pubmed/9285799?dopt=Abstract %R 10.1093/hmg/6.9.1595 %0 Journal Article %J Nat Genet %D 1996 %T A recombination hotspot responsible for two inherited peripheral neuropathies is located near a mariner transposon-like element. %A Reiter, L T %A Murakami, T %A Koeuth, T %A Pentao, L %A Donna M Muzny %A Richard A Gibbs %A James R Lupski %K Amino Acid Sequence %K Base Sequence %K Charcot-Marie-Tooth Disease %K DNA %K DNA Transposable Elements %K Gene Deletion %K Humans %K Molecular Sequence Data %K Multigene Family %K Peripheral Nervous System Diseases %K Recombination, Genetic %K Repetitive Sequences, Nucleic Acid %K Restriction Mapping %K Sequence Homology, Amino Acid %X

The Charcot-Marie Tooth disease type 1A (CMT1A) duplication and hereditary neuropathy with liability to pressure palsies (HNPP) deletion are reciprocal products of an unequal crossing-over event between misaligned flanking CMT1A-REP repeats. The molecular aetiology of this apparently homologous recombination event was examined by sequencing the crossover region. Through the detection of novel junction fragments from the recombinant CMT1A-REPs in both CMT1A and HNPP patients, a 1.7-kb recombination hotspot within the approximately 30-kb CMT1A-REPs was identified. This hotspot is 98% identical between CMT1A-REPs indicating that sequence identity is not likely the sole factor involved in promoting crossover events. Sequence analysis revealed a mariner transposon-like element (MITE) near the hotspot which we hypothesize could mediate strand exchange events via cleavage by a transposase at or near the 3' end of the element.

%B Nat Genet %V 12 %P 288-97 %8 1996 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/8589720?dopt=Abstract %R 10.1038/ng0396-288