%0 Journal Article %J J Cell Mol Med %D 2024 %T Novel, pathogenic insertion variant of GSDME associates with autosomal dominant hearing loss in a large Chinese pedigree. %A Cheng, Jingliang %A Li, Ting %A Tan, Qi %A Fu, Jiewen %A Zhang, Lianmei %A Yang, Luquan %A Zhou, Baixu %A Yang, Lisha %A Fu, Shangyi %A Linehan, Alora Grace %A Fu, Junjiang %K China %K Deafness %K Hearing Loss %K Hearing Loss, Sensorineural %K Humans %K Mutation %K Pedigree %X

Nonsyndromic hearing loss (NSHL) is a genetically diverse, highly heterogeneous condition characterised by deafness, and Gasdermin E (GSDME) variants have been identified as directly inducing autosomal dominant NSHL. While many NSHL cases associated with GSDME involve the skipping of exon 8, there is another, less understood pathogenic insertion variant specifically found in Chinese pedigrees that causes deafness, known as autosomal dominant 5 (DFNA5) hearing loss. In this study, we recruited a large Chinese pedigree, conducted whole-exome and Sanger sequencing to serve as a comprehensive clinical examination, and extracted genomic DNA samples for co-segregation analysis of the members. Conservation and expression analyses for GSDME were also conducted. Our clinical examinations revealed an autosomal dominant phenotype of hearing loss in the family. Genetic analysis identified a novel insertion variant in GSDME exon 8 (GSDME: NM_004403.3: c.1113_1114insGGGGTGCAGCTTACAGGGTGGGTGT: p. P372fs*36). This variant is segregated with the deafness phenotype of this pedigree. The GSDME gene was highly conserved in the different species we analysed, and its mRNA expression was ubiquitously low in different human tissues. In conclusion, we have successfully identified a novel pathogenic insertion variant of GSDME in a Chinese pedigree that causes deafness, shedding light on the genetic basis of hearing loss within this specific family. Our findings expand the spectrum of known variants associated with GSDME-related deafness and may further support both the underlying gain-of-function mechanism and functional associations of GSDME hearing loss variants.

%B J Cell Mol Med %V 28 %P e18004 %8 2024 Jan %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/37864300?dopt=Abstract %R 10.1111/jcmm.18004 %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 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 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 Pediatr Nephrol %D 2023 %T Variants in genes coding for collagen type IV α-chains are frequent causes of persistent, isolated hematuria during childhood. %A Alge, Joseph L %A Bekheirnia, Nasim %A Willcockson, Alexandra R %A Xiang Qin %A Steven E Scherer %A Braun, Michael C %A Bekheirnia, Mir Reza %K Autoantigens %K Child %K Collagen Type IV %K Hematuria %K Humans %K Kidney %K Mutation %K Nephritis, Hereditary %K Pedigree %X

BACKGROUND: Children with persistent, isolated microscopic hematuria typically undergo a limited diagnostic workup and are monitored for signs of kidney disease in long-term longitudinal follow-up, which can delay diagnosis and allow disease progression in some cases.

METHODS: To determine the clinical utility of genetic screening in this population, we performed targeted genetic testing using a custom, 32-gene next-generation sequencing panel for progressive kidney disease on children referred to the Texas Children's Hospital Pediatric Nephrology clinic for persistent, microscopic hematuria (n = 30; cohort 1). Patients with microscopic hematuria identified by urinalysis on at least two separate occasions were eligible for enrollment, but those with other evidence of kidney disease were excluded. Results were analyzed for sequence variants using the American College of Medical Genetics and Genomics (ACMG) guideline for data interpretation and were validated using a secondary analysis of a dataset of children with hematuria and normal kidney function who had undergone genetic testing as part of an industry-sponsored program (cohort 2; n = 67).

RESULTS: In cohort 1 33% of subjects (10/30) had pathogenic or likely pathogenic (P/LP) variants in the type IV collagen genes (COL4A3/A4/A5), and 10% (3/30) had variants of uncertain significance in these genes. The high diagnostic rate in type IV collagen genes was confirmed in cohort 2, where 27% (18/67) of subjects had P/LP variants in COL4A3/A4/A5 genes.

CONCLUSIONS: Children with persistent, isolated microscopic hematuria have a high likelihood of having pathogenic variants in type IV collagen genes and genetic screening should be considered. A higher resolution version of the Graphical abstract is available as Supplementary information.

%B Pediatr Nephrol %V 38 %P 687-695 %8 2023 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/35759000?dopt=Abstract %R 10.1007/s00467-022-05627-w %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 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 Identification of autosomal recessive novel genes and retinal phenotypes in members of the solute carrier (SLC) superfamily. %A Millo, Talya %A Rivera, Antonio %A Obolensky, Alexey %A Marks-Ohana, Devora %A Xu, Mingchu %A Yumei Li %A Wilhelm, Enosh %A Gopalakrishnan, Prakadeeswari %A Gross, Menachem %A Rosin, Boris %A Hanany, Mor %A Webster, Andrew %A Tracewska, Anna Maria %A Koenekoop, Robert K %A Rui Chen %A Arno, Gavin %A Schueler-Furman, Ora %A Roosing, Susanne %A Banin, Eyal %A Sharon, Dror %K DNA Mutational Analysis %K Genes, Recessive %K Genetic Association Studies %K Humans %K Mutation %K Pedigree %K Phenotype %K Retinitis Pigmentosa %X

PURPOSE: This study aimed to investigate the clinical and genetic aspects of solute carrier (SLC) genes in inherited retinal diseases (IRDs).

METHODS: Exome sequencing data were filtered to identify pathogenic variants in SLC genes. Analysis of transcript and protein expression was performed on fibroblast cell lines and retinal sections.

RESULTS: Comprehensive analysis of 433 SLC genes in 913 exome sequencing IRD samples revealed homozygous pathogenic variants in 6 SLC genes, including 2 candidate novel genes, which were 2 variants in SLC66A1, causing autosomal recessive retinitis pigmentosa (ARRP), and a variant in SLC39A12, causing autosomal recessive mild widespread retinal degeneration with marked macular involvement. In addition, we present 4 families with ARRP and homozygous null variants in SLC37A3 that were previously suggested to cause retinitis pigmentosa, 2 of which cause exon skipping. The recently reported SLC4A7- c.2007dup variant was found in 2 patients with ARRP resulting in the absence of protein. Finally, variants in SLC24A1 were found in 4 individuals with either ARRP or congenital stationary night blindness.

CONCLUSION: We report on SLC66A1 and SLC39A12 as candidate novel IRD genes, establish SLC37A3 pathogenicity, and provide further evidence of SLC4A7 as IRD genes. We extend the phenotypic spectrum of SLC24A1 and suggest that its ARRP phenotype may be more common than previously reported.

%B Genet Med %V 24 %P 1523-1535 %8 2022 Jul %G eng %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/35486108?dopt=Abstract %R 10.1016/j.gim.2022.03.020 %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 Ophthalmic Genet %D 2022 %T A novel stop codon mutation of TSPAN12 gene in Chinese patients with familial exudative vitreoretinopathy. %A Zou, Gang %A Qi, Rui %A Ma, Meijiao %A Fu, Shangyi %A Liang, Qingnan %A Bi, Xiaojun %A Wang, Chanjuan %A Hu, Xuejun %A Cai, Yujuan %A Sheng, Xunlun %K China %K Codon, Terminator %K DNA Mutational Analysis %K Eye Diseases, Hereditary %K Familial Exudative Vitreoretinopathies %K Humans %K Mutation %K Pedigree %K Phenotype %K Retinal Diseases %K Retrospective Studies %K Tetraspanins %X

BACKGROUND: Familial exudative vitreoretinopathy (FEVR) is a group of inherited eye diseases characterized by premature arrest of retinal vessel development. The purpose of our study was to characterize the genetic causes and clinical features in eight Chinese families with FEVR using next-generation sequencing (NGS) technology.

MATERIALS AND METHODS: Eight families with FEVR were included in genetic and clinical analyses. We screened the proband and the parents in eight pedigrees with FEVR using targeted NGS approach and in silico analysis to determine the causative mutation for their family's phenotype.

RESULTS: Four cases (4/8, 50.0%) were confirmed to harbor mutations in known genes, including 3 novel mutations and one previously reported mutation. Among the detected mutations, accounted for 75% (3/4). We identified a novel stop codon of , a heterozygous missense mutation NM_012338.4:c.633T>A, NP_036470.1:p.Tyr211Ter involved in highly conserved residues in the proband. Retrospective analysis of its clinical manifestation showed that the mutant carrier presented mild clinical features.

CONCLUSIONS: We found the novel stop codon mutation p.Tyr211Ter in the , which creates a milder phenotype. Discovery of this novel mutation expands the mutation spectrum of , and would be valuable for future genetic disease diagnosis.

%B Ophthalmic Genet %V 43 %P 210-217 %8 2022 Apr %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/34738848?dopt=Abstract %R 10.1080/13816810.2021.1998555 %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 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 Am J Med Genet A %D 2021 %T Clinical characterization of individuals with the distal 1q21.1 microdeletion. %A Edwards, Stacey D %A Schulze, Katharina V %A Rosenfeld, Jill A %A Westerfield, Lauren E %A Gerard, Amanda %A Bo Yuan %A Grigorenko, Elena L %A Posey, Jennifer E %A Bi, Weimin %A Liu, Pengfei %K Abnormalities, Multiple %K Adolescent %K Adult %K Child %K Child, Preschool %K Chromosome Deletion %K Chromosomes, Human, Pair 1 %K Developmental Disabilities %K DNA Copy Number Variations %K Failure to Thrive %K Female %K Genetic Counseling %K Genetic Testing %K Heart Defects, Congenital %K Humans %K Infant %K Intellectual Disability %K Male %K Megalencephaly %K Microcephaly %K Pedigree %K Seizures %K Young Adult %X

Distal 1q21.1 microdeletions have shown highly variable clinical expressivity and incomplete penetrance, with affected individuals manifesting a broad spectrum of nonspecific features. The goals of this study were to better describe the phenotypic spectrum of patients with distal 1q21.1 microdeletions and to compare the clinical features among affected individuals. We performed a retrospective chart review of 47 individuals with distal 1q21.1 microdeletions tested at a large clinical genetic testing laboratory, with most patients being clinically evaluated in the same children's hospital. Health information such as growth charts, results of imaging studies, developmental history, and progress notes were collected. Statistical analysis was performed using Fisher's exact test to compare clinical features among study subjects. Common features in our cohort include microcephaly (51.2%), seizures (29.8%), developmental delay (74.5%), failure to thrive (FTT) (68.1%), dysmorphic features (63.8%), and a variety of congenital anomalies such as cardiac abnormalities (23.4%) and genitourinary abnormalities (19.1%). Compared to prior literature, we found that seizures, brain anomalies, and FTT were more prevalent among our study cohort. Females were more likely than males to have microcephaly (p = 0.0199) and cardiac abnormalities (p = 0.0018). Based on existing genome-wide clinical testing results, at least a quarter of the cohort had additional genetic findings that may impact the phenotype of the individual. Our study represents the largest cohort of distal 1q21.1 microdeletion carriers available in the literature thus far, and it further illustrates the wide spectrum of clinical manifestations among symptomatic individuals. These results may allow for improved genetic counseling and management of affected individuals. Future studies may help to elucidate the underlying molecular mechanisms impacting the phenotypic variability observed with this microdeletion.

%B Am J Med Genet A %V 185 %P 1388-1398 %8 2021 05 %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/33576134?dopt=Abstract %R 10.1002/ajmg.a.62104 %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 Mol Genet Genomic Med %D 2021 %T Contribution of uniparental disomy in a clinical trio exome cohort of 2675 patients. %A Wang, Lei %A Liu, Pengfei %A Bi, Weimin %A Sim, Teresa %A Wang, Xia %A Walkiewicz, Magdalene %A Leduc, Magalie Sophie %A Meng, Linyan %A Xia, Fan %A Christine M Eng %A Yang, Yaping %A Bo Yuan %A Dai, Hongzheng %K Chromosome Disorders %K Humans %K Pedigree %K Uniparental Disomy %K Whole Exome Sequencing %X

BACKGROUND: Uniparental disomy (UPD) is the inheritance of two homologous chromosomes from the same parent. UPD may result in clinical phenotypes when occurring on chromosomes with specific imprinting pattern, when leading to homozygosity of a deleterious recessive allele inherited from one carrier parent, or when associated with a mosaic aneuploidy. Due to the importance of UPD in genetic disease etiology, UPD analysis has started to be implemented in the context of exome sequencing (ES) or genome sequencing.

METHODS: We developed an in-house algorithm TRIPS (Trio Parentage/UPD Studies) to identify UPD events in trio ES cases. This method identifies regions with uniparental inheritance by utilizing the trio genotyping data obtained from the concurrent SNP array to delineate the parental origin of the SNPs in the proband.

RESULTS: We identified 16 UPD events from 2675 ES trios. Among those, four events led to imprinting disorders, seven unmasked a pathogenic/likely pathogenic variant in a recessive disease gene, and two were consistent with a mosaic genome wide paternal UPD pattern. Twelve of these UPD events directly contributed to the molecular diagnosis of the patients.

CONCLUSION: Our study demonstrated the contribution of UPD to the molecular diagnosis in one clinical ES cohort, thus UPD analysis should be incorporated into routine clinical ES interpretation.

%B Mol Genet Genomic Med %V 9 %P e1792 %8 2021 11 %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/34587367?dopt=Abstract %R 10.1002/mgg3.1792 %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 Pediatr Diabetes %D 2021 %T Exome sequencing in children with clinically suspected maturity-onset diabetes of the young. %A Tosur, Mustafa %A Soler-Alfonso, Claudia %A Chan, Katie M %A Khayat, Michael M %A Jhangiani, Shalini N %A Meng, Qingchang %A Refaey, Ahmad %A Donna M Muzny %A Richard A Gibbs %A David R Murdock %A Posey, Jennifer E %A Balasubramanyam, Ashok %A Redondo, Maria J %A Aniko Sabo %K Adolescent %K Autoantibodies %K Child %K Diabetes Mellitus, Type 1 %K Diabetes Mellitus, Type 2 %K Diagnosis, Differential %K Exome Sequencing %K Female %K Frameshift Mutation %K Genetic Variation %K Humans %K Islets of Langerhans %K Male %K Mutation, Missense %K Pedigree %X

OBJECTIVE: Commercial gene panels identify pathogenic variants in as low as 27% of patients suspected to have MODY, suggesting the role of yet unidentified pathogenic variants. We sought to identify novel gene variants associated with MODY.

RESEARCH DESIGN AND METHODS: We recruited 10 children with a clinical suspicion of MODY but non-diagnostic commercial MODY gene panels. We performed exome sequencing (ES) in them and their parents.

RESULTS: Mean age at diabetes diagnosis was 10 (± 3.8) years. Six were females; 4 were non-Hispanic white, 5 Hispanic, and 1 Asian. Our variant prioritization analysis identified a pathogenic, de novo variant in INS (c.94G > A, p.Gly32Ser), confirmed by Sanger sequencing, in a proband who was previously diagnosed with "autoantibody-negative type 1 diabetes (T1D)" at 3 y/o. This rare variant, absent in the general population (gnomAD database), has been reported previously in neonatal diabetes. We also identified a frameshift deletion (c.2650delC, p.Gln884AsnfsTer57) in RFX6 in a child with a previous diagnosis of "autoantibody-negative T1D" at 12 y/o. The variant was inherited from the mother, who was diagnosed with "thin type 2 diabetes" at 25 y/o. Heterozygous protein-truncating variants in RFX6 gene have been recently reported in individuals with MODY.

CONCLUSIONS: We diagnosed two patients with MODY using ES in children initially classified as "T1D". One has a likely pathogenic novel gene variant not previously associated with MODY. We demonstrate the clinical utility of ES in patients with clinical suspicion of MODY.

%B Pediatr Diabetes %V 22 %P 960-968 %8 2021 Nov %G eng %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/34387403?dopt=Abstract %R 10.1111/pedi.13257 %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 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 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 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 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 Mol Ecol Resour %D 2021 %T Pedigree reconstruction and distant pairwise relatedness estimation from genome sequence data: A demonstration in a population of rhesus macaques (Macaca mulatta). %A Petty, Lauren E %A Phillippi-Falkenstein, Kathrine %A Kubisch, H Michael %A Raveendran, Muthuswamy %A R. Alan Harris %A Vallender, Eric J %A Huff, Chad D %A Bohm, Rudolf P %A Jeffrey Rogers %A Below, Jennifer E %K Animals %K Breeding %K Chromosome Mapping %K Genetics, Population %K Genome %K Genotype %K Macaca mulatta %K Male %K Pedigree %K Polymorphism, Single Nucleotide %X

A primary challenge in the analysis of free-ranging animal populations is the accurate estimation of relatedness among individuals. Many aspects of population analysis rely on knowledge of relatedness patterns, including socioecology, demography, heritability and gene mapping analyses, wildlife conservation and the management of breeding colonies. Methods for determining relatedness using genome-wide data have improved our ability to determine kinship and reconstruct pedigrees in humans. However, methods for reconstructing complex pedigree structures and estimating distant relatedness (beyond third-degree) have not been widely applied to other species. We sequenced the genomes of 150 male rhesus macaques from the Tulane National Primate Research Center colony to estimate pairwise relatedness, reconstruct closely related pedigrees, estimate more distant relationships and augment colony records. Methods for determining relatedness developed for human genetic data were applied and evaluated in the analysis of nonhuman primates, including identity-by-descent-based methods for pedigree reconstruction and shared segment-based inference of more distant relatedness. We compared the genotype-based pedigrees and estimated relationships to available colony pedigree records and found high concordance (95.5% agreement) between expected and identified relationships for close relatives. In addition, we detected distant relationships not captured in colony records, including some as distant as twelfth-degree. Furthermore, while deep sequence coverage is preferable, we show that this approach can also provide valuable information when only low-coverage (5×) sequence data is available. Our findings demonstrate the value of these methods for determination of relatedness in various animal populations, with diverse applications to conservation biology, evolutionary and ecological research and biomedical studies.

%B Mol Ecol Resour %V 21 %P 1333-1346 %8 2021 May %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/33386679?dopt=Abstract %R 10.1111/1755-0998.13317 %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 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 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 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 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 Genome sequencing analysis of a family with a child displaying severe abdominal distention and recurrent hypoglycemia. %A Liu, Jidong %A Ding, Guolian %A Zou, Kexin %A Jiang, Ziru %A Zhang, Junyu %A Lu, Yunhua %A Pignata, Antonella %A Eric Venner %A Liu, Pengfei %A Liu, Zhandong %A Wangler, Michael F %A Sun, Zheng %K Abdominal Neoplasms %K Child, Preschool %K Humans %K Hypoglycemia %K Loss of Function Mutation %K Male %K Neoplasms, Adipose Tissue %K Pedigree %K Phenotype %K PTEN Phosphohydrolase %K Seizures %K Syndrome %X

BACKGROUND: Germline mutations in PTEN are associated with the PTEN hamartoma tumor syndrome (PHTS), an umbrella term used to describe a spectrum of autosomal-dominant disorders characterized by variable phenotypic manifestations associated with cell or tissue overgrowth. We report a boy who developed severe progressive abdominal distention due to a dramatic adipose mass from the age of 7 months and developed recurrent hypoinsulinemic hypoglycemia that led to seizures at the age of 4 years.

METHODS: Trio-based whole-genome sequencing was performed by using blood DNA from the child and his parents. The possible pathogenic variants were verified by Sanger sequencing. Functional characterization of the identified variant was completed by western blot.

RESULTS: The child inherited a single-nucleotide deletion NM_000314.6:c.849delA (p.Glu284Argfs) in the tumor suppressor gene PTEN from his father. The paternal family members have a history of cancer. It is conceivable that PTEN loss-of-function induced the adipose tumor growth and hypoglycemia, although the proband did not meet the usual diagnosis criteria of Cowden syndrome or Bannayan-Riley-Ruvalcaba syndrome that are characterized by germline mutations of PTEN.

CONCLUSION: This case underlines the variability of phenotypes associated with PTEN germline mutations and provides useful information for diagnosis and genetic counseling of PTEN-related diseases for pediatric patients.

%B Mol Genet Genomic Med %V 8 %P e1130 %8 2020 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/31971667?dopt=Abstract %R 10.1002/mgg3.1130 %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 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 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 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 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 Am J Med Genet A %D 2019 %T Delineating the expanding phenotype associated with SCAPER gene mutation. %A Fasham, James %A Arno, Gavin %A Lin, Siying %A Xu, Mingchu %A Carss, Keren J %A Hull, Sarah %A Lane, Amelia %A Robson, Anthony G %A Wenger, Olivia %A Self, Jay E %A Harlalka, Gaurav V %A Salter, Claire G %A Schema, Lynn %A Moss, Timothy J %A Cheetham, Michael E %A Moore, Anthony T %A Raymond, F Lucy %A Rui Chen %A Baple, Emma L %A Webster, Andrew R %A Crosby, Andrew H %K Adolescent %K Adult %K Carrier Proteins %K Child %K Consanguinity %K DNA Mutational Analysis %K Female %K Genetic Association Studies %K Genetic Predisposition to Disease %K Humans %K Male %K Middle Aged %K Mutation %K Pedigree %K Phenotype %K Young Adult %B Am J Med Genet A %V 179 %P 1665-1671 %8 2019 Aug %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/31192531?dopt=Abstract %R 10.1002/ajmg.a.61202 %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 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 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 J Clin Res Pediatr Endocrinol %D 2019 %T A Patient with Berardinelli-Seip Syndrome, Novel Splicesite Mutation and Concomitant Development of Non-diabetic Polyneuropathy. %A Oswiecimska, Joanna %A Dawidziuk, Mateusz %A Gambin, Tomasz %A Ziora, Katarzyna %A Marek, Marta %A Rzonca, Sylwia %A Guilbride, D. Lys %A Jhangiani, Shalini N. %A Obuchowicz, Anna %A Sikora, Alicja %A Lupski, James R. %A Wiszniewski, Wojciech %A Gawlinski, Pawel %K Acyltransferases %K Adult %K Female %K Humans %K Infant %K Lipodystrophy, Congenital Generalized %K Male %K Mutation %K Pedigree %K Polyneuropathies %K Prognosis %K RNA Splice Sites %X

Primary polyneuropathy in the context of Seip-Berardinelli type 1 seipinopathy, or congenital generalized lipodystrophy type 1 (CGL1) has not been previously reported. We report the case history of a 27 year old female CGL1 patient presenting with an unusual additional development of non-diabetic peripheral neuropathy and learning disabilities in early adolescence. Whole exome sequencing (WES) of the patient genome identified a novel variant, homozygous for a 52 bp intronic deletion in the locus, coding for 1-acylglycerol-3-phosphate O-acyltransferase 2, which is uniquely associated with CGL1 seipinopathies, with no molecular evidence for dual diagnosis. Functional studies using RNA isolated from patient peripheral blood leucocytes showed abnormal RNA splicing resulting in the loss of 25 amino acids from the patient AGPAT2 protein coding sequence. Stability and transcription levels for the misspliced mRNA in our patient nonetheless remained normal. Any AGPAT2 protein produced in our patient is therefore likely to be dysfunctional. However, formal linkage of this deletion to the neuropathy observed remains to be shown. The classical clinical presentation of a patient with -associated lipodystrophy shows normal cognition and no development of polyneuropathy. Cognitive disabilities and polyneuropathy are features associated exclusively with clinical CGL type 2 arising from seipin gene mutations. This case study suggests that in some genetic contexts, mutations can also produce phenotypes with primary polyneuropathy.

%B J Clin Res Pediatr Endocrinol %V 11 %P 319-326 %8 2019 Sep 03 %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/30563316?dopt=Abstract %R 10.4274/jcrpe.galenos.2018.2018.0227 %0 Journal Article %J Retina %D 2019 %T PHENOTYPIC VARIABILITY OF RECESSIVE RDH12-ASSOCIATED RETINAL DYSTROPHY. %A Zou, Xuan %A Fu, Qing %A Fang, Sha %A Li, Hui %A Ge, Zhongqi %A Yang, Lizhu %A Xu, Mingchu %A Sun, Zixi %A Li, Huajin %A Yumei Li %A Dong, Fangtian %A Rui Chen %A Sui, Ruifang %K Adolescent %K Adult %K Alcohol Oxidoreductases %K Biological Variation, Population %K Child %K Child, Preschool %K DNA Mutational Analysis %K Electroretinography %K Eye Diseases, Hereditary %K Female %K Genotype %K Humans %K Male %K Middle Aged %K Mutation %K Pedigree %K Phenotype %K Retinal Dystrophies %K Visual Acuity %K Young Adult %X

PURPOSE: To characterize the phenotypic variability and report the genetic defects in a cohort of Chinese patients with biallelic variants of the retinol dehydrogenase 12 (RDH12) gene.

METHODS: The study included 38 patients from 38 unrelated families with biallelic pathogenic RDH12 variants. Systematic next-generation sequencing data analysis, Sanger sequencing validation, and segregation analysis were used to identify the pathogenic mutations. Detailed ophthalmic examinations, including electroretinogram, fundus photography, fundus autofluorescence and optical coherence tomography, and statistical analysis were performed to evaluate phenotype variability.

RESULTS: Twenty-five different mutations of RDH12 were identified in the 38 families. Six of these variants were novel. Val146Asp was observed at the highest frequency (23.7%), and it was followed by Arg62Ter (14.5%) and Thr49Met (9.2%). Twenty-three probands were diagnosed with early-onset severe retinal dystrophy, 6 with Leber congenital amaurosis, 7 with autosomal recessive retinitis pigmentosa, and 2 with cone-rod dystrophy. Self-reported nyctalopia occurred in about a half of patients (55.3%) and was significantly more common among older patients (P < 0.01). Nyctalopia was not significantly associated with best-corrected visual acuity (P = 0.72), but older patients had significantly greater best-corrected visual acuity loss (P < 0.01). Only 15.8% of the patients had nystagmus, which was significantly more likely to occur among 36.8% of the patients with hyperopia >3D (P < 0.01) and/or in cases of reduced best-corrected visual acuity (P = 0.01), but was not associated with age (P = 0.87).

CONCLUSION: Several high-frequency RDH12 variants were identified in patients with inherited retinal dystrophies, most of which were missense mutations. Variable but characteristic phenotypes of a progressive nature was observed. Overall, the findings indicated that biallelic RDH12 mutations are a common cause of early-onset retinal dystrophy and a rare cause of cone-rod dystrophy.

%B Retina %V 39 %P 2040-2052 %8 2019 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/30134391?dopt=Abstract %R 10.1097/IAE.0000000000002242 %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 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 Am J Med Genet A %D 2018 %T A heterozygous mutation in RPGR associated with X-linked retinitis pigmentosa in a patient with Turner syndrome mosaicism (45,X/46,XX). %A Zhou, Qi %A Yao, Fengxia %A Wang, Feng %A Li, Hui %A Rui Chen %A Sui, Ruifang %K Adult %K Eye Proteins %K Female %K Frameshift Mutation %K Genes, X-Linked %K Genomics %K Heterozygote %K Humans %K In Situ Hybridization, Fluorescence %K Male %K Mutation %K Pedigree %K Phenotype %K Retinitis Pigmentosa %K Sequence Analysis, DNA %K Turner Syndrome %X

Turner syndrome with retinitis pigmentosa (RP) is rare, with only three cases reported based on clinical examination alone. We summarized the 4-year follow-up and molecular findings in a 28-year-old patient with Turner syndrome and the typical features of short stature and neck webbing, who also had X-linked RP. Her main complaints were night blindness and progressive loss of vision since the age of 9 years. Ophthalmologic examination, optical coherent tomographic imaging, and visual electrophysiology tests showed classic manifestations of RP. The karyotype of peripheral blood showed mosaicism (45,X [72%]/46,XX[28%]). A novel heterozygous frameshift mutation (c.2403_2406delAGAG, p.T801fsX812) in the RP GTPase regulator (RPGR) gene was detected using next generation sequencing and validated by Sanger sequencing. We believe that this is the first report of X-linked RP in a patient with Turner syndrome associated with mosaicism, and an RPGR heterozygous mutation. We hypothesize that X-linked RP in this woman is not related to Turner syndrome, but may be a manifestation of the lack of a normal paternal X chromosome with intact but mutated RPGR.

%B Am J Med Genet A %V 176 %P 214-218 %8 2018 Jan %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/29135076?dopt=Abstract %R 10.1002/ajmg.a.38501 %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 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 One %D 2018 %T Novel genetic associations for blood pressure identified via gene-alcohol interaction in up to 570K individuals across multiple ancestries. %A Feitosa, Mary F %A Kraja, Aldi T %A Chasman, Daniel I %A Sung, Yun J %A Winkler, Thomas W %A Ntalla, Ioanna %A Guo, Xiuqing %A Franceschini, Nora %A Cheng, Ching-Yu %A Sim, Xueling %A Vojinovic, Dina %A Marten, Jonathan %A Musani, Solomon K %A Li, Changwei %A Bentley, Amy R %A Brown, Michael R %A Schwander, Karen %A Richard, Melissa A %A Noordam, Raymond %A Aschard, Hugues %A Bartz, Traci M %A Bielak, Lawrence F %A Dorajoo, Rajkumar %A Fisher, Virginia %A Hartwig, Fernando P %A Horimoto, Andrea R V R %A Lohman, Kurt K %A Manning, Alisa K %A Rankinen, Tuomo %A Smith, Albert V %A Tajuddin, Salman M %A Wojczynski, Mary K %A Alver, Maris %A Boissel, Mathilde %A Cai, Qiuyin %A Campbell, Archie %A Chai, Jin Fang %A Chen, Xu %A Divers, Jasmin %A Gao, Chuan %A Goel, Anuj %A Hagemeijer, Yanick %A Harris, Sarah E %A He, Meian %A Hsu, Fang-Chi %A Jackson, Anne U %A Kähönen, Mika %A Kasturiratne, Anuradhani %A Komulainen, Pirjo %A Kühnel, Brigitte %A Laguzzi, Federica %A Luan, Jian'an %A Matoba, Nana %A Nolte, Ilja M %A Padmanabhan, Sandosh %A Riaz, Muhammad %A Rueedi, Rico %A Robino, Antonietta %A Said, M Abdullah %A Scott, Robert A %A Sofer, Tamar %A Stančáková, Alena %A Takeuchi, Fumihiko %A Tayo, Bamidele O %A van der Most, Peter J %A Varga, Tibor V %A Vitart, Veronique %A Wang, Yajuan %A Ware, Erin B %A Warren, Helen R %A Weiss, Stefan %A Wen, Wanqing %A Yanek, Lisa R %A Zhang, Weihua %A Zhao, Jing Hua %A Afaq, Saima %A Amin, Najaf %A Amini, Marzyeh %A Arking, Dan E %A Aung, Tin %A Boerwinkle, Eric %A Borecki, Ingrid %A Broeckel, Ulrich %A Brown, Morris %A Brumat, Marco %A Burke, Gregory L %A Canouil, Mickaël %A Chakravarti, Aravinda %A Charumathi, Sabanayagam %A Ida Chen, Yii-Der %A Connell, John M %A Correa, Adolfo %A de Las Fuentes, Lisa %A de Mutsert, Renée %A de Silva, H Janaka %A Deng, Xuan %A Ding, Jingzhong %A Duan, Qing %A Eaton, Charles B %A Ehret, Georg %A Eppinga, Ruben N %A Evangelou, Evangelos %A Faul, Jessica D %A Felix, Stephan B %A Forouhi, Nita G %A Forrester, Terrence %A Franco, Oscar H %A Friedlander, Yechiel %A Gandin, Ilaria %A Gao, He %A Ghanbari, Mohsen %A Gigante, Bruna %A Gu, C Charles %A Gu, Dongfeng %A Hagenaars, Saskia P %A Hallmans, Goran %A Harris, Tamara B %A He, Jiang %A Heikkinen, Sami %A Heng, Chew-Kiat %A Hirata, Makoto %A Howard, Barbara V %A Ikram, M Arfan %A John, Ulrich %A Katsuya, Tomohiro %A Khor, Chiea Chuen %A Kilpeläinen, Tuomas O %A Koh, Woon-Puay %A Krieger, Jose E %A Kritchevsky, Stephen B %A Kubo, Michiaki %A Kuusisto, Johanna %A Lakka, Timo A %A Langefeld, Carl D %A Langenberg, Claudia %A Launer, Lenore J %A Lehne, Benjamin %A Lewis, Cora E %A Li, Yize %A Lin, Shiow %A Liu, Jianjun %A Liu, Jingmin %A Loh, Marie %A Louie, Tin %A Mägi, Reedik %A McKenzie, Colin A %A Meitinger, Thomas %A Metspalu, Andres %A Milaneschi, Yuri %A Milani, Lili %A Mohlke, Karen L %A Momozawa, Yukihide %A Nalls, Mike A %A Nelson, Christopher P %A Sotoodehnia, Nona %A Norris, Jill M %A O'Connell, Jeff R %A Palmer, Nicholette D %A Perls, Thomas %A Pedersen, Nancy L %A Peters, Annette %A Peyser, Patricia A %A Poulter, Neil %A Raffel, Leslie J %A Raitakari, Olli T %A Roll, Kathryn %A Rose, Lynda M %A Rosendaal, Frits R %A Rotter, Jerome I %A Schmidt, Carsten O %A Schreiner, Pamela J %A Schupf, Nicole %A Scott, William R %A Sever, Peter S %A Shi, Yuan %A Sidney, Stephen %A Sims, Mario %A Sitlani, Colleen M %A Smith, Jennifer A %A Snieder, Harold %A Starr, John M %A Strauch, Konstantin %A Stringham, Heather M %A Tan, Nicholas Y Q %A Tang, Hua %A Taylor, Kent D %A Teo, Yik Ying %A Tham, Yih Chung %A Turner, Stephen T %A Uitterlinden, André G %A Vollenweider, Peter %A Waldenberger, Melanie %A Wang, Lihua %A Wang, Ya Xing %A Wei, Wen Bin %A Williams, Christine %A Yao, Jie %A Yu, Caizheng %A Yuan, Jian-Min %A Zhao, Wei %A Zonderman, Alan B %A Becker, Diane M %A Boehnke, Michael %A Bowden, Donald W %A Chambers, John C %A Deary, Ian J %A Esko, Tõnu %A Farrall, Martin %A Franks, Paul W %A Freedman, Barry I %A Froguel, Philippe %A Gasparini, Paolo %A Gieger, Christian %A Jonas, Jost Bruno %A Kamatani, Yoichiro %A Kato, Norihiro %A Kooner, Jaspal S %A Kutalik, Zoltán %A Laakso, Markku %A Laurie, Cathy C %A Leander, Karin %A Lehtimäki, Terho %A Study, Lifelines Cohort %A Magnusson, Patrik K E %A Oldehinkel, Albertine J %A Penninx, Brenda W J H %A Polasek, Ozren %A Porteous, David J %A Rauramaa, Rainer %A Samani, Nilesh J %A Scott, James %A Shu, Xiao-Ou %A van der Harst, Pim %A Wagenknecht, Lynne E %A Wareham, Nicholas J %A Watkins, Hugh %A Weir, David R %A Wickremasinghe, Ananda R %A Wu, Tangchun %A Zheng, Wei %A Bouchard, Claude %A Christensen, Kaare %A Evans, Michele K %A Gudnason, Vilmundur %A Horta, Bernardo L %A Kardia, Sharon L R %A Liu, Yongmei %A Pereira, Alexandre C %A Psaty, Bruce M %A Ridker, Paul M %A van Dam, Rob M %A Gauderman, W James %A Zhu, Xiaofeng %A Mook-Kanamori, Dennis O %A Fornage, Myriam %A Rotimi, Charles N %A Cupples, L Adrienne %A Kelly, Tanika N %A Fox, Ervin R %A Hayward, Caroline %A van Duijn, Cornelia M %A Tai, E Shyong %A Wong, Tien Yin %A Kooperberg, Charles %A Palmas, Walter %A Rice, Kenneth %A Morrison, Alanna C %A Elliott, Paul %A Caulfield, Mark J %A Munroe, Patricia B %A Rao, Dabeeru C %A Province, Michael A %A Levy, Daniel %K Adolescent %K Adult %K Aged %K Aged, 80 and over %K Alcohol Drinking %K Blood Pressure %K Cohort Studies %K Female %K Gene-Environment Interaction %K Genetic Predisposition to Disease %K Genome-Wide Association Study %K Humans %K Hypertension %K Male %K Middle Aged %K Pedigree %K Polymorphism, Single Nucleotide %K Racial Groups %K Young Adult %X

Heavy alcohol consumption is an established risk factor for hypertension; the mechanism by which alcohol consumption impact blood pressure (BP) regulation remains unknown. We hypothesized that a genome-wide association study accounting for gene-alcohol consumption interaction for BP might identify additional BP loci and contribute to the understanding of alcohol-related BP regulation. We conducted a large two-stage investigation incorporating joint testing of main genetic effects and single nucleotide variant (SNV)-alcohol consumption interactions. In Stage 1, genome-wide discovery meta-analyses in ≈131K individuals across several ancestry groups yielded 3,514 SNVs (245 loci) with suggestive evidence of association (P < 1.0 x 10-5). In Stage 2, these SNVs were tested for independent external replication in ≈440K individuals across multiple ancestries. We identified and replicated (at Bonferroni correction threshold) five novel BP loci (380 SNVs in 21 genes) and 49 previously reported BP loci (2,159 SNVs in 109 genes) in European ancestry, and in multi-ancestry meta-analyses (P < 5.0 x 10-8). For African ancestry samples, we detected 18 potentially novel BP loci (P < 5.0 x 10-8) in Stage 1 that warrant further replication. Additionally, correlated meta-analysis identified eight novel BP loci (11 genes). Several genes in these loci (e.g., PINX1, GATA4, BLK, FTO and GABBR2) have been previously reported to be associated with alcohol consumption. These findings provide insights into the role of alcohol consumption in the genetic architecture of hypertension.

%B PLoS One %V 13 %P e0198166 %8 2018 %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/29912962?dopt=Abstract %R 10.1371/journal.pone.0198166 %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 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 Curr Biol %D 2018 %T Reproductive Longevity Predicts Mutation Rates in Primates. %A Thomas, Gregg W C %A Wang, Richard J %A Puri, Arthi %A R. Alan Harris %A Raveendran, Muthuswamy %A Hughes, Daniel S T %A Murali, Shwetha C %A Williams, Lawrence E %A Harshavardhan Doddapaneni %A Donna M Muzny %A Richard A Gibbs %A Abee, Christian R %A Galinski, Mary R %A Kim C Worley %A Jeffrey Rogers %A Radivojac, Predrag %A Hahn, Matthew W %K Animals %K Aotidae %K Genetic Fitness %K Genetics, Population %K Genome %K Humans %K Longevity %K Mutation %K Mutation Rate %K Pedigree %K Population Density %K Primates %K Reproduction %X

Mutation rates vary between species across several orders of magnitude, with larger organisms having the highest per-generation mutation rates. Hypotheses for this pattern typically invoke physiological or population-genetic constraints imposed on the molecular machinery preventing mutations [1]. However, continuing germline cell division in multicellular eukaryotes means that organisms with longer generation times and of larger size will leave more mutations to their offspring simply as a byproduct of their increased lifespan [2, 3]. Here, we deeply sequence the genomes of 30 owl monkeys (Aotus nancymaae) from six multi-generation pedigrees to demonstrate that paternal age is the major factor determining the number of de novo mutations in this species. We find that owl monkeys have an average mutation rate of 0.81 × 10 per site per generation, roughly 32% lower than the estimate in humans. Based on a simple model of reproductive longevity that does not require any changes to the mutational machinery, we show that this is the expected mutation rate in owl monkeys. We further demonstrate that our model predicts species-specific mutation rates in other primates, including study-specific mutation rates in humans based on the average paternal age. Our results suggest that variation in life history traits alone can explain variation in the per-generation mutation rate among primates, and perhaps among a wide range of multicellular organisms.

%B Curr Biol %V 28 %P 3193-3197.e5 %8 2018 Oct 08 %G eng %N 19 %1 https://www.ncbi.nlm.nih.gov/pubmed/30270182?dopt=Abstract %R 10.1016/j.cub.2018.08.050 %0 Journal Article %J Blood %D 2018 %T Syndromic congenital myelofibrosis associated with a loss-of-function variant in . %A Magoulas, Pilar L %A Shchelochkov, Oleg A %A Bainbridge, Matthew N %A Ben-Shachar, Shay %A Yatsenko, Svetlana %A Potocki, Lorraine %A Lewis, Richard A %A Searby, Charles %A Marcogliese, Andrea N %A Elghetany, M Tarek %A Zapata, Gladys %A Hernández, Paula P %A Gadkari, Manasi %A Einhaus, Derek %A Muzny, Donna M %A Gibbs, Richard A %A Bertuch, Alison A %A Scott, Daryl A %A Corvera, Silvia %A Franco, Luis M %K Abnormalities, Multiple %K Bone Marrow Transplantation %K Child %K Consanguinity %K Fatal Outcome %K Female %K Gonadal Dysgenesis, 46,XY %K Hematopoietic Stem Cell Transplantation %K Humans %K Infant %K Intellectual Disability %K Male %K Pedigree %K Phenotype %K Primary Myelofibrosis %K Syndrome %K Vesicular Transport Proteins %X

There is a Commentary on this article in this issue.

%B Blood %V 132 %P 658-662 %8 2018 Aug 09 %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/29784638?dopt=Abstract %R 10.1182/blood-2017-12-824433 %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 J Dent Res %D 2018 %T Whole-Exome Sequencing Identifies Novel Variants for Tooth Agenesis. %A Dinckan, N %A Du, R %A Petty, L E %A Coban-Akdemir, Z %A Jhangiani, S N %A Paine, I %A Baugh, E H %A Erdem, A P %A Kayserili, H %A Doddapaneni, H %A Hu, J %A Muzny, D M %A Boerwinkle, E %A Gibbs, R A %A Lupski, J R %A Uyguner, Z O %A Below, J E %A Letra, A %K Anodontia %K Exome Sequencing %K Female %K Genetic Linkage %K Genetic Variation %K Humans %K Intercellular Signaling Peptides and Proteins %K Laminin %K Low Density Lipoprotein Receptor-Related Protein-6 %K Male %K Membrane Proteins %K Mutation, Missense %K Pedigree %K Real-Time Polymerase Chain Reaction %K Turkey %K Wnt Proteins %X

Tooth agenesis is a common craniofacial abnormality in humans and represents failure to develop 1 or more permanent teeth. Tooth agenesis is complex, and variations in about a dozen genes have been reported as contributing to the etiology. Here, we combined whole-exome sequencing, array-based genotyping, and linkage analysis to identify putative pathogenic variants in candidate disease genes for tooth agenesis in 10 multiplex Turkish families. Novel homozygous and heterozygous variants in LRP6, DKK1, LAMA3, and COL17A1 genes, as well as known variants in WNT10A, were identified as likely pathogenic in isolated tooth agenesis. Novel variants in KREMEN1 were identified as likely pathogenic in 2 families with suspected syndromic tooth agenesis. Variants in more than 1 gene were identified segregating with tooth agenesis in 2 families, suggesting oligogenic inheritance. Structural modeling of missense variants suggests deleterious effects to the encoded proteins. Functional analysis of an indel variant (c.3607+3_6del) in LRP6 suggested that the predicted resulting mRNA is subject to nonsense-mediated decay. Our results support a major role for WNT pathways genes in the etiology of tooth agenesis while revealing new candidate genes. Moreover, oligogenic cosegregation was suggestive for complex inheritance and potentially complex gene product interactions during development, contributing to improved understanding of the genetic etiology of familial tooth agenesis.

%B J Dent Res %V 97 %P 49-59 %8 2018 Jan %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/28813618?dopt=Abstract %R 10.1177/0022034517724149 %0 Journal Article %J Hum Mol Genet %D 2018 %T Whole-exome sequencing revealed HKDC1 as a candidate gene associated with autosomal-recessive retinitis pigmentosa. %A Zhang, Lin %A Sun, Zixi %A Zhao, Peiquan %A Huang, Lulin %A Xu, Mingchu %A Yang, Yeming %A Chen, Xue %A Lu, Fang %A Zhang, Xiang %A Wang, Hui %A Zhang, Shanshan %A Liu, Wenjing %A Jiang, Zhilin %A Ma, Shi %A Rui Chen %A Zhao, Chen %A Yang, Zhenglin %A Sui, Ruifang %A Zhu, Xianjun %K Animals %K Disease Models, Animal %K Exome %K Exome Sequencing %K Female %K Genetic Association Studies %K Hexokinase %K Homozygote %K Humans %K Male %K Mice, Knockout %K Mutation %K Pedigree %K Retina %K Retinal Degeneration %K Retinitis Pigmentosa %X

Retinitis pigmentosa (RP) is an inheritable retina degenerative disease leading to blindness. Despite the identification of 70 genes associated with RP, the genetic cause of ∼40% of RP patients remains to be elucidated. Whole-exome sequencing was applied on the probands of a RP cohort of 68 unsolved cases to identify candidate genetic mutations. A homozygous missense variant (c.173C > T, p.T58 M) was found in HKDC1 in two unrelated families presenting late-onset retinal degeneration. This variant affects highly conserved amino acid residue and is very rare in several databases and absent in 4000 ethnic-matched controls. Mutant HKDC1 protein partially lost hexokinase activity. Hkdc1 is expressed in the mouse retina and localized to photoreceptor inner segments. To elucidate the in vivo roles of Hkdc1 in the retina, we generated Hkdc1 knockout (KO) mouse models using CRISPR/Cas9 technique. Two independent alleles were identified and backcrossed to C57BL/6 J for 6 generations. Absence of HKDC1 expression in the Hkdc1 KO retina was confirmed by western blot and immunostaning using HKDC1 antibody. Hkdc1 KO mice exhibited reduced scotopic electroretinogram response and thinner outer nuclear layer, similar to some of the human patient phenotypes. Loss of Hkdc1 led to mislocalization of rhodopsin to the inner segments and cell bodies of rods in some regions in the retina. Taken together, our data demonstrated that HKDC1 is associated with autosomal recessively inherited RP.

%B Hum Mol Genet %V 27 %P 4157-4168 %8 2018 Dec 01 %G eng %N 23 %1 https://www.ncbi.nlm.nih.gov/pubmed/30085091?dopt=Abstract %R 10.1093/hmg/ddy281 %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 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 Clin Genet %D 2017 %T Further delineation of a rare recessive encephalomyopathy linked to mutations in GFER thanks to data sharing of whole exome sequencing data. %A Nambot, S %A Gavrilov, D %A Thevenon, J %A Bruel, A L %A Bainbridge, M %A Rio, M %A Goizet, C %A Rötig, A %A Jaeken, J %A Niu, N %A Xia, F %A Vital, A %A Houcinat, N %A Mochel, F %A Kuentz, P %A Lehalle, D %A Duffourd, Y %A Rivière, J B %A Thauvin-Robinet, C %A Beaudet, A L %A Faivre, L %K Adolescent %K Adult %K Child %K Cytochrome Reductases %K Exome Sequencing %K Female %K Genetic Predisposition to Disease %K Heterozygote %K Humans %K Male %K Mitochondrial Encephalomyopathies %K Mutation %K Oxidoreductases Acting on Sulfur Group Donors %K Pedigree %K Young Adult %X

BACKGROUND: Alterations in GFER gene have been associated with progressive mitochondrial myopathy, congenital cataracts, hearing loss, developmental delay, lactic acidosis and respiratory chain deficiency in 3 siblings born to consanguineous Moroccan parents by homozygosity mapping and candidate gene approach (OMIM#613076). Next generation sequencing recently confirmed this association by the finding of compound heterozygous variants in 19-year-old girl with a strikingly similar phenotype, but this ultra-rare entity remains however unknown from most of the scientific community.

MATERIALS AND METHODS: Whole exome sequencing was performed as part of a "diagnostic odyssey" for suspected mitochondrial condition in 2 patients, presenting congenital cataracts, progressive encephalomyopathy and hypotrophy and detected unreported compound heterozygous variants in GFER.

RESULTS: Thanks to an international data sharing, we found 2 additional patients carrying compound heterozygous variants in GFER. Reverse phenotyping confirmed the phenotypical similarities between the 4 patients. Together with the first literature reports, the review of these 8 cases from 4 unrelated families enables us to better describe this apparently homogeneous disorder, with the clinical and biological stigmata of mitochondrial disease.

CONCLUSION: This report highlights the clinical utility of whole exome sequencing and reverse phenotyping for the diagnosis of ultra-rare diseases and underlines the importance of a broad data sharing for accurate clinical delineation of previously unrecognized entities.

%B Clin Genet %V 92 %P 188-198 %8 2017 Aug %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/28155230?dopt=Abstract %R 10.1111/cge.12985 %0 Journal Article %J Invest Ophthalmol Vis Sci %D 2017 %T The Genetic Causes of Nonsyndromic Congenital Retinal Detachment: A Genetic and Phenotypic Study of Pakistani Families. %A Keser, Vafa %A Khan, Ayesha %A Siddiqui, Sorath %A Lopez, Irma %A Ren, Huanan %A Qamar, Raheel %A Nadaf, Javad %A Majewski, Jacek %A Chen, Rui %A Koenekoop, Robert K %K Basic Helix-Loop-Helix Transcription Factors %K Child %K Child, Preschool %K DNA Mutational Analysis %K Female %K Genotype %K Helix-Loop-Helix Motifs %K Humans %K Incidence %K Infant %K Male %K Mutation %K Pakistan %K Pedigree %K Phenotype %K Polymorphism, Single Nucleotide %K Retina %K Retinal Diseases %X

PURPOSE: To evaluate consanguineous pedigrees from Pakistan with a clinical diagnosis of nonsyndromic congenital retinal nonattachment (NCRNA) and identify genes responsible for the disease as currently only one NCRNA gene is known (atonal basic helix-loop-helix transcription factor 7: ATOH7).

METHODS: We implemented a three-step genotyping platform: single nucleotide polymorphism genotyping to identify loss of heterozygosity regions in patients, Retinal Information Network panel screening for mutations in currently known retinal genes. Negative patients were then subjected to whole exome sequencing.

RESULTS: We evaluated 21 consanguineous NCRNA pedigrees and identified the causal mutations in known retinal genes in 13 out of our 21 families. We found mutations in ATOH7 in three families. Surprisingly, we then found mutations in familial exudative vitreoretinopathy (FEVR) genes; low-density lipoprotein receptor-related protein 5 mutations (six families), tetraspanin 12 mutations (two families), and NDP mutations (two families). Thus, 62% of the patients were successfully genotyped in our study with seven novel and six previously reported mutations in known retinal genes.

CONCLUSIONS: Although the clinical diagnosis of all children was NCRNA with severe congenital fibrotic retinal detachments, the molecular diagnosis determined that the disease process was in fact a very severe form of FEVR in 10 families. Because severe congenital retinal detachment has not been previously associated with all the FEVR genes, we have thus expanded the phenotypic spectrum of FEVR, a highly variable retinal detachment phenotype that has clinical overlap with NCRNA. We identified seven novel mutations. We also established for the first time genetic overlap between the Iranian and Pakistani populations. We identified eight NCRNA families that do not harbor mutations in any known retinal genes, suggesting novel causal genes in these families.

%B Invest Ophthalmol Vis Sci %V 58 %P 1028-1036 %8 2017 Feb 01 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/28192794?dopt=Abstract %R 10.1167/iovs.16-20281 %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 BMC Med Genet %D 2017 %T Identification of established arrhythmogenic right ventricular cardiomyopathy mutation in a patient with the contrasting phenotype of hypertrophic cardiomyopathy. %A Bainbridge, Matthew Neil %A Li, Lili %A Tan, Yanli %A Cheong, Benjamin Y %A Marian, Ali J %K Cardiomyopathy, Hypertrophic %K DNA %K DNA Mutational Analysis %K Echocardiography %K Female %K Heart %K Heart Ventricles %K Humans %K Magnetic Resonance Imaging %K Middle Aged %K Pedigree %K Phenotype %K Plakophilins %X

BACKGROUND: Advances in the nucleic acid sequencing technologies have ushered in the era of genetic-based "precision medicine". Applications of the genetic discoveries to practice of medicine, however, are hindered by phenotypic variability of the genetic variants. The report illustrates extreme pleiotropic phenotypes associated with an established causal mutation for hereditary cardiomyopathy.

CASE PRESENTATION: We report a 61-year old white female who presented with syncope and echocardiographic and cardiac magnetic resonance (CMR) imaging findings consistent with the diagnosis of hypertrophic cardiomyopathy (HCM). The electrocardiogram, however, showed a QRS pattern resembling an Epsilon wave, a feature of arrhythmogenic right ventricular cardiomyopathy (ARVC). Whole exome sequencing (mean depth of coverage of exons 178X) analysis did not identify a pathogenic variant in the known HCM genes but identified an established causal mutation for ARVC. The mutation involves a canonical splice accepter site (c.2146-1G > C) in the PKP2 gene, which encodes plakophillin 2. Sanger sequencing confirmed the mutation. PKP2 is the most common causal gene for ARVC but has not been implicated in HCM. Findings on echocardiography and CMR during the course of 4-year follow up showed septal hypertrophy and a hyperdynamic left ventricle, consistent with the diagnosis of HCM. However, neither baseline nor follow up echocardiography and CMR studies showed evidence of ARVC. The right ventricle was normal in size, thickness, and function and there was no evidence of fibro-fatty infiltration in the myocardium.

CONCLUSIONS: The patient carries an established pathogenic mutation for ARVC and a subtle finding of ARVC but exhibits the classic phenotype of HCM, a contrasting phenotype to ARVC. The case illustrates the need for detailed phenotypic characterization for patients with hereditary cardiomyopathies as well as the challenges physicians face in applying the genetic discoveries in practicing genetic-based "precision medicine".

%B BMC Med Genet %V 18 %P 24 %8 2017 Mar 03 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/28253841?dopt=Abstract %R 10.1186/s12881-017-0385-8 %0 Journal Article %J Hum Mutat %D 2017 %T Leveraging splice-affecting variant predictors and a minigene validation system to identify Mendelian disease-causing variants among exon-captured variants of uncertain significance. %A Soens, Zachry T %A Branch, Justin %A Wu, Shijing %A Yuan, Zhisheng %A Li, Yumei %A Li, Hui %A Wang, Keqing %A Xu, Mingchu %A Rajan, Lavan %A Motta, Fabiana L %A Simões, Renata T %A Lopez-Solache, Irma %A Ajlan, Radwan %A Birch, David G %A Zhao, Peiquan %A Porto, Fernanda B %A Sallum, Juliana %A Koenekoop, Robert K %A Sui, Ruifang %A Chen, Rui %K Alleles %K Chromosome Mapping %K Computational Biology %K Exons %K Gene Expression %K Genes, Reporter %K Genetic Association Studies %K Genetic Diseases, Inborn %K Genetic Predisposition to Disease %K Genetic Variation %K Genotype %K High-Throughput Nucleotide Sequencing %K Humans %K Molecular Sequence Annotation %K Pedigree %K Reproducibility of Results %K RNA Splicing %X

The genetic heterogeneity of Mendelian disorders results in a significant proportion of patients that are unable to be assigned a confident molecular diagnosis after conventional exon sequencing and variant interpretation. Here, we evaluated how many patients with an inherited retinal disease (IRD) have variants of uncertain significance (VUS) that are disrupting splicing in a known IRD gene by means other than affecting the canonical dinucleotide splice site. Three in silico splice-affecting variant predictors were leveraged to annotate and prioritize variants for splicing functional validation. An in vitro minigene system was used to assay each variant's effect on splicing. Starting with 745 IRD patients lacking a confident molecular diagnosis, we validated 23 VUS as splicing variants that likely explain disease in 26 patients. Using our results, we optimized in silico score cutoffs to guide future variant interpretation. Variants that alter base pairs other than the canonical GT-AG dinucleotide are often not considered for their potential effect on RNA splicing but in silico tools and a minigene system can be utilized for the prioritization and validation of such splice-disrupting variants. These variants can be overlooked causes of human disease but can be identified using conventional exon sequencing with proper interpretation guidelines.

%B Hum Mutat %V 38 %P 1521-1533 %8 2017 Nov %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/28714225?dopt=Abstract %R 10.1002/humu.23294 %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 J Med Genet %D 2017 %T is mutated in a distinct type of Usher syndrome. %A Fu, Qing %A Xu, Mingchu %A Chen, Xue %A Sheng, Xunlun %A Yuan, Zhisheng %A Liu, Yani %A Li, Huajin %A Sun, Zixi %A Li, Huiping %A Yang, Lizhu %A Wang, Keqing %A Zhang, Fangxia %A Li, Yumei %A Zhao, Chen %A Sui, Ruifang %A Chen, Rui %K Adult %K Cell Cycle Proteins %K Child %K Consanguinity %K Exome %K Female %K Frameshift Mutation %K Genome, Human %K Hair Cells, Auditory, Inner %K High-Throughput Nucleotide Sequencing %K Homozygote %K Humans %K Male %K Pedigree %K Retinitis Pigmentosa %K Usher Syndromes %X

BACKGROUND: Usher syndrome is a genetically heterogeneous disorder featured by combined visual impairment and hearing loss. Despite a dozen of genes involved in Usher syndrome having been identified, the genetic basis remains unknown in 20-30% of patients. In this study, we aimed to identify the novel disease-causing gene of a distinct subtype of Usher syndrome.

METHODS: Ophthalmic examinations and hearing tests were performed on patients with Usher syndrome in two consanguineous families. Target capture sequencing was initially performed to screen causative mutations in known retinal disease-causing loci. Whole exome sequencing (WES) and whole genome sequencing (WGS) were applied for identifying novel disease-causing genes. RT-PCR and Sanger sequencing were performed to evaluate the splicing-altering effect of identified variants.

RESULTS: Patients from the two independent families show a mild Usher syndrome phenotype featured by juvenile or adult-onset cone-rod dystrophy and sensorineural hearing loss. WES and WGS identified two homozygous rare variants that affect mRNA splicing of a ciliary gene . RT-PCR confirmed that the two variants indeed lead to abnormal splicing, resulting in premature stop of protein translation due to frameshift.

CONCLUSIONS: Our results provide evidence that is a novel disease-causing gene for Usher syndrome, demonstrating an additional link between ciliopathy and Usher protein network in photoreceptor cells and inner ear hair cells.

%B J Med Genet %V 54 %P 190-195 %8 2017 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/27627988?dopt=Abstract %R 10.1136/jmedgenet-2016-104166 %0 Journal Article %J Am J Hum Genet %D 2017 %T Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies. %A Xu, Mingchu %A Xie, Yajing Angela %A Abouzeid, Hana %A Gordon, Christopher T %A Fiorentino, Alessia %A Sun, Zixi %A Lehman, Anna %A Osman, Ihab S %A Dharmat, Rachayata %A Riveiro-Álvarez, Rosa %A Bapst-Wicht, Linda %A Babino, Darwin %A Arno, Gavin %A Busetto, Virginia %A Zhao, Li %A Li, Hui %A Lopez-Martinez, Miguel A %A Azevedo, Liliana F %A Hubert, Laurence %A Pontikos, Nikolas %A Eblimit, Aiden %A Lorda-Sanchez, Isabel %A Kheir, Valeria %A Plagnol, Vincent %A Oufadem, Myriam %A Soens, Zachry T %A Yang, Lizhu %A Bole-Feysot, Christine %A Pfundt, Rolph %A Allaman-Pillet, Nathalie %A Nitschké, Patrick %A Cheetham, Michael E %A Lyonnet, Stanislas %A Agrawal, Smriti A %A Li, Huajin %A Pinton, Gaëtan %A Michaelides, Michel %A Besmond, Claude %A Li, Yumei %A Yuan, Zhisheng %A von Lintig, Johannes %A Webster, Andrew R %A Le Hir, Hervé %A Stoilov, Peter %A Amiel, Jeanne %A Hardcastle, Alison J %A Ayuso, Carmen %A Sui, Ruifang %A Chen, Rui %A Allikmets, Rando %A Schorderet, Daniel F %K Abnormalities, Multiple %K Adolescent %K Animals %K Child %K Child, Preschool %K Cyclophilins %K Female %K Humans %K Male %K Mice %K Mutation %K Pedigree %K Peptidylprolyl Isomerase %K Retinal Degeneration %K Young Adult %X

Pre-mRNA splicing factors play a fundamental role in regulating transcript diversity both temporally and spatially. Genetic defects in several spliceosome components have been linked to a set of non-overlapping spliceosomopathy phenotypes in humans, among which skeletal developmental defects and non-syndromic retinitis pigmentosa (RP) are frequent findings. Here we report that defects in spliceosome-associated protein CWC27 are associated with a spectrum of disease phenotypes ranging from isolated RP to severe syndromic forms. By whole-exome sequencing, recessive protein-truncating mutations in CWC27 were found in seven unrelated families that show a range of clinical phenotypes, including retinal degeneration, brachydactyly, craniofacial abnormalities, short stature, and neurological defects. Remarkably, variable expressivity of the human phenotype can be recapitulated in Cwc27 mutant mouse models, with significant embryonic lethality and severe phenotypes in the complete knockout mice while mice with a partial loss-of-function allele mimic the isolated retinal degeneration phenotype. Our study describes a retinal dystrophy-related phenotype spectrum as well as its genetic etiology and highlights the complexity of the spliceosomal gene network.

%B Am J Hum Genet %V 100 %P 592-604 %8 2017 Apr 06 %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/28285769?dopt=Abstract %R 10.1016/j.ajhg.2017.02.008 %0 Journal Article %J Am J Med Genet A %D 2017 %T Neonatal fractures as a presenting feature of LMOD3-associated congenital myopathy. %A Abbott, Megan %A Jain, Mahim %A Pferdehirt, Rachel %A Chen, Yuqing %A Tran, Alyssa %A Duz, Mehmet B %A Seven, Mehmet %A Gibbs, Richard A %A Muzny, Donna %A Lee, Brendan %A Marom, Ronit %A Burrage, Lindsay C %K Female %K Fractures, Bone %K Homozygote %K Humans %K Infant, Newborn %K Male %K Microfilament Proteins %K Muscle Proteins %K Mutation %K Myopathies, Structural, Congenital %K Pedigree %X

Nemaline myopathy is a rare inherited disorder characterized by weakness, hypotonia, and depressed deep tendon reflexes. It is clinically and genetically heterogeneous, with the most severe phenotype presenting as perinatal akinesia, severe muscle weakness, feeding difficulties and respiratory failure, leading to early mortality. Pathogenic variants in 12 genes, encoding components of the sarcomere or factors related to myogenesis, have been reported in patients affected with the disorder. Here, we describe an early, lethal presentation of decreased fetal movements, hypotonia, muscle weakness, and neonatal respiratory failure requiring ventilator support in three siblings from a consanguineous family. All exhibited perinatal fractures, and thus, a skeletal dysplasia was considered as possibly contributing to the phenotype. However, whole exome sequencing revealed a homozygous, loss-of-function pathogenic variant in LMOD3, which has recently been associated with nemaline myopathy and, in a subset of patients, perinatal fractures. This case demonstrates the importance of considering congenital neuromuscular disorders in the differential diagnosis of perinatal fractures.

%B Am J Med Genet A %V 173 %P 2789-2794 %8 2017 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/28815944?dopt=Abstract %R 10.1002/ajmg.a.38383 %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 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 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 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 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 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 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 Am J Med Genet A %D 2016 %T CRIPT exonic deletion and a novel missense mutation in a female with short stature, dysmorphic features, microcephaly, and pigmentary abnormalities. %A Leduc, Magalie S %A Niu, Zhiyv %A Bi, Weimin %A Zhu, Wenmiao %A Miloslavskaya, Irene %A Chiang, Theodore %A Streff, Haley %A Seavitt, John R %A Murray, Stephen A %A Eng, Christine %A Chan, Audrey %A Yang, Yaping %A Lalani, Seema R %K Abnormalities, Multiple %K Adaptor Proteins, Signal Transducing %K Alleles %K Amino Acid Substitution %K Child, Preschool %K DNA Mutational Analysis %K Dwarfism %K Exons %K Facies %K Female %K Genetic Association Studies %K Humans %K Microcephaly %K Mutation, Missense %K Pedigree %K Phenotype %K Sequence Deletion %X

Mutations in CRIPT encoding cysteine-rich PDZ domain-binding protein are rare, and to date have been reported in only two patients with autosomal recessive primordial dwarfism and distinctive facies. Here, we describe a female with biallelic mutations in CRIPT presenting with postnatal growth retardation, global developmental delay, and dysmorphic features including frontal bossing, high forehead, and sparse hair and eyebrows. Additional clinical features included high myopia, admixed hyper- and hypopigmented macules primarily on the face, arms, and legs, and syndactyly of 4-5 toes bilaterally. Using whole exome sequencing (WES) and chromosomal microarray analysis (CMA), we detected a c.8G>A (p.C3Y) missense variant in exon 1 of the CRIPT gene inherited from the mother and a 1,331 bp deletion encompassing exon 1, inherited from the father. The c.8G>A (p.C3Y) missense variant in CRIPT was apparently homozygous in the proband due to the exon 1 deletion. Our findings illustrate the clinical utility of combining WES with copy number variant (CNV) analysis to provide a molecular diagnosis to patients with rare Mendelian disorders. Our findings also illustrate the clinical spectrum of CRIPT related mutations. © 2016 Wiley Periodicals, Inc.

%B Am J Med Genet A %V 170 %P 2206-11 %8 2016 Aug %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/27250922?dopt=Abstract %R 10.1002/ajmg.a.37780 %0 Journal Article %J J Clin Invest %D 2016 %T Destabilized SMC5/6 complex leads to chromosome breakage syndrome with severe lung disease. %A van der Crabben, Saskia N %A Hennus, Marije P %A McGregor, Grant A %A Ritter, Deborah I %A Nagamani, Sandesh C S %A Wells, Owen S %A Harakalova, Magdalena %A Chinn, Ivan K %A Alt, Aaron %A Vondrova, Lucie %A Hochstenbach, Ron %A van Montfrans, Joris M %A Terheggen-Lagro, Suzanne W %A van Lieshout, Stef %A van Roosmalen, Markus J %A Renkens, Ivo %A Duran, Karen %A Nijman, Isaac J %A Kloosterman, Wigard P %A Hennekam, Eric %A Orange, Jordan S %A van Hasselt, Peter M %A Wheeler, David A %A Palecek, Jan J %A Lehmann, Alan R %A Oliver, Antony W %A Pearl, Laurence H %A Plon, Sharon E %A Murray, Johanne M %A van Haaften, Gijs %K Abnormalities, Multiple %K Alleles %K B-Lymphocytes %K Cell Cycle Proteins %K Cell Proliferation %K Child %K Child, Preschool %K Chromosomal Proteins, Non-Histone %K Chromosome Breakage %K Chromosome Segregation %K Chromosomes %K DNA Damage %K DNA Repair %K DNA Replication %K Family Health %K Female %K Fibroblasts %K Homozygote %K Humans %K Infant %K Intracellular Signaling Peptides and Proteins %K Lung Diseases %K Male %K Meiosis %K Mitosis %K Mutation, Missense %K Pedigree %K Recombination, Genetic %K Syndrome %K T-Lymphocytes %X

The structural maintenance of chromosomes (SMC) family of proteins supports mitotic proliferation, meiosis, and DNA repair to control genomic stability. Impairments in chromosome maintenance are linked to rare chromosome breakage disorders. Here, we have identified a chromosome breakage syndrome associated with severe lung disease in early childhood. Four children from two unrelated kindreds died of severe pulmonary disease during infancy following viral pneumonia with evidence of combined T and B cell immunodeficiency. Whole exome sequencing revealed biallelic missense mutations in the NSMCE3 (also known as NDNL2) gene, which encodes a subunit of the SMC5/6 complex that is essential for DNA damage response and chromosome segregation. The NSMCE3 mutations disrupted interactions within the SMC5/6 complex, leading to destabilization of the complex. Patient cells showed chromosome rearrangements, micronuclei, sensitivity to replication stress and DNA damage, and defective homologous recombination. This work associates missense mutations in NSMCE3 with an autosomal recessive chromosome breakage syndrome that leads to defective T and B cell function and acute respiratory distress syndrome in early childhood.

%B J Clin Invest %V 126 %P 2881-92 %8 2016 Aug 01 %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/27427983?dopt=Abstract %R 10.1172/JCI82890 %0 Journal Article %J Evolution %D 2016 %T Evolutionary and developmental implications of asymmetric brain folding in a large primate pedigree. %A Atkinson, Elizabeth G %A Jeffrey Rogers %A Cheverud, James M %K Animals %K Biological Evolution %K Cerebrum %K Female %K Male %K Pedigree %K Primates %X

Bilateral symmetry is a fundamental property of the vertebrate central nervous system. Local deviations from symmetry provide various types of information about the development, evolution, and function of elements within the CNS, especially the cerebral hemispheres. Here, we quantify the pattern and extent of asymmetry in cortical folding within the cerebrum of Papio baboons and assess the evolutionary and developmental implications of the findings. Analyses of directional asymmetry show a population-level trend in length measurements indicating that baboons are genetically predisposed to be asymmetrical, with the right side longer than the left in the anterior cerebrum while the left side is longer than the right posteriorly. We also find a corresponding bias to display a right frontal petalia (overgrowth of the anterior pole of the cerebral cortex on the right side). By quantifying fluctuating asymmetry, we assess canalization of brain features and the susceptibility of the baboon brain to developmental perturbations. We find that features are differentially canalized depending on their ontogenetic timing. We further deduce that development of the two hemispheres is to some degree independent. This independence has important implications for the evolution of cerebral hemispheres and their separate specialization. Asymmetry is a major feature of primate brains and is characteristic of both brain structure and function.

%B Evolution %V 70 %P 707-15 %8 2016 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/26813679?dopt=Abstract %R 10.1111/evo.12867 %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 Am J Hum Genet %D 2016 %T Isolated and Syndromic Retinal Dystrophy Caused by Biallelic Mutations in RCBTB1, a Gene Implicated in Ubiquitination. %A Coppieters, Frauke %A Ascari, Giulia %A Dannhausen, Katharina %A Nikopoulos, Konstantinos %A Peelman, Frank %A Karlstetter, Marcus %A Xu, Mingchu %A Brachet, Cécile %A Meunier, Isabelle %A Tsilimbaris, Miltiadis K %A Tsika, Chrysanthi %A Blazaki, Styliani V %A Vergult, Sarah %A Farinelli, Pietro %A Van Laethem, Thalia %A Bauwens, Miriam %A De Bruyne, Marieke %A Chen, Rui %A Langmann, Thomas %A Sui, Ruifang %A Meire, Françoise %A Rivolta, Carlo %A Hamel, Christian P %A Leroy, Bart P %A De Baere, Elfride %K Adolescent %K Adult %K Age of Onset %K Alleles %K Child %K Consanguinity %K Cullin Proteins %K Exome %K Female %K Founder Effect %K Genes, Recessive %K Guanine Nucleotide Exchange Factors %K Haplotypes %K Homozygote %K Humans %K Lymphocytes %K Male %K Mutation, Missense %K NF-E2-Related Factor 2 %K Pedigree %K Phenotype %K Retina %K Retinal Dystrophies %K RNA, Messenger %K Syndrome %K Turkey %K Ubiquitination %X

Inherited retinal dystrophies (iRDs) are a group of genetically and clinically heterogeneous conditions resulting from mutations in over 250 genes. Here, homozygosity mapping and whole-exome sequencing (WES) in a consanguineous family revealed a homozygous missense mutation, c.973C>T (p.His325Tyr), in RCBTB1. In affected individuals, it was found to segregate with retinitis pigmentosa (RP), goiter, primary ovarian insufficiency, and mild intellectual disability. Subsequent analysis of WES data in different cohorts uncovered four additional homozygous missense mutations in five unrelated families in whom iRD segregates with or without syndromic features. Ocular phenotypes ranged from typical RP starting in the second decade to chorioretinal dystrophy with a later age of onset. The five missense mutations affect highly conserved residues either in the sixth repeat of the RCC1 domain or in the BTB1 domain. A founder haplotype was identified for mutation c.919G>A (p.Val307Met), occurring in two families of Mediterranean origin. We showed ubiquitous mRNA expression of RCBTB1 and demonstrated predominant RCBTB1 localization in human inner retina. RCBTB1 was very recently shown to be involved in ubiquitination, more specifically as a CUL3 substrate adaptor. Therefore, the effect on different components of the CUL3 and NFE2L2 (NRF2) pathway was assessed in affected individuals' lymphocytes, revealing decreased mRNA expression of NFE2L2 and several NFE2L2 target genes. In conclusion, our study puts forward mutations in RCBTB1 as a cause of autosomal-recessive non-syndromic and syndromic iRD. Finally, our data support a role for impaired ubiquitination in the pathogenetic mechanism of RCBTB1 mutations.

%B Am J Hum Genet %V 99 %P 470-80 %8 2016 Aug 04 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/27486781?dopt=Abstract %R 10.1016/j.ajhg.2016.06.017 %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 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 JAMA Ophthalmol %D 2016 %T Molecular and Clinical Findings in Patients With Knobloch Syndrome. %A Hull, Sarah %A Arno, Gavin %A Ku, Cristy A %A Ge, Zhongqi %A Waseem, Naushin %A Chandra, Aman %A Webster, Andrew R %A Robson, Anthony G %A Michaelides, Michel %A Weleber, Richard G %A Davagnanam, Indran %A Rui Chen %A Holder, Graham E %A Pennesi, Mark E %A Moore, Anthony T %K Adolescent %K Adult %K Child %K Child, Preschool %K Collagen Type VIII %K Collagen Type XVIII %K DNA Mutational Analysis %K Electroretinography %K Encephalocele %K Exfoliation Syndrome %K Exons %K Female %K Glaucoma, Open-Angle %K Humans %K Magnetic Resonance Imaging %K Male %K Molecular Biology %K Mutation %K Myopia, Degenerative %K Pedigree %K Photoreceptor Cells, Vertebrate %K Polymerase Chain Reaction %K Retinal Degeneration %K Retinal Detachment %K Vision Disorders %K Young Adult %X

IMPORTANCE: Knobloch syndrome is a rare, recessively inherited disorder classically characterized by high myopia, retinal detachment, and occipital encephalocele, but it is now known to have an increasingly variable phenotype. There is a lack of reported electrophysiologic data, and some key clinical features have yet to be described.

OBJECTIVE: To expand on current clinical, electrophysiologic, and molecular genetic findings in Knobloch syndrome.

DESIGN, SETTING, AND PARTICIPANTS: Twelve patients from 7 families underwent full ophthalmic examination and retinal imaging. Further investigations included electroretinography and neuroradiologic imaging. Bidirectional Sanger sequencing of COL18A1 was performed with segregation on available relatives. The study was conducted from July 4, 2013, to October 5, 2015. Data analysis was performed from May 20, 2014, to November 3, 2015.

MAIN OUTCOMES AND MEASURES: Results of ophthalmic and neuroradiologic assessment and sequence analysis of COL18A1.

RESULTS: Of the 12 patients (6 males; mean age at last review, 16 years [range, 2-38 years]), all had high myopia in at least 1 eye and severely reduced vision. A sibling pair had unilateral high myopia in their right eyes and near emmetropia in their left eyes from infancy. Anterior segment abnormalities included absent iris crypts, iris transillumination, lens subluxation, and cataract. Two patients with iris transillumination had glaucoma. Fundus characteristics included abnormal collapsed vitreous, macular atrophy, and a tesselated fundus. Five patients had previous retinal detachment. Electroretinography revealed a cone-rod pattern of dysfunction in 8 patients, was severely reduced or undetectable in 2 patients, and demonstrated cone-rod dysfunction in 1 eye with undetectable responses in the other eye in 2 patients. Radiologic imaging demonstrated occipital encephalocele or meningocele in 3 patients, occipital skull defects in 4 patients, minor occipital changes in 2 patients, and no abnormalities in 2 patients. Cutaneous scalp changes were present in 5 patients. Systemic associations were identified in 8 patients, including learning difficulties, epilepsy, and congenital renal abnormalities. Biallelic mutations including 2 likely novel mutations in COL18A1, were identified in 6 families that were consistent with autosomal recessive inheritance with a single mutation identified in a family with 2 affected children.

CONCLUSIONS AND RELEVANCE: This report describes new features in patients with Knobloch syndrome, including pigment dispersion syndrome and glaucoma as well as cone-rod dysfunction on electroretinography. Two patients had normal neuroradiologic findings, emphasizing that some affected individuals have isolated ocular disease. Awareness of the ocular phenotype may aid early diagnosis, appropriate genetic counseling, and monitoring for potential complications.

%B JAMA Ophthalmol %V 134 %P 753-62 %8 2016 Jul 01 %G eng %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/27259167?dopt=Abstract %R 10.1001/jamaophthalmol.2016.1073 %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 Mol Genet %D 2016 %T Mutations in POMGNT1 cause non-syndromic retinitis pigmentosa. %A Xu, Mingchu %A Yamada, Takeyuki %A Sun, Zixi %A Eblimit, Aiden %A Lopez, Irma %A Wang, Feng %A Manya, Hiroshi %A Xu, Shan %A Zhao, Li %A Li, Yumei %A Kimchi, Adva %A Sharon, Dror %A Sui, Ruifang %A Endo, Tamao %A Koenekoop, Robert K %A Chen, Rui %K Adult %K Aged %K Animals %K Cells, Cultured %K Exome %K Female %K Genes, Recessive %K Genetic Predisposition to Disease %K Glycosylation %K Humans %K Male %K Mice %K Middle Aged %K Mutation %K N-Acetylglucosaminyltransferases %K Pedigree %K Photoreceptor Cells, Vertebrate %K Retinitis Pigmentosa %K Sequence Analysis, DNA %X

A growing number of human diseases have been linked to defects in protein glycosylation that affects a wide range of organs. Among them, O-mannosylation is an unusual type of protein glycosylation that is largely restricted to the muscular and nerve system. Consistently, mutations in genes involved in the O-mannosylation pathway result in infantile-onset, severe developmental defects involving skeleton muscle, brain and eye, such as the muscle-eye-brain disease (MIM no. 253280). However, the functional importance of O-mannosylation in these tissues at later stages remains largely unknown. In our study, we have identified recessive mutations in POMGNT1, which encodes an essential component in O-mannosylation pathway, in three unrelated families with autosomal recessive retinitis pigmentosa (RP), but without extraocular involvement. Enzymatic assay of these mutant alleles demonstrate that they greatly reduce the POMGNT1 enzymatic activity and are likely to be hypomorphic. Immunohistochemistry shows that POMGNT1 is specifically expressed in photoreceptor basal body. Taken together, our work identifies a novel disease-causing gene for RP and indicates that proper protein O-mannosylation is not only essential for early organ development, but also important for maintaining survival and function of the highly specialized retinal cells at later stages.

%B Hum Mol Genet %V 25 %P 1479-88 %8 2016 Apr 15 %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/26908613?dopt=Abstract %R 10.1093/hmg/ddw022 %0 Journal Article %J Sci Rep %D 2016 %T Next-generation sequencing-based molecular diagnosis of 35 Hispanic retinitis pigmentosa probands. %A Zhang, Qi %A Xu, Mingchu %A Verriotto, Jennifer D %A Li, Yumei %A Wang, Hui %A Gan, Lin %A Lam, Byron L %A Chen, Rui %K Alleles %K Eye Proteins %K Female %K High-Throughput Nucleotide Sequencing %K Hispanic or Latino %K Humans %K Male %K Mutation %K Pedigree %K Retinitis Pigmentosa %K RNA Splicing %X

Retinitis pigmentosa (RP) is a heterogeneous group of inherited retinal diseases. The prevalence of RP and the mutation spectrum vary across populations. Hispanic people account for approximately 17% of the United States population, and the genetic etiologies of RP of this ethnic group still remain not well defined. Utilizing next-generation sequencing (NGS), we screened mutations in known retinal disease-causing genes in an RP cohort of 35 unrelated Hispanic probands from the Miami area. We achieved a solving rate of 66% and identified 15 novel putative pathogenic mutations, including a frequent founder mutation disrupting PRPF31 splicing. Our data show that the mutation spectrum of Hispanic RP receives a significant impact from disease-causing alleles of Spanish origin and may also contain population-specific alleles.

%B Sci Rep %V 6 %P 32792 %8 2016 Sep 06 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/27596865?dopt=Abstract %R 10.1038/srep32792 %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 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 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 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 Am J Med Genet A %D 2016 %T Whole exome sequencing identifies the first STRADA point mutation in a patient with polyhydramnios, megalencephaly, and symptomatic epilepsy syndrome (PMSE). %A Bi, Weimin %A Glass, Ian A %A Donna M Muzny %A Richard A Gibbs %A Eng, Christine M %A Yang, Yaping %A Sun, Angela %K Adaptor Proteins, Vesicular Transport %K Child, Preschool %K DNA Mutational Analysis %K Epilepsy %K Exome %K Facies %K Genetic Association Studies %K Genotype %K High-Throughput Nucleotide Sequencing %K Humans %K Male %K Megalencephaly %K Pedigree %K Phenotype %K Physical Examination %K Point Mutation %K Polyhydramnios %K Psychomotor Disorders %K Syndrome %X

Polyhydramnios, megalencephaly, and symptomatic epilepsy syndrome (PMSE) is an ultra rare neurodevelopmental disorder characterized by severe, infantile-onset intractable epilepsy, neurocognitive delay, macrocephaly, and craniofacial dysmorphism. The molecular diagnosis of this condition has thus far only been made in 16 Old Order Mennonite patients carrying a homozygous 7 kb founder deletion of exons 9-13 of STRADA. We performed clinical whole exome sequencing (WES) on a 4-year-old Indian male with global developmental delay, history of failure to thrive, infantile spasms, repetitive behaviors, hypotonia, low muscle mass, marked joint laxity, and dysmorphic facial features including tall forehead, long face, arched eyebrows, small chin, wide mouth, and tented upper lip. A homozygous single nucleotide duplication, c.842dupA (p.D281fs), in exon 10 of STRADA was identified. Sanger sequencing confirmed the mutation in the individual and identified both parents as carriers. In light of the molecular discoveries, the patient's clinical phenotype was considered to be a good fit for PMSE. We identified for the first time a homozygous point mutation in STRADA causing PMSE. Additional bi-allelic mutations related to PMSE thus far have not been observed in Baylor ∼6,000 consecutive clinical WES cases, supporting the rarity of this disorder. Our findings may have treatment implications for the patient since previous studies have shown rapamycin as a potential therapeutic agent for the seizures and cognitive problems in PMSE patients. © 2016 Wiley Periodicals, Inc.

%B Am J Med Genet A %V 170 %P 2181-5 %8 2016 Aug %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/27170158?dopt=Abstract %R 10.1002/ajmg.a.37727 %0 Journal Article %J Sci Rep %D 2016 %T X-Linked Retinoschisis: Phenotypic Variability in a Chinese Family. %A Xiao, Yangyan %A Liu, Xiao %A Tang, Luosheng %A Wang, Xia %A Coursey, Terry G %A Guo, Xiaojian %A Li, Zhuo %K Adult %K Aged, 80 and over %K Asian People %K China %K Codon, Initiator %K Eye Proteins %K Family %K Female %K Humans %K Male %K Middle Aged %K Mutation %K Pedigree %K Retinoschisis %X

X-linked juvenile retinoschisis (XLRS), a leading cause of juvenile macular degeneration, is characterized by a spoke-wheel pattern in the macular region of the retina and splitting of the neurosensory retina. Our study is to describe the clinical characteristics of a four generations of this family (a total of 18 members)with X-linked retinoschisis (XLRS) and detected a novel mutations of c.3G > A (p.M1?) in the initiation codon of the RS1 gene. by direct sequencing.Identification of this mutation in this family provides evidence about potential genetic or environmental factors on its phenotypic variance, as patients presented with different phenotypes regardless of having the same mutation. Importantly, OCT has proven vital for XLRS diagnosis in children.

%B Sci Rep %V 6 %P 20118 %8 2016 Jan 29 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/26823236?dopt=Abstract %R 10.1038/srep20118 %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 Orphanet J Rare Dis %D 2015 %T Comprehensive molecular diagnosis of 67 Chinese Usher syndrome probands: high rate of ethnicity specific mutations in Chinese USH patients. %A Jiang, Lichun %A Liang, Xiaofang %A Li, Yumei %A Wang, Jing %A Zaneveld, Jacques Eric %A Wang, Hui %A Xu, Shan %A Wang, Keqing %A Wang, Binbin %A Chen, Rui %A Sui, Ruifang %K China %K Cohort Studies %K Ethnicity %K Female %K Humans %K Male %K Molecular Diagnostic Techniques %K Mutation %K Pedigree %K Phenotype %K Usher Syndromes %X

BACKGROUND: Usher syndrome (USH) is the most common disease causing combined deafness and blindness. It is predominantly an autosomal recessive genetic disorder with occasionally digenic cases. Molecular diagnosis of USH patients is important for disease management. Few studies have tried to find the genetic cause of USH in Chinese patients. This study was designed to determine the mutation spectrum of Chinese USH patients.

METHODS: We applied next generation sequencing to characterize the mutation spectrum in 67 independent Chinese families with at least one member diagnosed with USH. Blood was collected at Peking Union Medical College Hospital. This cohort is one of the largest USH cohorts reported. We utilized customized panel and whole exome sequencing, variant analysis, Sanger validation and segregation tests to find disease causing mutations in these families.

RESULTS: We identified biallelic disease causing mutations in known USH genes in 70 % (49) of our patients. As has been previously reported, MYO7A is the most frequently mutated gene in our USH type I patients while USH2A is the most mutated gene in our USH type II patients. In addition, we identify mutations in CLRN1, DFNB31, GPR98 and PCDH15 for the first time in Chinese USH patients. Together, mutations in CLRN1, DNFB31, GPR98 and PCDH15 account for 11.4 % of disease in our cohort. Interestingly, although the spectrum of disease genes is quite similar between our Chinese patient cohort and other patient cohorts from different (and primarily Caucasian) ethnic backgrounds, the mutations themselves are dramatically different. In particular, 76 % (52/68) of alleles found in this study have never been previously reported. Interestingly, we observed a strong enrichment for severe protein truncating mutations expected to have severe functional consequence on the protein in USH II patients compared to the reported mutation spectrum in RP patients, who often carry partial protein truncating mutations.

CONCLUSIONS: Our study provides the first comprehensive genetic characterization of a large collection of Chinese USH patients. Up to 90 % of USH patients have disease caused by mutations in known USH disease genes. By combining NGS-based molecular diagnosis and patient clinical information, a more accurate diagnosis, prognosis and personalized treatment of USH patients can be achieved.

%B Orphanet J Rare Dis %V 10 %P 110 %8 2015 Sep 04 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/26338283?dopt=Abstract %R 10.1186/s13023-015-0329-3 %0 Journal Article %J Invest Ophthalmol Vis Sci %D 2015 %T Comprehensive Molecular Diagnosis of a Large Chinese Leber Congenital Amaurosis Cohort. %A Wang, Hui %A Wang, Xia %A Zou, Xuan %A Xu, Shan %A Li, Hui %A Soens, Zachry Tore %A Wang, Keqing %A Li, Yumei %A Dong, Fangtian %A Chen, Rui %A Sui, Ruifang %K Adolescent %K Adult %K Asian People %K Child %K Child, Preschool %K Female %K Humans %K Infant %K Leber Congenital Amaurosis %K Male %K Molecular Diagnostic Techniques %K Mutation %K Pedigree %K Phenotype %X

PURPOSE: Leber congenital amaurosis (LCA) is an inherited retinal disease that causes early-onset severe visual impairment. To evaluate the mutation spectrum in the Chinese population, we performed a mutation screen in 145 Chinese LCA families.

METHODS: First, we performed direct Sanger sequencing of 7 LCA disease genes in 81 LCA families. Next, we developed a capture panel that enriches the entire coding exons and splicing sites of 163 known retinal disease genes and other candidate retinal disease genes. The capture panel allowed us to quickly identify disease-causing mutations in a large number of genes at a relatively low cost. Thus, this method was applied to the 53 LCA families that were unsolved by direct Sanger sequencing of 7 LCA disease genes and an additional 64 LCA families. Systematic next-generation sequencing (NGS) data analysis, Sanger sequencing validation, and segregation analysis were used to identify pathogenic mutations.

RESULTS: Homozygous or compound heterozygous mutations were identified in 107 families, heterozygous autosomal dominant mutations were identified in 3 families and an X-linked mutation was found in 1 family, for a combined solving rate of 76.6%. In total, 136 novel pathogenic mutations were found in this study. In combination with two previous studies carried out in Chinese LCA patients, we concluded that the mutation spectrum in the Chinese population is distinct compared to that in the European population. After revisiting, we also refined the clinical diagnosis of 10 families based on their molecular diagnosis.

CONCLUSIONS: Our results highlight the importance of a molecular diagnosis as an integral part of the clinical diagnostic process.

%B Invest Ophthalmol Vis Sci %V 56 %P 3642-55 %8 2015 Jun %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/26047050?dopt=Abstract %R 10.1167/iovs.14-15972 %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 Genetics %D 2015 %T Cortical Folding of the Primate Brain: An Interdisciplinary Examination of the Genetic Architecture, Modularity, and Evolvability of a Significant Neurological Trait in Pedigreed Baboons (Genus Papio). %A Atkinson, Elizabeth G %A Rogers, Jeffrey %A Mahaney, Michael C %A Cox, Laura A %A Cheverud, James M %K Animals %K Biological Evolution %K Brain %K Cerebral Cortex %K Chromosome Mapping %K Cluster Analysis %K Papio %K Pedigree %K Primates %K Quantitative Trait Loci %K Reproducibility of Results %X

Folding of the primate brain cortex allows for improved neural processing power by increasing cortical surface area for the allocation of neurons. The arrangement of folds (sulci) and ridges (gyri) across the cerebral cortex is thought to reflect the underlying neural network. Gyrification, an adaptive trait with a unique evolutionary history, is affected by genetic factors different from those affecting brain volume. Using a large pedigreed population of ∼1000 Papio baboons, we address critical questions about the genetic architecture of primate brain folding, the interplay between genetics, brain anatomy, development, patterns of cortical-cortical connectivity, and gyrification's potential for future evolution. Through Mantel testing and cluster analyses, we find that the baboon cortex is quite evolvable, with high integration between the genotype and phenotype. We further find significantly similar partitioning of variation between cortical development, anatomy, and connectivity, supporting the predictions of tension-based models for sulcal development. We identify a significant, moderate degree of genetic control over variation in sulcal length, with gyrus-shape features being more susceptible to environmental effects. Finally, through QTL mapping, we identify novel chromosomal regions affecting variation in brain folding. The most significant QTL contain compelling candidate genes, including gene clusters associated with Williams and Down syndromes. The QTL distribution suggests a complex genetic architecture for gyrification with both polygeny and pleiotropy. Our results provide a solid preliminary characterization of the genetic basis of primate brain folding, a unique and biomedically relevant phenotype with significant implications in primate brain evolution.

%B Genetics %V 200 %P 651-65 %8 2015 Jun %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/25873632?dopt=Abstract %R 10.1534/genetics.114.173443 %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 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 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 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 Behav Genet %D 2015 %T Genetic influences on response to novel objects and dimensions of personality in Papio baboons. %A Johnson, Zachary %A Brent, Linda %A Alvarenga, Juan Carlos %A Comuzzie, Anthony G %A Shelledy, Wendy %A Ramirez, Stephanie %A Cox, Laura %A Mahaney, Michael C %A Huang, Yung-Yu %A Mann, J John %A Kaplan, Jay R %A Rogers, Jeffrey %K Animals %K Behavior, Animal %K Ethylene Glycols %K Female %K Genetic Linkage %K Genetic Variation %K Homovanillic Acid %K Male %K Multivariate Analysis %K Papio %K Pedigree %K Personality %K Phenols %K Phenotype %K Polymorphism, Single Nucleotide %K Quantitative Trait Loci %K Social Behavior %K Synaptosomal-Associated Protein 25 %X

Behavioral variation within and between populations and species of the genus Papio has been studied extensively, but little is known about the genetic causes of individual- or population-level differences. This study investigates the influence of genetic variation on personality (sometimes referred to as temperament) in baboons and identifies a candidate gene partially responsible for the variation in that phenotype. To accomplish these goals, we examined individual variation in response to both novel objects and an apparent novel social partner (using a mirror test) among pedigreed baboons (n = 578) from the Southwest National Primate Research Center. We investigated the frequency and duration of individual behaviors in response to novel objects and used multivariate factor analysis to identify trait-like dimensions of personality. Exploratory factor analysis identified two distinct dimensions of personality within this population. Factor 1 accounts for 46.8 % of the variance within the behavioral matrix, and consists primarily of behaviors related to the "boldness" of the subject. Factor 2 accounts for 18.8 % of the variation, and contains several "anxiety" like behaviors. Several specific behaviors, and the two personality factors, were significantly heritable, with the factors showing higher heritability than most individual behaviors. Subsequent analyses show that the behavioral reactions observed in the test protocol are associated with animals' social behavior observed later in their home social groups. Finally we used linkage analysis to map quantitative trait loci for the measured phenotypes. Single nucleotide polymorphisms in a positional candidate gene (SNAP25) are associated with variation in one of the personality factors, and CSF levels of homovanillic acid and 3-methoxy-4-hydroxyphenylglycol. This study documents heritable variation in personality among baboons and suggests that sequence variation in SNAP25 may influence differences in behavior and neurochemistry in these nonhuman primates.

%B Behav Genet %V 45 %P 215-27 %8 2015 Mar %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/25604451?dopt=Abstract %R 10.1007/s10519-014-9702-6 %0 Journal Article %J J Natl Cancer Inst %D 2015 %T Germline mutations in shelterin complex genes are associated with familial glioma. %A Bainbridge, Matthew N %A Armstrong, Georgina N %A Gramatges, M Monica %A Bertuch, Alison A %A Jhangiani, Shalini N %A Doddapaneni, Harsha %A Lewis, Lora %A Tombrello, Joseph %A Tsavachidis, Spyros %A Liu, Yanhong %A Jalali, Ali %A Plon, Sharon E %A Lau, Ching C %A Parsons, Donald W %A Claus, Elizabeth B %A Barnholtz-Sloan, Jill %A Il'yasova, Dora %A Schildkraut, Joellen %A Ali-Osman, Francis %A Sadetzki, Siegal %A Johansen, Christoffer %A Houlston, Richard S %A Jenkins, Robert B %A Lachance, Daniel %A Olson, Sara H %A Bernstein, Jonine L %A Merrell, Ryan T %A Wrensch, Margaret R %A Walsh, Kyle M %A Davis, Faith G %A Lai, Rose %A Shete, Sanjay %A Aldape, Kenneth %A Amos, Christopher I %A Thompson, Patricia A %A Muzny, Donna M %A Gibbs, Richard A %A Melin, Beatrice S %A Bondy, Melissa L %K Adult %K Aged %K Brain Neoplasms %K Exome %K Female %K Genetic Predisposition to Disease %K Germ-Line Mutation %K Glioma %K Humans %K Male %K Middle Aged %K Oligodendroglioma %K Pedigree %K Shelterin Complex %K Telomere-Binding Proteins %X

Gliomas are the most common brain tumor, with several histological subtypes of various malignancy grade. The genetic contribution to familial glioma is not well understood. Using whole exome sequencing of 90 individuals from 55 families, we identified two families with mutations in POT1 (p.G95C, p.E450X), a member of the telomere shelterin complex, shared by both affected individuals in each family and predicted to impact DNA binding and TPP1 binding, respectively. Validation in a separate cohort of 264 individuals from 246 families identified an additional mutation in POT1 (p.D617Efs), also predicted to disrupt TPP1 binding. All families with POT1 mutations had affected members with oligodendroglioma, a specific subtype of glioma more sensitive to irradiation. These findings are important for understanding the origin of glioma and could have importance for the future diagnostics and treatment of glioma.

%B J Natl Cancer Inst %V 107 %P 384 %8 2015 Jan %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/25482530?dopt=Abstract %R 10.1093/jnci/dju384 %0 Journal Article %J Circ Cardiovasc Genet %D 2015 %T Loss of Function Mutations in NNT Are Associated With Left Ventricular Noncompaction. %A Bainbridge, Matthew N %A Davis, Erica E %A Choi, Wen-Yee %A Dickson, Amy %A Martinez, Hugo R %A Wang, Min %A Dinh, Huyen %A Muzny, Donna M %A Pignatelli, Ricardo %A Katsanis, Nicholas %A Boerwinkle, Eric %A Gibbs, Richard A %A Jefferies, John L %K Animals %K Animals, Genetically Modified %K Embryo, Nonmammalian %K Exome %K Family Health %K Female %K Frameshift Mutation %K Genetic Complementation Test %K Genetic Predisposition to Disease %K Humans %K Isolated Noncompaction of the Ventricular Myocardium %K Luminescent Proteins %K Male %K Microscopy, Confocal %K Mitochondrial Proteins %K NADP Transhydrogenase, AB-Specific %K Pedigree %K Sequence Analysis, DNA %K Zebrafish %X

BACKGROUND: Left ventricular noncompaction (LVNC) is an autosomal-dominant, genetically heterogeneous cardiomyopathy with variable severity, which may co-occur with cardiac hypertrophy.

METHODS AND RESULTS: Here, we generated whole exome sequence data from multiple members from 5 families with LVNC. In 4 of 5 families, the candidate causative mutation segregates with disease in known LVNC genes MYH7 and TPM1. Subsequent sequencing of MYH7 in a larger LVNC cohort identified 7 novel likely disease causing variants. In the fifth family, we identified a frameshift mutation in NNT, a nuclear-encoded mitochondrial protein, not implicated previously in human cardiomyopathies. Resequencing of NNT in additional LVNC families identified a second likely pathogenic missense allele. Suppression of nnt in zebrafish caused early ventricular malformation and contractility defects, probably driven by altered cardiomyocyte proliferation. In vivo complementation studies showed that mutant human NNT failed to rescue nnt morpholino-induced heart dysfunction, indicating a probable haploinsufficiency mechanism.

CONCLUSIONS: Together, our data expand the genetic spectrum of LVNC and demonstrate how the intersection of whole exome sequence with in vivo functional studies can accelerate the identification of genes that drive human genetic disorders.

%B Circ Cardiovasc Genet %V 8 %P 544-52 %8 2015 Aug %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/26025024?dopt=Abstract %R 10.1161/CIRCGENETICS.115.001026 %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 Hum Genet %D 2015 %T Mutations in human IFT140 cause non-syndromic retinal degeneration. %A Xu, Mingchu %A Yang, Lizhu %A Wang, Feng %A Li, Huajin %A Wang, Xia %A Wang, Weichen %A Ge, Zhongqi %A Wang, Keqing %A Zhao, Li %A Li, Hui %A Li, Yumei %A Sui, Ruifang %A Chen, Rui %K Adult %K Amino Acid Sequence %K Carrier Proteins %K Child %K Female %K Genetic Association Studies %K Humans %K Leber Congenital Amaurosis %K Male %K Middle Aged %K Mutation, Missense %K Pedigree %K Retinitis Pigmentosa %X

Leber congenital amaurosis (LCA) and retinitis pigmentosa (RP) are two genetically heterogeneous retinal degenerative disorders. Despite the identification of a number of genes involved in LCA and RP, the genetic etiology remains unknown in many patients. In this study, we aimed to identify novel disease-causing genes of LCA and RP. Retinal capture sequencing was initially performed to screen mutations in known disease-causing genes in different cohorts of LCA and RP patients. For patients with negative results, we performed whole exome sequencing and applied a series of variant filtering strategies. Sanger sequencing was done to validate candidate causative IFT140 variants. Exome sequencing data analysis led to the identification of IFT140 variants in multiple unrelated non-syndromic LCA and RP cases. All the variants are extremely rare and predicted to be damaging. All the variants passed Sanger validation and segregation tests provided that the family members' DNA was available. The results expand the phenotype spectrum of IFT140 mutations to non-syndromic retinal degeneration, thus extending our understanding of intraflagellar transport and primary cilia biology in the retina. This work also improves the molecular diagnosis of retinal degenerative disease.

%B Hum Genet %V 134 %P 1069-78 %8 2015 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/26216056?dopt=Abstract %R 10.1007/s00439-015-1586-x %0 Journal Article %J Nat Commun %D 2015 %T Mutations in PNPLA6 are linked to photoreceptor degeneration and various forms of childhood blindness. %A Kmoch, S %A Majewski, J %A Ramamurthy, V %A Cao, S %A Fahiminiya, S %A Ren, H %A MacDonald, I M %A Lopez, I %A Sun, V %A Keser, V %A Khan, A %A Stránecký, V %A Hartmannová, H %A Přistoupilová, A %A Hodaňová, K %A Piherová, L %A Kuchař, L %A Baxová, A %A Chen, R %A Barsottini, O G P %A Pyle, A %A Griffin, H %A Splitt, M %A Sallum, J %A Tolmie, J L %A Sampson, J R %A Chinnery, P %A Banin, E %A Sharon, D %A Dutta, S %A Grebler, R %A Helfrich-Foerster, C %A Pedroso, J L %A Kretzschmar, D %A Cayouette, M %A Koenekoop, R K %K Amino Acid Sequence %K Animals %K Blindness %K Child %K Child, Preschool %K Drosophila %K Female %K Humans %K Male %K Mice %K Mice, Inbred C57BL %K Microscopy, Fluorescence %K Molecular Sequence Data %K Mutation %K Pedigree %K Phenotype %K Phospholipases %K Phospholipids %K Retina %K Retinal Degeneration %K Sequence Analysis, DNA %K Sequence Homology, Amino Acid %K Spectrometry, Mass, Electrospray Ionization %X

Blindness due to retinal degeneration affects millions of people worldwide, but many disease-causing mutations remain unknown. PNPLA6 encodes the patatin-like phospholipase domain containing protein 6, also known as neuropathy target esterase (NTE), which is the target of toxic organophosphates that induce human paralysis due to severe axonopathy of large neurons. Mutations in PNPLA6 also cause human spastic paraplegia characterized by motor neuron degeneration. Here we identify PNPLA6 mutations in childhood blindness in seven families with retinal degeneration, including Leber congenital amaurosis and Oliver McFarlane syndrome. PNPLA6 localizes mostly at the inner segment plasma membrane in photoreceptors and mutations in Drosophila PNPLA6 lead to photoreceptor cell death. We also report that lysophosphatidylcholine and lysophosphatidic acid levels are elevated in mutant Drosophila. These findings show a role for PNPLA6 in photoreceptor survival and identify phospholipid metabolism as a potential therapeutic target for some forms of blindness.

%B Nat Commun %V 6 %P 5614 %8 2015 Jan 09 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/25574898?dopt=Abstract %R 10.1038/ncomms6614 %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 Sci Rep %D 2015 %T NGS-based Molecular diagnosis of 105 eyeGENE(®) probands with Retinitis Pigmentosa. %A Ge, Zhongqi %A Bowles, Kristen %A Goetz, Kerry %A Scholl, Hendrik P N %A Wang, Feng %A Wang, Xinjing %A Xu, Shan %A Wang, Keqing %A Wang, Hui %A Chen, Rui %K Antigens, Neoplasm %K Cell Cycle Proteins %K Child %K Child, Preschool %K Cohort Studies %K Cytoskeletal Proteins %K Female %K Genetic Association Studies %K Genetic Testing %K High-Throughput Nucleotide Sequencing %K Humans %K Inheritance Patterns %K Male %K Molecular Diagnostic Techniques %K Mutation %K Neoplasm Proteins %K Pedigree %K Phenotype %K Receptors, G-Protein-Coupled %K Receptors, Glutamate %K Retinitis Pigmentosa %X

The National Ophthalmic Disease Genotyping and Phenotyping Network (eyeGENE(®)) was established in an effort to facilitate basic and clinical research of human inherited eye disease. In order to provide high quality genetic testing to eyeGENE(®)'s enrolled patients which potentially aids clinical diagnosis and disease treatment, we carried out a pilot study and performed Next-generation sequencing (NGS) based molecular diagnosis for 105 Retinitis Pigmentosa (RP) patients randomly selected from the network. A custom capture panel was designed, which incorporated 195 known retinal disease genes, including 61 known RP genes. As a result, disease-causing mutations were identified in 52 out of 105 probands (solving rate of 49.5%). A total of 82 mutations were identified, and 48 of them were novel. Interestingly, for three probands the molecular diagnosis was inconsistent with the initial clinical diagnosis, while for five probands the molecular information suggested a different inheritance model other than that assigned by the physician. In conclusion, our study demonstrated that NGS target sequencing is efficient and sufficiently precise for molecular diagnosis of a highly heterogeneous patient cohort from eyeGENE(®).

%B Sci Rep %V 5 %P 18287 %8 2015 Dec 15 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/26667666?dopt=Abstract %R 10.1038/srep18287 %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 Sci Rep %D 2015 %T Targeted sequencing in chromosome 17q linkage region identifies familial glioma candidates in the Gliogene Consortium. %A Jalali, Ali %A Amirian, E Susan %A Bainbridge, Matthew N %A Armstrong, Georgina N %A Liu, Yanhong %A Tsavachidis, Spyros %A Jhangiani, Shalini N %A Plon, Sharon E %A Lau, Ching C %A Claus, Elizabeth B %A Barnholtz-Sloan, Jill S %A Il'yasova, Dora %A Schildkraut, Joellen %A Ali-Osman, Francis %A Sadetzki, Siegal %A Johansen, Christoffer %A Houlston, Richard S %A Jenkins, Robert B %A Lachance, Daniel %A Olson, Sara H %A Bernstein, Jonine L %A Merrell, Ryan T %A Wrensch, Margaret R %A Davis, Faith G %A Lai, Rose %A Shete, Sanjay %A Aldape, Kenneth %A Amos, Christopher I %A Muzny, Donna M %A Gibbs, Richard A %A Melin, Beatrice S %A Bondy, Melissa L %K Adult %K Brain Neoplasms %K Chromosomes, Human, Pair 17 %K Family %K Female %K Genetic Linkage %K Genetic Variation %K Glioma %K Humans %K Male %K Middle Aged %K Mutation %K Pedigree %K Sequence Analysis, DNA %K Young Adult %X

Glioma is a rare, but highly fatal, cancer that accounts for the majority of malignant primary brain tumors. Inherited predisposition to glioma has been consistently observed within non-syndromic families. Our previous studies, which involved non-parametric and parametric linkage analyses, both yielded significant linkage peaks on chromosome 17q. Here, we use data from next generation and Sanger sequencing to identify familial glioma candidate genes and variants on chromosome 17q for further investigation. We applied a filtering schema to narrow the original list of 4830 annotated variants down to 21 very rare (<0.1% frequency), non-synonymous variants. Our findings implicate the MYO19 and KIF18B genes and rare variants in SPAG9 and RUNDC1 as candidates worthy of further investigation. Burden testing and functional studies are planned.

%B Sci Rep %V 5 %P 8278 %8 2015 Feb 05 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/25652157?dopt=Abstract %R 10.1038/srep08278 %0 Journal Article %J J Transl Med %D 2015 %T Whole exome sequencing confirms the clinical diagnosis of Marfan syndrome combined with X-linked hypophosphatemia. %A Sheng, Xunlun %A Chen, Xue %A Lei, Bo %A Chen, Rui %A Wang, Hui %A Zhang, Fangxia %A Rong, Weining %A Ha, Ruoshui %A Liu, Yani %A Zhao, Feng %A Yang, Peizeng %A Zhao, Chen %K Adult %K Amino Acid Sequence %K Base Sequence %K Child %K Exome %K Familial Hypophosphatemic Rickets %K Family %K Female %K Fibrillin-1 %K Fibrillins %K Humans %K Male %K Marfan Syndrome %K Microfilament Proteins %K Molecular Sequence Data %K Mutation %K Pedigree %K PHEX Phosphate Regulating Neutral Endopeptidase %K Reproducibility of Results %K Sequence Analysis, DNA %X

BACKGROUND: To determine the genetic lesions and to modify the clinical diagnosis for a Chinese family with significant intrafamilial phenotypic diversities and unusual presentations.

METHODS: Three affected patients and the asymptomatic father were included and received comprehensive systemic examinations. Whole exome sequencing (WES) was performed for mutation detection. Structural modeling test was applied to analyze the potential structural changes caused by the missense substitution.

RESULTS: The proband showed a wide spectrum of systemic anomalies, including bilateral ectopia lentis, atrial septal defect, ventricular septal defect, widening of tibial metaphysis with medial bowing, and dolichostenomelia in digits, while her mother and elder brother only demonstrated similar skeletal changes. A recurrent mutation, PHEX p.R291*, was found in all patients, while a de novo mutation, FBN1 p.C792F, was only detected in the proband. The FBN1 substitution was also predicted to cause significant conformational change in fibrillin-1 protein, thus changing its physical and biological properties.

CONCLUSIONS: Taken together, we finalized the diagnosis for this family as X-linked hypophosphatemia (XLH), and diagnosed this girl as Marfan syndrome combined with XLH, and congenital heart disease. Our study also emphasizes the importance of WES in assisting the clinical diagnosis for complicated cases when the original diagnoses are challenged.

%B J Transl Med %V 13 %P 179 %8 2015 Jun 04 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/26040324?dopt=Abstract %R 10.1186/s12967-015-0534-9 %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 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 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 J Clin Endocrinol Metab %D 2014 %T Exome sequencing identifies a novel homozygous mutation in the phosphate transporter SLC34A1 in hypophosphatemia and nephrocalcinosis. %A Rajagopal, Abbhirami %A Braslavsky, Débora %A Lu, James T %A Kleppe, Soledad %A Clément, Florencia %A Cassinelli, Hamilton %A Liu, David S %A Liern, Jose Miguel %A Vallejo, Graciela %A Bergadá, Ignacio %A Gibbs, Richard A %A Campeau, Phillipe M %A Lee, Brendan H %K Child %K Child, Preschool %K DNA Mutational Analysis %K Exome %K Female %K Humans %K Hypercalcemia %K Hypercalciuria %K Hypophosphatemia %K Male %K Mutation %K Nephrocalcinosis %K Parathyroid Hormone %K Pedigree %K Phenotype %K Sodium-Phosphate Cotransporter Proteins, Type IIa %X

CONTEXT: Two Argentinean siblings (a boy and a girl) from a nonconsanguineous family presented with hypercalcemia, hypercalciuria, hypophosphatemia, low parathyroid hormone (PTH), and nephrocalcinosis.

OBJECTIVE: The goal of this study was to identify genetic causes of the clinical findings in the two siblings.

DESIGN: Whole exome sequencing was performed to identify disease-causing mutations in the youngest sibling, and a candidate variant was screened in other family members by Sanger sequencing. In vitro experiments were conducted to determine the effects of the mutation that was identified.

PATIENTS AND OTHER PARTICIPANTS: Affected siblings (2 y.o. female and 10 y.o male) and their parents were included in the study. Informed consent was obtained for genetic studies.

RESULTS: A novel homozygous mutation in the gene encoding the renal sodium-dependent phosphate transporter SLC34A1 was identified in both siblings (c.1484G>A, p.Arg495His). In vitro studies showed that the p.Arg495His mutation resulted in decreased phosphate uptake when compared to wild-type SLC34A1.

CONCLUSIONS: The homozygous G>A transition that results in the substitution of histidine for arginine at position 495 of the renal sodium-dependent phosphate transporter, SLC34A1, is involved in disease pathogenesis in these patients. Our report of the second family with two mutated SLC34A1 alleles expands the known phenotype of this rare condition.

%B J Clin Endocrinol Metab %V 99 %P E2451-6 %8 2014 Nov %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/25050900?dopt=Abstract %R 10.1210/jc.2014-1517 %0 Journal Article %J Neuro Oncol %D 2014 %T Germline rearrangements in families with strong family history of glioma and malignant melanoma, colon, and breast cancer. %A Andersson, Ulrika %A Wibom, Carl %A Cederquist, Kristina %A Aradottir, Steina %A Borg, Ake %A Armstrong, Georgina N %A Shete, Sanjay %A Lau, Ching C %A Bainbridge, Matthew N %A Claus, Elizabeth B %A Barnholtz-Sloan, Jill %A Lai, Rose %A Il'yasova, Dora %A Houlston, Richard S %A Schildkraut, Joellen %A Bernstein, Jonine L %A Olson, Sara H %A Jenkins, Robert B %A Lachance, Daniel H %A Wrensch, Margaret %A Davis, Faith G %A Merrell, Ryan %A Johansen, Christoffer %A Sadetzki, Siegal %A Bondy, Melissa L %A Melin, Beatrice S %K Adaptor Proteins, Signal Transducing %K Adult %K Brain Neoplasms %K Breast Neoplasms %K Checkpoint Kinase 2 %K Child, Preschool %K Colonic Neoplasms %K Cyclin-Dependent Kinase Inhibitor p15 %K Cyclin-Dependent Kinase Inhibitor p16 %K Female %K Genetic Predisposition to Disease %K Germ-Line Mutation %K Glioma %K Humans %K Male %K Melanoma %K Middle Aged %K MutL Protein Homolog 1 %K MutS Homolog 2 Protein %K Nuclear Proteins %K Pedigree %K Tumor Suppressor Protein p53 %K Young Adult %X

BACKGROUND: Although familial susceptibility to glioma is known, the genetic basis for this susceptibility remains unidentified in the majority of glioma-specific families. An alternative approach to identifying such genes is to examine cancer pedigrees, which include glioma as one of several cancer phenotypes, to determine whether common chromosomal modifications might account for the familial aggregation of glioma and other cancers.

METHODS: Germline rearrangements in 146 glioma families (from the Gliogene Consortium; http://www.gliogene.org/) were examined using multiplex ligation-dependent probe amplification. These families all had at least 2 verified glioma cases and a third reported or verified glioma case in the same family or 2 glioma cases in the family with at least one family member affected with melanoma, colon, or breast cancer.The genomic areas covering TP53, CDKN2A, MLH1, and MSH2 were selected because these genes have been previously reported to be associated with cancer pedigrees known to include glioma.

RESULTS: We detected a single structural rearrangement, a deletion of exons 1-6 in MSH2, in the proband of one family with 3 cases with glioma and one relative with colon cancer.

CONCLUSIONS: Large deletions and duplications are rare events in familial glioma cases, even in families with a strong family history of cancers that may be involved in known cancer syndromes.

%B Neuro Oncol %V 16 %P 1333-40 %8 2014 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/24723567?dopt=Abstract %R 10.1093/neuonc/nou052 %0 Journal Article %J Invest Ophthalmol Vis Sci %D 2014 %T A homozygous missense mutation in NEUROD1 is associated with nonsyndromic autosomal recessive retinitis pigmentosa. %A Wang, Feng %A Li, Huajin %A Xu, Mingchu %A Li, Hui %A Zhao, Li %A Yang, Lizhu %A Zaneveld, Jacques E %A Wang, Keqing %A Li, Yumei %A Sui, Ruifang %A Chen, Rui %K Adult %K Basic Helix-Loop-Helix Transcription Factors %K DNA %K DNA Mutational Analysis %K Female %K Genes, Recessive %K Homozygote %K Humans %K Male %K Mutation, Missense %K Pedigree %K Phenotype %K Retinitis Pigmentosa %X

PURPOSE: Mutations in the same gene can lead to different clinical phenotypes. In this study, we aim to identify novel genotype-phenotype correlations and novel disease genes by analyzing an unsolved autosomal recessive retinitis pigmentosa (ARRP) Han Chinese family.

METHODS: Whole exome sequencing was performed for one proband from the consanguineous ARRP family. Stringent variants filtering and prioritizations were applied to identify the causative mutation.

RESULTS: A homozygous missense variant, c.724G>A; p.V242I, in NEUROD1 was identified as the most likely cause of disease. This allele perfectly segregates in the family and affects an amino acid, which is highly conserved among mammals. A previous study showed that a homozygous null allele in NEUROD1 causes severe syndromic disease with neonatal diabetes, systematic neurological abnormalities, and early-onset retinal dystrophy. Consistent with these results, our patients who are homozygous for a less severe missense allele presented only late-onset retinal degeneration without any syndromic symptoms.

CONCLUSIONS: We identified a potential novel genotype-phenotype correlation between NEUROD1 and nonsyndromic ARRP. Our study supports the idea that NEUROD1 is important for maintenance of the retina function and partial loss-of-function mutation in NEUROD1 is likely a rare cause of nonsyndromic ARRP.

%B Invest Ophthalmol Vis Sci %V 56 %P 150-5 %8 2014 Dec 04 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/25477324?dopt=Abstract %R 10.1167/iovs.14-15382 %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 Invest Ophthalmol Vis Sci %D 2014 %T A missense mutation in HK1 leads to autosomal dominant retinitis pigmentosa. %A Wang, Feng %A Wang, Yandong %A Zhang, Bin %A Zhao, Li %A Lyubasyuk, Vera %A Wang, Keqing %A Xu, Mingchu %A Li, Yumei %A Wu, Frances %A Wen, Cindy %A Bernstein, Paul S %A Lin, Danni %A Zhu, Susanna %A Wang, Hui %A Zhang, Kang %A Chen, Rui %K Adolescent %K Child %K Child, Preschool %K DNA %K DNA Mutational Analysis %K Female %K Genes, Dominant %K Genetic Linkage %K Genetic Predisposition to Disease %K Heterozygote %K Hexokinase %K Humans %K Male %K Mutation, Missense %K Pedigree %K Phenotype %K Retinitis Pigmentosa %K Young Adult %X

PURPOSE: Retinitis pigmentosa (RP) is a genetically heterogeneous disease with over 60 causative genes known to date. Nevertheless, approximately 40% of RP cases remain genetically unsolved, suggesting that many novel disease-causing genes are yet to be identified. In this study, we aimed to identify the causative mutation for a large autosomal dominant RP (adRP) family with negative results from known retinal disease gene screening.

METHODS: Linkage analysis followed by whole-exome sequencing was performed. Stringent variant filtering and prioritization was carried out to identify the causative mutation.

RESULTS: Linkage analysis identified a minimal disease region of 8 Mb on chromosome 10 with a peak parametric logarithm (base 10) of odds (LOD) score of 3.500. Further whole-exome sequencing identified a heterozygous missense mutation (NM_000188.2:c.2539G>A, p.E847K) in hexokinase 1 (HK1) that segregated with the disease phenotype in the family. Biochemical assays showed that the E847K mutation does not affect hexokinase enzymatic activity or the protein stability, suggesting that the mutation may impact other uncharacterized function or result in a gain of function of HK1.

CONCLUSIONS: Here, we identified HK1 as a novel causative gene for adRP. This is the first report that associates the glucose metabolic pathway with human retinal degenerative disease, suggesting a potential new disease mechanism.

%B Invest Ophthalmol Vis Sci %V 55 %P 7159-64 %8 2014 Oct 14 %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/25316723?dopt=Abstract %R 10.1167/iovs.14-15520 %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 Genet Med %D 2014 %T Mutations in NGLY1 cause an inherited disorder of the endoplasmic reticulum-associated degradation pathway. %A Enns, Gregory M %A Shashi, Vandana %A Bainbridge, Matthew %A Gambello, Michael J %A Zahir, Farah R %A Bast, Thomas %A Crimian, Rebecca %A Schoch, Kelly %A Platt, Julia %A Cox, Rachel %A Bernstein, Jonathan A %A Scavina, Mena %A Walter, Rhonda S %A Bibb, Audrey %A Jones, Melanie %A Hegde, Madhuri %A Graham, Brett H %A Need, Anna C %A Oviedo, Angelica %A Schaaf, Christian P %A Boyle, Sean %A Butte, Atul J %A Chen, Rui %A Chen, Rong %A Clark, Michael J %A Haraksingh, Rajini %A Cowan, Tina M %A He, Ping %A Langlois, Sylvie %A Zoghbi, Huda Y %A Snyder, Michael %A Gibbs, Richard A %A Freeze, Hudson H %A Goldstein, David B %K Abnormalities, Multiple %K Adolescent %K Child, Preschool %K Developmental Disabilities %K Endoplasmic Reticulum-Associated Degradation %K Exome %K Family Health %K Fatal Outcome %K Female %K Genome-Wide Association Study %K Humans %K Infant %K Male %K Microcephaly %K Movement Disorders %K Muscle Hypotonia %K Mutation %K Pedigree %K Peptide-N4-(N-acetyl-beta-glucosaminyl) Asparagine Amidase %K Retrospective Studies %K Seizures %K Sequence Analysis, DNA %K Signal Transduction %K Young Adult %X

PURPOSE: The endoplasmic reticulum-associated degradation pathway is responsible for the translocation of misfolded proteins across the endoplasmic reticulum membrane into the cytosol for subsequent degradation by the proteasome. To define the phenotype associated with a novel inherited disorder of cytosolic endoplasmic reticulum-associated degradation pathway dysfunction, we studied a series of eight patients with deficiency of N-glycanase 1.

METHODS: Whole-genome, whole-exome, or standard Sanger sequencing techniques were employed. Retrospective chart reviews were performed in order to obtain clinical data.

RESULTS: All patients had global developmental delay, a movement disorder, and hypotonia. Other common findings included hypolacrima or alacrima (7/8), elevated liver transaminases (6/7), microcephaly (6/8), diminished reflexes (6/8), hepatocyte cytoplasmic storage material or vacuolization (5/6), and seizures (4/8). The nonsense mutation c.1201A>T (p.R401X) was the most common deleterious allele.

CONCLUSION: NGLY1 deficiency is a novel autosomal recessive disorder of the endoplasmic reticulum-associated degradation pathway associated with neurological dysfunction, abnormal tear production, and liver disease. The majority of patients detected to date carry a specific nonsense mutation that appears to be associated with severe disease. The phenotypic spectrum is likely to enlarge as cases with a broader range of mutations are detected.

%B Genet Med %V 16 %P 751-8 %8 2014 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/24651605?dopt=Abstract %R 10.1038/gim.2014.22 %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 Hum Genet %D 2014 %T Next generation sequencing-based molecular diagnosis of retinitis pigmentosa: identification of a novel genotype-phenotype correlation and clinical refinements. %A Wang, Feng %A Wang, Hui %A Tuan, Han-Fang %A Nguyen, Duy H %A Sun, Vincent %A Keser, Vafa %A Bowne, Sara J %A Sullivan, Lori S %A Luo, Hongrong %A Zhao, Ling %A Wang, Xia %A Zaneveld, Jacques E %A Salvo, Jason S %A Siddiqui, Sorath %A Mao, Louise %A Wheaton, Dianna K %A Birch, David G %A Branham, Kari E %A Heckenlively, John R %A Wen, Cindy %A Flagg, Ken %A Ferreyra, Henry %A Pei, Jacqueline %A Khan, Ayesha %A Ren, Huanan %A Wang, Keqing %A Lopez, Irma %A Qamar, Raheel %A Zenteno, Juan C %A Ayala-Ramirez, Raul %A Buentello-Volante, Beatriz %A Fu, Qing %A Simpson, David A %A Li, Yumei %A Sui, Ruifang %A Silvestri, Giuliana %A Daiger, Stephen P %A Koenekoop, Robert K %A Zhang, Kang %A Chen, Rui %K Alleles %K Computational Biology %K Exons %K Genes, Recessive %K Genetic Association Studies %K Genetic Testing %K Genotype %K High-Throughput Nucleotide Sequencing %K Humans %K Membrane Glycoproteins %K Molecular Chaperones %K Mutation %K Pedigree %K Phenotype %K Polymorphism, Single Nucleotide %K Reproducibility of Results %K Retinitis Pigmentosa %K Sequence Analysis, DNA %X

Retinitis pigmentosa (RP) is a devastating form of retinal degeneration, with significant social and professional consequences. Molecular genetic information is invaluable for an accurate clinical diagnosis of RP due to its high genetic and clinical heterogeneity. Using a gene capture panel that covers 163 of the currently known retinal disease genes, including 48 RP genes, we performed a comprehensive molecular screening in a collection of 123 RP unsettled probands from a wide variety of ethnic backgrounds, including 113 unrelated simplex and 10 autosomal recessive RP (arRP) cases. As a result, 61 mutations were identified in 45 probands, including 38 novel pathogenic alleles. Interestingly, we observed that phenotype and genotype were not in full agreement in 21 probands. Among them, eight probands were clinically reassessed, resulting in refinement of clinical diagnoses for six of these patients. Finally, recessive mutations in CLN3 were identified in five retinal degeneration patients, including four RP probands and one cone-rod dystrophy patient, suggesting that CLN3 is a novel non-syndromic retinal disease gene. Collectively, our results underscore that, due to the high molecular and clinical heterogeneity of RP, comprehensive screening of all retinal disease genes is effective in identifying novel pathogenic mutations and provides an opportunity to discover new genotype-phenotype correlations. Information gained from this genetic screening will directly aid in patient diagnosis, prognosis, and treatment, as well as allowing appropriate family planning and counseling.

%B Hum Genet %V 133 %P 331-45 %8 2014 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/24154662?dopt=Abstract %R 10.1007/s00439-013-1381-5 %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 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 J Med Genet %D 2013 %T Comprehensive molecular diagnosis of 179 Leber congenital amaurosis and juvenile retinitis pigmentosa patients by targeted next generation sequencing. %A Wang, Xia %A Wang, Hui %A Sun, Vincent %A Tuan, Han-Fang %A Keser, Vafa %A Wang, Keqing %A Ren, Huanan %A Lopez, Irma %A Zaneveld, Jacques E %A Siddiqui, Sorath %A Bowles, Stephanie %A Khan, Ayesha %A Salvo, Jason %A Jacobson, Samuel G %A Iannaccone, Alessandro %A Wang, Feng %A Birch, David %A Heckenlively, John R %A Fishman, Gerald A %A Traboulsi, Elias I %A Li, Yumei %A Wheaton, Dianna %A Koenekoop, Robert K %A Chen, Rui %K Alleles %K Amino Acid Sequence %K Base Sequence %K Exome %K Female %K Genotype %K High-Throughput Nucleotide Sequencing %K Humans %K Leber Congenital Amaurosis %K Mutation %K Pedigree %K Polymorphism, Single Nucleotide %K Reproducibility of Results %K Retinitis Pigmentosa %K Sensitivity and Specificity %X

BACKGROUND: Leber congenital amaurosis (LCA) and juvenile retinitis pigmentosa (RP) are inherited retinal diseases that cause early onset severe visual impairment. An accurate molecular diagnosis can refine the clinical diagnosis and allow gene specific treatments.

METHODS: We developed a capture panel that enriches the exonic DNA of 163 known retinal disease genes. Using this panel, we performed targeted next generation sequencing (NGS) for a large cohort of 179 unrelated and prescreened patients with the clinical diagnosis of LCA or juvenile RP. Systematic NGS data analysis, Sanger sequencing validation, and segregation analysis were utilised to identify the pathogenic mutations. Patients were revisited to examine the potential phenotypic ambiguity at the time of initial diagnosis.

RESULTS: Pathogenic mutations for 72 patients (40%) were identified, including 45 novel mutations. Of these 72 patients, 58 carried mutations in known LCA or juvenile RP genes and exhibited corresponding phenotypes, while 14 carried mutations in retinal disease genes that were not consistent with their initial clinical diagnosis. We revisited patients in the latter case and found that homozygous mutations in PRPH2 can cause LCA/juvenile RP. Guided by the molecular diagnosis, we reclassified the clinical diagnosis in two patients.

CONCLUSIONS: We have identified a novel gene and a large number of novel mutations that are associated with LCA/juvenile RP. Our results highlight the importance of molecular diagnosis as an integral part of clinical diagnosis.

%B J Med Genet %V 50 %P 674-88 %8 2013 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/23847139?dopt=Abstract %R 10.1136/jmedgenet-2013-101558 %0 Journal Article %J BMC Med Genet %D 2013 %T Exome sequencing of a patient with suspected mitochondrial disease reveals a likely multigenic etiology. %A Craigen, William J %A Graham, Brett H %A Wong, Lee-Jun %A Scaglia, Fernando %A Lewis, Richard Alan %A Bonnen, Penelope E %K Adult %K Computational Biology %K DNA Helicases %K Exome %K Genetic Diseases, X-Linked %K Genetic Loci %K Homozygote %K Humans %K Male %K Mitochondrial Diseases %K Multifunctional Enzymes %K Mutation, Missense %K Nephrolithiasis %K Oculocerebrorenal Syndrome %K Pedigree %K Phenotype %K Phosphoric Monoester Hydrolases %K RNA Helicases %K RNA, Ribosomal, 16S %K Sequence Analysis, DNA %K Spinocerebellar Ataxias %K Spinocerebellar Degenerations %X

BACKGROUND: The clinical features of mitochondrial disease are complex and highly variable, leading to challenges in establishing a specific diagnosis. Despite being one of the most commonly occurring inherited genetic diseases with an incidence of 1/5000, ~90% of these complex patients remain without a DNA-based diagnosis. We report our efforts to identify the pathogenetic cause for a patient with typical features of mitochondrial disease including infantile cataracts, CPEO, ptosis, progressive distal muscle weakness, and ataxia who carried a diagnosis of mitochondrial disease for over a decade.

METHODS: Whole exome sequencing and bioinformatic analysis of these data were conducted on the proband.

RESULTS: Exome sequencing studies showed a homozygous splice site mutation in SETX, which is known to cause Spinocerebellar Ataxia, Autosomal Recessive 1 (SCAR1). Additionally a missense mutation was identified in a highly conserved position of the OCRL gene, which causes Lowe Syndrome and Dent Disease 2.

CONCLUSIONS: This patient's complex phenotype reflects a complex genetic etiology in which no single gene explained the complete clinical presentation. These genetic studies reveal that this patient does not have mitochondrial disease but rather a genocopy caused by more than one mutant locus. This study demonstrates the benefit of exome sequencing in providing molecular diagnosis to individuals with complex clinical presentations.

%B BMC Med Genet %V 14 %P 83 %8 2013 Aug 16 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/23947751?dopt=Abstract %R 10.1186/1471-2350-14-83 %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 Pediatr Blood Cancer %D 2013 %T Identification of TP53 as an acute lymphocytic leukemia susceptibility gene through exome sequencing. %A Powell, Bradford C %A Jiang, Lichun %A Muzny, Donna M %A Treviño, Lisa R %A Dreyer, Zoann E %A Strong, Louise C %A Wheeler, David A %A Gibbs, Richard A %A Plon, Sharon E %K Exome %K Female %K Genetic Predisposition to Disease %K Humans %K Male %K Pedigree %K Precursor Cell Lymphoblastic Leukemia-Lymphoma %K Tumor Suppressor Protein p53 %X

Although acute lymphocytic leukemia (ALL) is the most common childhood cancer, genetic predisposition to ALL remains poorly understood. Whole-exome sequencing was performed in an extended kindred in which five individuals had been diagnosed with leukemia. Analysis revealed a nonsense variant of TP53 which has been previously reported in families with sarcomas and other typical Li Fraumeni syndrome-associated cancers but never in a familial leukemia kindred. This unexpected finding enabled identification of an appropriate sibling bone marrow donor and illustrates that exome sequencing will reveal atypical clinical presentations of even well-studied genes.

%B Pediatr Blood Cancer %V 60 %P E1-3 %8 2013 Jun %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/23255406?dopt=Abstract %R 10.1002/pbc.24417 %0 Journal Article %J Am J Hum Genet %D 2013 %T Mutations in FBXL4 cause mitochondrial encephalopathy and a disorder of mitochondrial DNA maintenance. %A Bonnen, Penelope E %A Yarham, John W %A Besse, Arnaud %A Wu, Ping %A Faqeih, Eissa A %A Al-Asmari, Ali Mohammad %A Saleh, Mohammad A M %A Eyaid, Wafaa %A Hadeel, Alrukban %A He, Langping %A Smith, Frances %A Yau, Shu %A Simcox, Eve M %A Miwa, Satomi %A Donti, Taraka %A Abu-Amero, Khaled K %A Wong, Lee-Jun %A Craigen, William J %A Graham, Brett H %A Scott, Kenneth L %A McFarland, Robert %A Taylor, Robert W %K Acidosis, Lactic %K Base Sequence %K Child %K Child, Preschool %K Chromosome Segregation %K DNA, Mitochondrial %K Electron Transport %K F-Box Proteins %K Female %K Fibroblasts %K Gene Dosage %K Genes, Recessive %K Genetic Predisposition to Disease %K Humans %K Infant %K Infant, Newborn %K Male %K Mitochondrial Encephalomyopathies %K Molecular Sequence Data %K Muscle, Skeletal %K Mutation %K Oxidative Phosphorylation %K Pedigree %K Protein Transport %K Ubiquitin-Protein Ligases %X

Nuclear genetic disorders causing mitochondrial DNA (mtDNA) depletion are clinically and genetically heterogeneous, and the molecular etiology remains undiagnosed in the majority of cases. Through whole-exome sequencing, we identified recessive nonsense and splicing mutations in FBXL4 segregating in three unrelated consanguineous kindreds in which affected children present with a fatal encephalopathy, lactic acidosis, and severe mtDNA depletion in muscle. We show that FBXL4 is an F-box protein that colocalizes with mitochondria and that loss-of-function and splice mutations in this protein result in a severe respiratory chain deficiency, loss of mitochondrial membrane potential, and a disturbance of the dynamic mitochondrial network and nucleoid distribution in fibroblasts from affected individuals. Expression of the wild-type FBXL4 transcript in cell lines from two subjects fully rescued the levels of mtDNA copy number, leading to a correction of the mitochondrial biochemical deficit. Together our data demonstrate that mutations in FBXL4 are disease causing and establish FBXL4 as a mitochondrial protein with a possible role in maintaining mtDNA integrity and stability.

%B Am J Hum Genet %V 93 %P 471-81 %8 2013 Sep 05 %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/23993193?dopt=Abstract %R 10.1016/j.ajhg.2013.07.017 %0 Journal Article %J Am J Hum Genet %D 2013 %T Mutations in KCTD1 cause scalp-ear-nipple syndrome. %A Marneros, Alexander G %A Beck, Anita E %A Turner, Emily H %A McMillin, Margaret J %A Edwards, Matthew J %A Field, Michael %A de Macena Sobreira, Nara Lygia %A Perez, Ana Beatriz A %A Fortes, Jose A R %A Lampe, Anne K %A Giovannucci Uzielli, Maria Luisa %A Gordon, Christopher T %A Plessis, Ghislaine %A Le Merrer, Martine %A Amiel, Jeanne %A Reichenberger, Ernst %A Shively, Kathryn M %A Cerrato, Felecia %A Labow, Brian I %A Tabor, Holly K %A Smith, Joshua D %A Shendure, Jay %A Nickerson, Deborah A %A Bamshad, Michael J %K Abnormalities, Multiple %K Amino Acid Sequence %K Branchio-Oto-Renal Syndrome %K Co-Repressor Proteins %K Ear, External %K Ectodermal Dysplasia %K Exome %K Female %K Humans %K Hypospadias %K Male %K Molecular Sequence Data %K Muscle Hypotonia %K Mutation, Missense %K Nipples %K Pedigree %K Phenotype %K Protein Structure, Tertiary %K Repressor Proteins %K Scalp %K Sequence Homology, Amino Acid %X

Scalp-ear-nipple (SEN) syndrome is a rare, autosomal-dominant disorder characterized by cutis aplasia of the scalp; minor anomalies of the external ears, digits, and nails; and malformations of the breast. We used linkage analysis and exome sequencing of a multiplex family affected by SEN syndrome to identify potassium-channel tetramerization-domain-containing 1 (KCTD1) mutations that cause SEN syndrome. Evaluation of a total of ten families affected by SEN syndrome revealed KCTD1 missense mutations in each family tested. All of the mutations occurred in a KCTD1 region encoding a highly conserved bric-a-brac, tram track, and broad complex (BTB) domain that is required for transcriptional repressor activity. KCTD1 inhibits the transactivation of the transcription factor AP-2α (TFAP2A) via its BTB domain, and mutations in TFAP2A cause cutis aplasia in individuals with branchiooculofacial syndrome (BOFS), suggesting a potential overlap in the pathogenesis of SEN syndrome and BOFS. The identification of KCTD1 mutations in SEN syndrome reveals a role for this BTB-domain-containing transcriptional repressor during ectodermal development.

%B Am J Hum Genet %V 92 %P 621-6 %8 2013 Apr 04 %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/23541344?dopt=Abstract %R 10.1016/j.ajhg.2013.03.002 %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 PLoS One %D 2013 %T Union makes strength: a worldwide collaborative genetic and clinical study to provide a comprehensive survey of RD3 mutations and delineate the associated phenotype. %A Perrault, Isabelle %A Estrada-Cuzcano, Alejandro %A Lopez, Irma %A Kohl, Susanne %A Li, Shiqiang %A Testa, Francesco %A Zekveld-Vroon, Renate %A Wang, Xia %A Pomares, Esther %A Andorf, Jean %A Aboussair, Nisrine %A Banfi, Sandro %A Delphin, Nathalie %A den Hollander, Anneke I %A Edelson, Catherine %A Florijn, Ralph %A Jean-Pierre, Marc %A Leowski, Corinne %A Megarbane, Andre %A Villanueva, Cristina %A Flores, Blanca %A Munnich, Arnold %A Ren, Huanan %A Zobor, Ditta %A Bergen, Arthur %A Chen, Rui %A Cremers, Frans P M %A Gonzalez-Duarte, Roser %A Koenekoop, Robert K %A Simonelli, Francesca %A Stone, Edwin %A Wissinger, Bernd %A Zhang, Qingjiong %A Kaplan, Josseline %A Rozet, Jean-Michel %K Adolescent %K Adult %K Canada %K Child %K Child, Preschool %K China %K Cohort Studies %K Europe %K Eye Proteins %K Female %K Humans %K Infant %K Leber Congenital Amaurosis %K Linkage Disequilibrium %K Male %K Mutation %K Pedigree %K Phenotype %K Polymorphism, Genetic %K Retina %K Retinal Degeneration %K United States %K Young Adult %X

Leber congenital amaurosis (LCA) is the earliest and most severe retinal degeneration (RD), and the most common cause of incurable blindness diagnosed in children. It is occasionally the presenting symptom of multisystemic ciliopathies which diagnosis will require a specific care of patients. Nineteen LCA genes are currently identified and three of them account for both non-syndromic and syndromic forms of the disease. RD3 (LCA12) was implicated as a LCA gene based on the identification of homozygous truncating mutations in two LCA families despite the screening of large cohorts of patients. Here we provide a comprehensive survey of RD3 mutations and of their clinical expression through the screening of a cohort of 852 patients originating worldwide affected with LCA or early-onset and severe RD. We identified three RD3 mutations in seven unrelated consanguineous LCA families - i.e., a 2 bp deletion and two nonsense mutations - predicted to cause complete loss of function. Five families originating from the Southern Shores of the Mediterranean segregated a similar mutation (c.112C>T, p.R38*) suggesting that this change may have resulted from an ancient founder effect. Considering the low frequency of RD3 carriers, the recurrence risk for LCA in non-consanguineous unions is negligible for both heterozygote and homozygote RD3 individuals. The LCA12 phenotype in our patients is highly similar to those of patients with mutant photoreceptor-specific guanylate cyclase (GUCY2D/LCA1). This observation is consistent with the report of the role of RD3 in trafficking of GUCYs and gives further support to a common mechanism of photoreceptor degeneration in LCA12 and LCA1, i.e., inability to increase cytoplasmic cGMP concentration in outer segments and thus to recover the dark-state. Similar to LCA1, LCA12 patients have no extraocular symptoms despite complete inactivation of both RD3 alleles, supporting the view that extraocular investigations in LCA infants with RD3 mutations should be avoided.

%B PLoS One %V 8 %P e51622 %8 2013 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/23308101?dopt=Abstract %R 10.1371/journal.pone.0051622 %0 Journal Article %J Nat Genet %D 2012 %T Loss-of-function mutations in TGFB2 cause a syndromic presentation of thoracic aortic aneurysm. %A Lindsay, Mark E %A Schepers, Dorien %A Bolar, Nikhita Ajit %A Doyle, Jefferson J %A Gallo, Elena %A Fert-Bober, Justyna %A Kempers, Marlies J E %A Fishman, Elliot K %A Chen, Yichun %A Myers, Loretha %A Bjeda, Djahita %A Oswald, Gretchen %A Elias, Abdallah F %A Levy, Howard P %A Anderlid, Britt-Marie %A Yang, Margaret H %A Bongers, Ernie M H F %A Timmermans, Janneke %A Braverman, Alan C %A Canham, Natalie %A Mortier, Geert R %A Brunner, Han G %A Byers, Peter H %A Van Eyk, Jennifer %A Van Laer, Lut %A Dietz, Harry C %A Loeys, Bart L %K Animals %K Aortic Aneurysm, Thoracic %K Disease Models, Animal %K Female %K Fibrillin-1 %K Fibrillins %K Haploinsufficiency %K Humans %K Loeys-Dietz Syndrome %K Male %K Marfan Syndrome %K Mice %K Mice, Knockout %K Mice, Mutant Strains %K Microfilament Proteins %K Mutation %K Pedigree %K Phenotype %K Signal Transduction %K Syndrome %K Transforming Growth Factor beta2 %X

Loeys-Dietz syndrome (LDS) associates with a tissue signature for high transforming growth factor (TGF)-β signaling but is often caused by heterozygous mutations in genes encoding positive effectors of TGF-β signaling, including either subunit of the TGF-β receptor or SMAD3, thereby engendering controversy regarding the mechanism of disease. Here, we report heterozygous mutations or deletions in the gene encoding the TGF-β2 ligand for a phenotype within the LDS spectrum and show upregulation of TGF-β signaling in aortic tissue from affected individuals. Furthermore, haploinsufficient Tgfb2(+/-) mice have aortic root aneurysm and biochemical evidence of increased canonical and noncanonical TGF-β signaling. Mice that harbor both a mutant Marfan syndrome (MFS) allele (Fbn1(C1039G/+)) and Tgfb2 haploinsufficiency show increased TGF-β signaling and phenotypic worsening in association with normalization of TGF-β2 expression and high expression of TGF-β1. Taken together, these data support the hypothesis that compensatory autocrine and/or paracrine events contribute to the pathogenesis of TGF-β-mediated vasculopathies.

%B Nat Genet %V 44 %P 922-7 %8 2012 Jul 08 %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/22772368?dopt=Abstract %R 10.1038/ng.2349 %0 Journal Article %J Am J Med Genet A %D 2012 %T WDR35 mutation in siblings with Sensenbrenner syndrome: a ciliopathy with variable phenotype. %A Bacino, Carlos A %A Dhar, Shweta U %A Brunetti-Pierri, Nicola %A Lee, Brendan %A Bonnen, Penelope E %K Amino Acid Sequence %K Base Sequence %K Bone and Bones %K Craniosynostoses %K Cytoskeletal Proteins %K Ectodermal Dysplasia %K Exome %K Female %K Hedgehog Proteins %K Homozygote %K Humans %K Infant %K Intracellular Signaling Peptides and Proteins %K Male %K Mutation %K Mutation, Missense %K Pedigree %K Phenotype %K Proteins %K Siblings %X

Sensenbrenner syndrome and unclassified short rib-polydactyly conditions are ciliopathies with overlapping phenotypes and genetic heterogeneity. Mutations in WDR35 were identified recently in a sub-group of patients with Sensenbrenner syndrome and in a single family that presented with an unclassified form of short-rib polydactyly (SRP) syndrome. We report on siblings with an unusual combination of phenotypes: narrow thorax, short stature, minor anomalies, developmental delay, and severe hepatic fibrosis leading to liver failure and early death in two of the children. Both parents were unaffected suggesting autosomal recessive inheritance. The family and their affected children were followed over a decade. Exome sequencing was performed in one affected individual. It showed a homozygous missense mutation in a highly conserved position of the WDR35 gene. This family represents a WDR35-ciliopathy with a complex clinical presentation that includes significant overlap of the phenotypes described in Sensenbrenner syndrome and the unclassified SRPs. The accurate molecular diagnosis of this family exemplifies the power of exome sequencing in the diagnosis of Mendelian disorders and enabled us to broaden and refine our understanding of Sensenbrenner syndrome and SRP. Detailed genotype-phenotype information is provided as well as discussion of previously reported cases.

%B Am J Med Genet A %V 158A %P 2917-24 %8 2012 Nov %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/22987818?dopt=Abstract %R 10.1002/ajmg.a.35608 %0 Journal Article %J Am J Med Genet A %D 2012 %T WDR62 missense mutation in a consanguineous family with primary microcephaly. %A Bacino, Carlos A %A Arriola, Luis A %A Wiszniewska, Joanna %A Bonnen, Penelope E %K Cell Cycle Proteins %K Consanguinity %K Female %K Homozygote %K Humans %K Infant %K Male %K Microcephaly %K Mutation, Missense %K Nerve Tissue Proteins %K Pedigree %K Polymorphism, Single Nucleotide %X

We report on a consanguineous couple with two affected sons who presented with primary microcephaly and moderate to severe intellectual disabilities. A SNP array uncovered two overlapping regions of copy-neutral absence of heterozygosity (AOH) in both sibs. This led to sequencing of WDR62, a gene that codes for a spindle pole protein recently identified as a cause of primary microcephaly. A homozygous missense mutation in WDR62, p.E400K, was found in both boys and segregated with the condition in this family. WDR62 is one of seven genes responsible for autosomal recessive primary microcephaly (MCPH), and appears to be one of the most frequently involved in MCPH following ASPM. Studies of ASPM and WDR62 should perhaps be pursued in all cases of primary microcephaly with or without gross brain malformations.

%B Am J Med Genet A %V 158A %P 622-5 %8 2012 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/22308068?dopt=Abstract %R 10.1002/ajmg.a.34417 %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 Circ Cardiovasc Genet %D 2011 %T Familial thoracic aortic aneurysms and dissections: identification of a novel locus for stable aneurysms with a low risk for progression to aortic dissection. %A Guo, Dong-chuan %A Regalado, Ellen S %A Minn, Charles %A Tran-Fadulu, Van %A Coney, Joshua %A Cao, Jiumei %A Wang, Min %A Yu, Robert K %A Estrera, Anthony L %A Safi, Hazim J %A Shete, Sanjay S %A Milewicz, Dianna M %K Adult %K Aged %K Aged, 80 and over %K Aorta %K Aortic Aneurysm, Thoracic %K Aortic Dissection %K Chromosomes, Human, Pair 12 %K Disease Progression %K Family %K Female %K Genetic Association Studies %K Genetic Loci %K Genetic Predisposition to Disease %K Genome, Human %K Haplotypes %K Humans %K Lod Score %K Male %K Middle Aged %K Pedigree %K Risk Factors %K Sequence Analysis, DNA %X

BACKGROUND: Thoracic aortic aneurysms leading to acute aortic dissections are the major diseases that affect the thoracic aorta. Approximately 20% of patients with thoracic aortic aneurysms and dissections (TAAD) have a family history of TAAD, and these patients present younger with more rapidly enlarging aneurysms than patients without a family history of aortic disease.

METHODS AND RESULTS: A large family with multiple members with TAAD inherited in an autosomal-dominant manner was identified. The ascending aortic aneurysms were associated with slow enlargement, a low risk of dissection, and decreased penetrance in women. Genome-wide linkage analysis was performed, and a novel locus on chromosome 12 was identified for the mutant gene causing disease in this family. Of the 12 male members who carry the disease-linked microsatellite haplotype, 9 had ascending aortic aneurysms with an average diameter of 4.7 cm at an average age of 52.4 years (range, 32 to 76 years) at the time of diagnosis; only 1 individual had progressed to acute aortic dissection, and no other members with aortic dissections were identified. Women harboring the disease-linked haplotype did not have thoracic aortic disease, including 1 aged 84 years. Sequencing of 9 genes within the critical interval at the chromosome 12 locus did not identify the mutant gene.

CONCLUSIONS: Mapping a locus for ascending thoracic aortic aneurysms associated with a low risk of aortic dissection supports our hypothesis that genes leading to familial disease can be associated with less-aggressive thoracic aortic disease.

%B Circ Cardiovasc Genet %V 4 %P 36-42 %8 2011 Feb %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/21163914?dopt=Abstract %R 10.1161/CIRCGENETICS.110.958066 %0 Journal Article %J Cancer Res %D 2011 %T Genome-wide high-density SNP linkage search for glioma susceptibility loci: results from the Gliogene Consortium. %A Shete, Sanjay %A Lau, Ching C %A Houlston, Richard S %A Claus, Elizabeth B %A Barnholtz-Sloan, Jill %A Lai, Rose %A Il'yasova, Dora %A Schildkraut, Joellen %A Sadetzki, Siegal %A Johansen, Christoffer %A Bernstein, Jonine L %A Olson, Sara H %A Jenkins, Robert B %A Yang, Ping %A Vick, Nicholas A %A Wrensch, Margaret %A Davis, Faith G %A McCarthy, Bridget J %A Leung, Eastwood Hon-chiu %A Davis, Caleb %A Cheng, Rita %A Hosking, Fay J %A Armstrong, Georgina N %A Liu, Yanhong %A Yu, Robert K %A Henriksson, Roger %A Melin, Beatrice S %A Bondy, Melissa L %K Adolescent %K Adult %K Aged %K Brain Neoplasms %K Child %K Chromosome Mapping %K Family Health %K Female %K Genetic Heterogeneity %K Genetic Predisposition to Disease %K Genome, Human %K Genome-Wide Association Study %K Genotype %K Glioma %K Humans %K Linkage Disequilibrium %K Lod Score %K Male %K Middle Aged %K Pedigree %K Polymorphism, Single Nucleotide %K United States %K Young Adult %X

Gliomas, which generally have a poor prognosis, are the most common primary malignant brain tumors in adults. Recent genome-wide association studies have shown that inherited susceptibility plays a role in the development of glioma. Although first-degree relatives of patients exhibit a two-fold increased risk of glioma, the search for susceptibility loci in familial forms of the disease has been challenging because the disease is relatively rare, fatal, and heterogeneous, making it difficult to collect sufficient biosamples from families for statistical power. To address this challenge, the Genetic Epidemiology of Glioma International Consortium (Gliogene) was formed to collect DNA samples from families with two or more cases of histologically confirmed glioma. In this study, we present results obtained from 46 U.S. families in which multipoint linkage analyses were undertaken using nonparametric (model-free) methods. After removal of high linkage disequilibrium single-nucleotide polymorphism, we obtained a maximum nonparametric linkage score (NPL) of 3.39 (P = 0.0005) at 17q12-21.32 and the Z-score of 4.20 (P = 0.000007). To replicate our findings, we genotyped 29 independent U.S. families and obtained a maximum NPL score of 1.26 (P = 0.008) and the Z-score of 1.47 (P = 0.035). Accounting for the genetic heterogeneity using the ordered subset analysis approach, the combined analyses of 75 families resulted in a maximum NPL score of 3.81 (P = 0.00001). The genomic regions we have implicated in this study may offer novel insights into glioma susceptibility, focusing future work to identify genes that cause familial glioma.

%B Cancer Res %V 71 %P 7568-75 %8 2011 Dec 15 %G eng %N 24 %1 https://www.ncbi.nlm.nih.gov/pubmed/22037877?dopt=Abstract %R 10.1158/0008-5472.CAN-11-0013 %0 Journal Article %J PLoS Genet %D 2011 %T Recurrent chromosome 16p13.1 duplications are a risk factor for aortic dissections. %A Kuang, Shao-Qing %A Guo, Dong-chuan %A Prakash, Siddharth K %A McDonald, Merry-Lynn N %A Johnson, Ralph J %A Wang, Min %A Regalado, Ellen S %A Russell, Ludivine %A Cao, Jiu-Mei %A Kwartler, Callie %A Fraivillig, Kurt %A Coselli, Joseph S %A Safi, Hazim J %A Estrera, Anthony L %A Leal, Suzanne M %A LeMaire, Scott A %A Belmont, John W %A Milewicz, Dianna M %K Adult %K Aged %K Aorta %K Aortic Aneurysm, Thoracic %K Aortic Dissection %K Case-Control Studies %K Chromosome Duplication %K Chromosomes, Human, Pair 16 %K Female %K Gene Expression Regulation %K Genetic Predisposition to Disease %K Humans %K Male %K Middle Aged %K Myosin Heavy Chains %K Pedigree %K Phenotype %K Risk Factors %X

Chromosomal deletions or reciprocal duplications of the 16p13.1 region have been implicated in a variety of neuropsychiatric disorders such as autism, schizophrenia, epilepsies, and attention-deficit hyperactivity disorder (ADHD). In this study, we investigated the association of recurrent genomic copy number variants (CNVs) with thoracic aortic aneurysms and dissections (TAAD). By using SNP arrays to screen and comparative genomic hybridization microarrays to validate, we identified 16p13.1 duplications in 8 out of 765 patients of European descent with adult-onset TAAD compared with 4 of 4,569 controls matched for ethnicity (P = 5.0 × 10⁻⁵, OR = 12.2). The findings were replicated in an independent cohort of 467 patients of European descent with TAAD (P = 0.005, OR = 14.7). Patients with 16p13.1 duplications were more likely to harbor a second rare CNV (P = 0.012) and to present with aortic dissections (P = 0.010) than patients without duplications. Duplications of 16p13.1 were identified in 2 of 130 patients with familial TAAD, but the duplications did not segregate with TAAD in the families. MYH11, a gene known to predispose to TAAD, lies in the duplicated region of 16p13.1, and increased MYH11 expression was found in aortic tissues from TAAD patients with 16p13.1 duplications compared with control aortas. These data suggest chromosome 16p13.1 duplications confer a risk for TAAD in addition to the established risk for neuropsychiatric disorders. It also indicates that recurrent CNVs may predispose to disorders involving more than one organ system, an observation critical to the understanding of the role of recurrent CNVs in human disease and a finding that may be common to other recurrent CNVs involving multiple genes.

%B PLoS Genet %V 7 %P e1002118 %8 2011 Jun %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/21698135?dopt=Abstract %R 10.1371/journal.pgen.1002118 %0 Journal Article %J Nat Genet %D 2011 %T TTC21B contributes both causal and modifying alleles across the ciliopathy spectrum. %A Davis, Erica E %A Zhang, Qi %A Liu, Qin %A Diplas, Bill H %A Davey, Lisa M %A Hartley, Jane %A Stoetzel, Corinne %A Szymanska, Katarzyna %A Ramaswami, Gokul %A Logan, Clare V %A Muzny, Donna M %A Young, Alice C %A Wheeler, David A %A Cruz, Pedro %A Morgan, Margaret %A Lewis, Lora R %A Cherukuri, Praveen %A Maskeri, Baishali %A Hansen, Nancy F %A Mullikin, James C %A Blakesley, Robert W %A Bouffard, Gerard G %A Gyapay, Gábor %A Rieger, Susanne %A Tönshoff, Burkhard %A Kern, Ilse %A Soliman, Neveen A %A Neuhaus, Thomas J %A Swoboda, Kathryn J %A Kayserili, Hulya %A Gallagher, Tomas E %A Lewis, Richard A %A Bergmann, Carsten %A Otto, Edgar A %A Saunier, Sophie %A Scambler, Peter J %A Beales, Philip L %A Gleeson, Joseph G %A Maher, Eamonn R %A Attié-Bitach, Tania %A Dollfus, Hélène %A Johnson, Colin A %A Green, Eric D %A Gibbs, Richard A %A Hildebrandt, Friedhelm %A Pierce, Eric A %A Katsanis, Nicholas %K Adaptor Proteins, Signal Transducing %K Alleles %K Animals %K Ciliary Motility Disorders %K Genetic Variation %K Humans %K Mice %K Mutation %K Pedigree %K Photoreceptor Cells %K Zebrafish %X

Ciliary dysfunction leads to a broad range of overlapping phenotypes, collectively termed ciliopathies. This grouping is underscored by genetic overlap, where causal genes can also contribute modifier alleles to clinically distinct disorders. Here we show that mutations in TTC21B, which encodes the retrograde intraflagellar transport protein IFT139, cause both isolated nephronophthisis and syndromic Jeune asphyxiating thoracic dystrophy. Moreover, although resequencing of TTC21B in a large, clinically diverse ciliopathy cohort and matched controls showed a similar frequency of rare changes, in vivo and in vitro evaluations showed a significant enrichment of pathogenic alleles in cases (P < 0.003), suggesting that TTC21B contributes pathogenic alleles to ∼5% of ciliopathy cases. Our data illustrate how genetic lesions can be both causally associated with diverse ciliopathies and interact in trans with other disease-causing genes and highlight how saturated resequencing followed by functional analysis of all variants informs the genetic architecture of inherited disorders.

%B Nat Genet %V 43 %P 189-96 %8 2011 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/21258341?dopt=Abstract %R 10.1038/ng.756 %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 Nature %D 2010 %T Amygdalar and hippocampal substrates of anxious temperament differ in their heritability. %A Oler, Jonathan A %A Fox, Andrew S %A Shelton, Steven E %A Rogers, Jeffrey %A Dyer, Thomas D %A Davidson, Richard J %A Shelledy, Wendy %A Oakes, Terrence R %A Blangero, John %A Kalin, Ned H %K Amygdala %K Animals %K Anxiety %K Depression %K Female %K Freezing Reaction, Cataleptic %K Genetic Predisposition to Disease %K Glucose %K Heredity %K Hippocampus %K Macaca mulatta %K Male %K Models, Animal %K Neural Pathways %K Pedigree %K Phenotype %K Positron-Emission Tomography %K Stress, Psychological %K Temperament %K Temporal Lobe %K Vocalization, Animal %X

Anxious temperament (AT) in human and non-human primates is a trait-like phenotype evident early in life that is characterized by increased behavioural and physiological reactivity to mildly threatening stimuli. Studies in children demonstrate that AT is an important risk factor for the later development of anxiety disorders, depression and comorbid substance abuse. Despite its importance as an early predictor of psychopathology, little is known about the factors that predispose vulnerable children to develop AT and the brain systems that underlie its expression. To characterize the neural circuitry associated with AT and the extent to which the function of this circuit is heritable, we studied a large sample of rhesus monkeys phenotyped for AT. Using 238 young monkeys from a multigenerational single-family pedigree, we simultaneously assessed brain metabolic activity and AT while monkeys were exposed to the relevant ethological condition that elicits the phenotype. High-resolution (18)F-labelled deoxyglucose positron-emission tomography (FDG-PET) was selected as the imaging modality because it provides semi-quantitative indices of absolute glucose metabolic rate, allows for simultaneous measurement of behaviour and brain activity, and has a time course suited for assessing temperament-associated sustained brain responses. Here we demonstrate that the central nucleus region of the amygdala and the anterior hippocampus are key components of the neural circuit predictive of AT. We also show significant heritability of the AT phenotype by using quantitative genetic analysis. Additionally, using voxelwise analyses, we reveal significant heritability of metabolic activity in AT-associated hippocampal regions. However, activity in the amygdala region predictive of AT is not significantly heritable. Furthermore, the heritabilities of the hippocampal and amygdala regions significantly differ from each other. Even though these structures are closely linked, the results suggest differential influences of genes and environment on how these brain regions mediate AT and the ongoing risk of developing anxiety and depression.

%B Nature %V 466 %P 864-8 %8 2010 Aug 12 %G eng %N 7308 %1 https://www.ncbi.nlm.nih.gov/pubmed/20703306?dopt=Abstract %R 10.1038/nature09282 %0 Journal Article %J Eur J Hum Genet %D 2010 %T European admixture on the Micronesian island of Kosrae: lessons from complete genetic information. %A Bonnen, Penelope E %A Lowe, Jennifer K %A Altshuler, David M %A Breslow, Jan L %A Stoffel, Markus %A Friedman, Jeffrey M %A Pe'er, Itsik %K Chromosomes, Human, Y %K DNA, Mitochondrial %K Europe %K Female %K Gene Pool %K Genetic Markers %K Genetics, Population %K Genome, Human %K Geography %K Haplotypes %K Humans %K Inheritance Patterns %K Male %K Micronesia %K Pedigree %K Phylogeny %K Software %K Time Factors %X

The architecture of natural variation present in a contemporary population is a result of multiple population genetic forces, including population bottleneck and expansion, selection, drift, and admixture. We seek to untangle the contribution of admixture to genetic diversity on the Micronesian island of Kosrae. Toward this goal, we used a complete genetic approach by combining a dense genome-wide map of 100,000 single-nucleotide polymorphisms (SNPs) with data from uniparental markers from the mitochondrial genome and the nonrecombining portion of the Y chromosome. These markers were typed in approximately 3200 individuals from Kosrae, representing 80% of the adult population of the island. We developed novel software that uses SNP data to delineate ancestry for individual segments of the genome. Through this analysis, we determined that 39% of Kosraens have some European ancestry. However, the vast majority of admixed individuals (77%) have European alleles spanning less than 10% of their genomes. Data from uniparental markers show most of this admixture to be male, introduced in the late nineteenth century. Furthermore, pedigree analysis shows that the majority of European admixture on Kosrae is because of the contribution of one individual. This approach shows the benefit of combining information from autosomal and uniparental polymorphisms and provides new methodology for determining ancestry in a population.

%B Eur J Hum Genet %V 18 %P 309-16 %8 2010 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/19844264?dopt=Abstract %R 10.1038/ejhg.2009.180 %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 Circ Cardiovasc Genet %D 2009 %T Genome-wide identification of allelic expression in hypertensive rats. %A Dmitrieva, Renata I %A Hinojos, Cruz A %A Grove, Megan L %A Bell, Rebecca J %A Boerwinkle, Eric %A Fornage, Myriam %A Doris, Peter A %K Alleles %K Animals %K Blood Pressure %K Disease Models, Animal %K Female %K Gene Expression Profiling %K Genome-Wide Association Study %K Humans %K Hypertension %K Kidney %K Male %K Pedigree %K Polymorphism, Single Nucleotide %K Rats %K Rats, Inbred SHR %K Rats, Inbred WKY %X

BACKGROUND: Identification of genes involved in complex cardiovascular disease traits has proven challenging. Inbred animal models can facilitate genetic studies of disease traits. The spontaneously hypertensive rat (SHR) is an inbred model of hypertension that exists in several closely related but genetically distinct lines.

METHODS AND RESULTS: We used renal gene-expression profiling across 3 distinct SHR lines to identify genes that show different expression in SHR than in the genetically related normotensive control strain, Wistar-Kyoto. To ensure robust discovery of genes showing SHR-specific expression differences, we considered only those genes in which differential expression is replicated in multiple animals of each of multiple hypertensive rat lines at multiple time points during the ontogeny of hypertension. Mutation analysis was performed on the identified genes to uncover allelic variation. We identified those genes in which all SHR lines share a single allele of the gene when normotensive controls (Wistar-Kyoto) have fixed the alternative allele. We then identified which of the differentially expressed genes show expression that is controlled by the alleleic variation present in and around the gene. Allelic expression was demonstrated by observing the effect on gene expression of alleles inherited in the freely segregating F(2) progeny of a cross between SHR and Wistar-Kyoto animals.

CONCLUSIONS: The result of these studies is the identification of several genes (Ptprj, Ela1, Dapk-2, and Gstt2) in which each of 4 SHR lines examined have fixed the same allele and in which each of 2 Wistar-Kyoto lines have a contrasting allele for which the inherited allele influences the level of gene expression. We further show that alleles of these genes lie in extensive haplotype blocks that have been inherited identical by descent in the hypertensive lines.

%B Circ Cardiovasc Genet %V 2 %P 106-15 %8 2009 Apr %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/20031574?dopt=Abstract %R 10.1161/CIRCGENETICS.108.809509 %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 Exp Biol Med (Maywood) %D 2009 %T Quantitative loci regulating plasma levels of gamma glutamyl transferase and albumin and their genetic correlations with cardiovascular risk factors. %A Bose, Tanushree %A Voruganti, V Saroja %A Tejero, M Elizabeth %A Proffitt, J Michael %A Cox, Laura A %A VandeBerg, John L %A Mahaney, Michael C %A Rogers, Jeffrey %A Freeland-Graves, Jeanne H %A Cole, Shelley A %A Comuzzie, Anthony G %K Animals %K Biomarkers %K Cardiovascular Diseases %K gamma-Glutamyltransferase %K Genetic Markers %K Genetic Predisposition to Disease %K Humans %K Liver %K Lod Score %K Papio hamadryas %K Pedigree %K Phenotype %K Quantitative Trait Loci %K Risk Factors %K Serum Albumin %X

gamma Glutamyl transferase (GGT) and albumin (ALB) are two markers of liver function. These two proteins have been associated with non-alcoholic fatty liver disease and cardiovascular disease. The objectives of this study were to explore the genetic factors that influence variation in the plasma levels of GGT and ALB and to evaluate their genetic correlations with cardiovascular risk factors. Baboons from the Southwest National Primate Research Center at the Southwest Foundation for Biomedical Research, San Antonio, TX, were used as an animal model. The baboons were fed a standard monkey chow diet ad libitum. Fasting plasma concentrations of GGT, ALB, triglycerides, total cholesterol and LDL cholesterol were measured in 350 pedigreed adult baboons by standard assay procedures. A maximum likelihood-based variance decomposition approach implemented in the computer program SOLAR was used to conduct genetic analyses. The heritabilities of GGT (h(2) = 0.55; P < 0.0001) and ALB (h(2) = 0.42; P < 0.01) were significant. No statistically significant associations were found between GGT and the cardiovascular-related phenotypes. Genetic correlations between ALB and total cholesterol, LDL cholesterol and triglycerides were significant. A QTL (LOD = 2.8) for GGT plasma levels was identified on the baboon homologue of human chromosome 22 between markers D22S304 and D22S280. A QTL (LOD = 2.3) near marker D10S1432 was detected on the baboon homologue of human chromosome 10 for ALB. These results imply that variations in the plasma levels of GGT and ALB are under significant genetic regulation and that a common genetic component influences ALB and cardiovascular risk factor phenotypes.

%B Exp Biol Med (Maywood) %V 234 %P vi, 1519-24 %8 2009 Dec %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/19934372?dopt=Abstract %R 10.3181/0903-RM-115 %0 Journal Article %J Am J Hypertens %D 2008 %T Regional association-based fine-mapping for sodium-lithium countertransport on chromosome 10. %A Morrison, Alanna C %A Boerwinkle, Eric %A Turner, Stephen T %A Ferrell, Robert E %K Adolescent %K Adult %K Aged %K Antiporters %K Blood Pressure %K Child %K Chromosome Mapping %K Chromosomes, Human, Pair 10 %K Erythrocytes %K Female %K Gene Frequency %K Genetic Predisposition to Disease %K Genotype %K Humans %K Hypertension %K Linkage Disequilibrium %K Male %K Mannose-Binding Lectin %K Middle Aged %K Minnesota %K Pedigree %K Phenotype %K Polymorphism, Single Nucleotide %K Risk Factors %X

BACKGROUND: Increased erythrocyte sodium-lithium countertransport (SLC) has been observed in patients with essential hypertension. Consistent evidence of genetic linkage was shown for SLC on chromosome 10, and a region of interest was localized between 26 and 56 Mb.

METHODS: This study surveyed single nucleotide polymorphisms (SNPs) in 54 genes that reside in the region of interest, and investigated their association with SLC and blood pressure. These SNPs were genotyped in 1,133 non-Hispanic white individuals from 255 pedigrees comprising the second phase of the Rochester Family Heart Study. The variance-components-based genetics software package SOLAR was used for evaluating whether an SNP contributed to a significant fraction of the trait heritability.

RESULTS: Of the 77 SNPs surveyed in this study across the region of interest, four SNPs were associated with SLC (P < 0.04), five SNPs were associated with blood pressure (P < 0.04), and two SNPs in mannose-binding lectin 2 (MBL2) were associated with both phenotypes. In general, the pairwise linkage disequilibrium among the genotyped SNPs was low.

CONCLUSIONS: This fine-mapping survey of genetic variation in a linkage region of interest provides overall support for association-mapping for SLC on chromosome 10. Genes significantly associated with systolic blood pressure and/or SLC in these families will be prioritized for future studies.

%B Am J Hypertens %V 21 %P 117-21 %8 2008 Jan %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/18091754?dopt=Abstract %R 10.1038/ajh.2007.17 %0 Journal Article %J Cancer Res %D 2007 %T EGFR-T790M is a rare lung cancer susceptibility allele with enhanced kinase activity. %A Vikis, Haris %A Sato, Mitsuo %A James, Michael %A Wang, Daolong %A Wang, Yian %A Wang, Min %A Jia, Dongmei %A Liu, Yan %A Bailey-Wilson, Joan E %A Amos, Christopher I %A Pinney, Susan M %A Petersen, Gloria M %A de Andrade, Mariza %A Yang, Ping %A Wiest, Jonathan S %A Fain, Pamela R %A Schwartz, Ann G %A Gazdar, Adi %A Gaba, Colette %A Rothschild, Henry %A Mandal, Diptasri %A Kupert, Elena %A Seminara, Daniela %A Viswanathan, Avinash %A Govindan, Ramaswamy %A Minna, John %A Anderson, Marshall W %A You, Ming %K Alleles %K Animals %K Chlorocebus aethiops %K COS Cells %K DNA, Neoplasm %K ErbB Receptors %K Genes, erbB-1 %K Genetic Predisposition to Disease %K Germ-Line Mutation %K Humans %K Lung Neoplasms %K Pedigree %K Phosphorylation %X

The use of tyrosine kinase inhibitors (TKI) has yielded great success in treatment of lung adenocarcinomas. However, patients who develop resistance to TKI treatment often acquire a somatic resistance mutation (T790M) located in the catalytic cleft of the epidermal growth factor receptor (EGFR) enzyme. Recently, a report describing EGFR-T790M as a germ-line mutation suggested that this mutation may be associated with inherited susceptibility to lung cancer. Contrary to previous reports, our analysis indicates that the T790M mutation confers increased Y992 and Y1068 phosphorylation levels. In a human bronchial epithelial cell line, overexpression of EGFR-T790M displayed a growth advantage over wild-type (WT) EGFR. We also screened 237 lung cancer family probands, in addition to 45 bronchoalveolar tumors, and found that none of them contained the EGFR-T790M mutation. Our observations show that EGFR-T790M provides a proliferative advantage with respect to WT EGFR and suggest that the enhanced kinase activity of this mutant is the basis for rare cases of inherited susceptibility to lung cancer.

%B Cancer Res %V 67 %P 4665-70 %8 2007 May 15 %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/17510392?dopt=Abstract %R 10.1158/0008-5472.CAN-07-0217 %0 Journal Article %J Hum Brain Mapp %D 2007 %T Heritability of brain volume, surface area and shape: an MRI study in an extended pedigree of baboons. %A Rogers, Jeffrey %A Kochunov, Peter %A Lancaster, Jack %A Shelledy, Wendy %A Glahn, David %A Blangero, John %A Fox, Peter %K Animals %K Brain %K Brain Mapping %K Female %K Genetic Linkage %K Magnetic Resonance Imaging %K Male %K Papio %K Pedigree %X

To evaluate baboons (Papio hamadryas) as a primate model for the study of the genetic control of brain size and internal structure, we performed high resolution (<500 microm) magnetic resonance imaging on 109 pedigreed baboons. Quantitative genetic analysis of these MR images using a variance components approach indicates that native (untransformed) brain volume exhibits significant heritability among these baboons (h(2) = 0.52, P = 0.0049), with age and sex also accounting for substantial variation. Using global spatial normalization, we transformed all images to a standard population-specific reference, and recalculated the heritability of brain volume. The transformed images generated heritability estimates of h(2) = 0.82 (P = 0.00022) for total brain volume, h(2) = 0.86 (P = 0.0006) for cerebral volume, h(2) = 0.73 (P = 0.0069) for exposed surface area of the cerebrum and h(2) = 0.67 (P = 0.01) for gray matter volume. Regional differences in the genetic effects on brain structure were calculated using a voxel-based morphometry (VBM) approach. This analysis of regional variation shows that some areas of motor cortex and the superior temporal gyrus show relatively high heritability while other regions (e.g. superior parietal cortex) exhibit lower heritability. The general pattern of regional differences is similar to that observed in previous studies of humans. The present study demonstrates that there is substantial genetic variation underlying individual variation in brain size and structure among Papio baboons, and that broad patterns of genetic influence on variation in brain structure may be similar in baboons and humans.

%B Hum Brain Mapp %V 28 %P 576-83 %8 2007 Jun %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/17437285?dopt=Abstract %R 10.1002/hbm.20407 %0 Journal Article %J Nat Genet %D 2007 %T Mutations in smooth muscle alpha-actin (ACTA2) lead to thoracic aortic aneurysms and dissections. %A Guo, Dong-chuan %A Pannu, Hariyadarshi %A Tran-Fadulu, Van %A Papke, Christina L %A Yu, Robert K %A Avidan, Nili %A Bourgeois, Scott %A Estrera, Anthony L %A Safi, Hazim J %A Sparks, Elizabeth %A Amor, David %A Ades, Lesley %A McConnell, Vivienne %A Willoughby, Colin E %A Abuelo, Dianne %A Willing, Marcia %A Lewis, Richard A %A Kim, Dong H %A Steven E Scherer %A Tung, Poyee P %A Ahn, Chul %A Buja, L Maximilian %A Raman, C S %A Shete, Sanjay S %A Milewicz, Dianna M %K Actins %K Aorta %K Aortic Aneurysm, Thoracic %K Aortic Dissection %K Female %K Genetic Predisposition to Disease %K Humans %K Male %K Mutation, Missense %K Myocytes, Smooth Muscle %K Pedigree %X

The major function of vascular smooth muscle cells (SMCs) is contraction to regulate blood pressure and flow. SMC contractile force requires cyclic interactions between SMC alpha-actin (encoded by ACTA2) and the beta-myosin heavy chain (encoded by MYH11). Here we show that missense mutations in ACTA2 are responsible for 14% of inherited ascending thoracic aortic aneurysms and dissections (TAAD). Structural analyses and immunofluorescence of actin filaments in SMCs derived from individuals heterozygous for ACTA2 mutations illustrate that these mutations interfere with actin filament assembly and are predicted to decrease SMC contraction. Aortic tissues from affected individuals showed aortic medial degeneration, focal areas of medial SMC hyperplasia and disarray, and stenotic arteries in the vasa vasorum due to medial SMC proliferation. These data, along with the previously reported MYH11 mutations causing familial TAAD, indicate the importance of SMC contraction in maintaining the structural integrity of the ascending aorta.

%B Nat Genet %V 39 %P 1488-93 %8 2007 Dec %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/17994018?dopt=Abstract %R 10.1038/ng.2007.6 %0 Journal Article %J Hum Mol Genet %D 2007 %T MYH11 mutations result in a distinct vascular pathology driven by insulin-like growth factor 1 and angiotensin II. %A Pannu, Hariyadarshi %A Tran-Fadulu, Van %A Papke, Christina L %A Scherer, Steve %A Liu, Yaozhong %A Presley, Caroline %A Guo, Dongchuan %A Estrera, Anthony L %A Safi, Hazim J %A Brasier, Allan R %A Vick, G Wesley %A Marian, A J %A Raman, C S %A Buja, L Maximilian %A Milewicz, Dianna M %K Adult %K Amino Acid Sequence %K Angiotensin II %K Aortic Aneurysm, Thoracic %K Child, Preschool %K Ductus Arteriosus, Patent %K Female %K Genetic Testing %K Humans %K Insulin-Like Growth Factor I %K Male %K Middle Aged %K Models, Molecular %K Molecular Sequence Data %K Mutation %K Myosin Heavy Chains %K Pedigree %K Sequence Homology, Amino Acid %K Vascular Diseases %X

Non-syndromic thoracic aortic aneurysms and dissections (TAADs) are inherited in an autosomal dominant manner in approximately 20% of cases. Familial TAAD is genetically heterogeneous and four loci have been mapped for this disease to date, including a locus at 16p for TAAD associated with patent ductus arteriosus (PDA). The defective gene at the 16p locus has recently been identified as the smooth muscle cell (SMC)-specific myosin heavy chain gene (MYH11). On sequencing MYH11 in 93 families with TAAD alone and three families with TAAD/PDA, we identified novel mutations in two families with TAAD/PDA, but none in families with TAAD alone. Histopathological analysis of aortic sections from two individuals with MYH11 mutations revealed SMC disarray and focal hyperplasia of SMCs in the aortic media. SMC hyperplasia leading to significant lumen narrowing in some of the vessels of the adventitia was also observed. Insulin-like growth factor-1 (IGF-1) was upregulated in mutant aortas as well as explanted SMCs, but no increase in transforming growth factor-beta expression or downstream targets was observed. Enhanced expression of angiotensin-converting enzyme and markers of Angiotensin II (Ang II) vascular inflammation (macrophage inflammatory protein-1alpha and beta) were also found. These data suggest that MYH11 mutations are likely to be specific to the phenotype of TAAD/PDA and result in a distinct aortic and occlusive vascular pathology potentially driven by IGF-1 and Ang II.

%B Hum Mol Genet %V 16 %P 2453-62 %8 2007 Oct 15 %G eng %N 20 %1 https://www.ncbi.nlm.nih.gov/pubmed/17666408?dopt=Abstract %R 10.1093/hmg/ddm201 %0 Journal Article %J Genomics %D 2006 %T Designing new microsatellite markers for linkage and population genetic analyses in rhesus macaques and other nonhuman primates. %A Raveendran, Muthuswamy %A R. Alan Harris %A Milosavljevic, Aleksandar %A Johnson, Zach %A Shelledy, Wendy %A Cameron, Judy %A Jeffrey Rogers %K Animals %K Chromosome Mapping %K Genetic Markers %K Genetic Techniques %K Genetics, Population %K Humans %K Macaca mulatta %K Microsatellite Repeats %K Papio hamadryas %K Pedigree %K Polymorphism, Genetic %X

Identification of polymorphic microsatellite loci in nonhuman primates is useful for various biomedical and evolutionary studies of these species. Prior methods for identifying microsatellites in nonhuman primates are inefficient. We describe a new strategy for marker development that uses the available whole genome sequence for rhesus macaques. Fifty-four novel rhesus-derived microsatellites were genotyped in large pedigrees of rhesus monkeys. Linkage analysis was used to place 51 of these loci into the existing rhesus linkage map. In addition, we find that microsatellites identified this way are polymorphic in other Old World monkeys such as baboons. This approach to marker development is more efficient than previous methods and produces polymorphisms with known locations in the rhesus genome assembly. Finally, we propose a nomenclature system that can be used for rhesus-derived microsatellites genotyped in any species or for novel loci derived from the genome sequence of any nonhuman primate.

%B Genomics %V 88 %P 706-710 %8 2006 Dec %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/17010566?dopt=Abstract %R 10.1016/j.ygeno.2006.08.009 %0 Journal Article %J Am J Hum Genet %D 2006 %T Spectrum of CHD7 mutations in 110 individuals with CHARGE syndrome and genotype-phenotype correlation. %A Lalani, Seema R %A Safiullah, Arsalan M %A Fernbach, Susan D %A Harutyunyan, Karine G %A Thaller, Christina %A Peterson, Leif E %A McPherson, John D %A Gibbs, Richard A %A White, Lisa D %A Hefner, Margaret %A Davenport, Sandra L H %A Graham, John M %A Bacino, Carlos A %A Glass, Nancy L %A Towbin, Jeffrey A %A Craigen, William J %A Neish, Steven R %A Lin, Angela E %A Belmont, John W %K Abnormalities, Multiple %K Adolescent %K Animals %K Child %K Child, Preschool %K Coloboma %K DNA Helicases %K DNA Mutational Analysis %K DNA-Binding Proteins %K Embryo, Mammalian %K Facial Asymmetry %K Female %K Genotype %K Heart Defects, Congenital %K Humans %K In Situ Hybridization, Fluorescence %K Male %K Mice %K Molecular Sequence Data %K Mutation %K Pedigree %K Phenotype %K RNA Splice Sites %K RNA, Messenger %K Syndrome %X

CHARGE syndrome is a well-established multiple-malformation syndrome with distinctive consensus diagnostic criteria. Characteristic associated anomalies include ocular coloboma, choanal atresia, cranial nerve defects, distinctive external and inner ear abnormalities, hearing loss, cardiovascular malformations, urogenital anomalies, and growth retardation. Recently, mutations of the chromodomain helicase DNA-binding protein gene CHD7 were reported to be a major cause of CHARGE syndrome. We sequenced the CHD7 gene in 110 individuals who had received the clinical diagnosis of CHARGE syndrome, and we detected mutations in 64 (58%). Mutations were distributed throughout the coding exons and conserved splice sites of CHD7. Of the 64 mutations, 47 (73%) predicted premature truncation of the protein. These included nonsense and frameshift mutations, which most likely lead to haploinsufficiency. Phenotypically, the mutation-positive group was more likely to exhibit cardiovascular malformations (54 of 59 in the mutation-positive group vs. 30 of 42 in the mutation-negative group; P=.014), coloboma of the eye (55 of 62 in the mutation-positive group vs. 30 of 43 in the mutation-negative group; P=.022), and facial asymmetry, often caused by seventh cranial nerve abnormalities (36 of 56 in the mutation-positive group vs. 13 of 39 in the mutation-negative group; P=.004). Mouse embryo whole-mount and section in situ hybridization showed the expression of Chd7 in the outflow tract of the heart, optic vesicle, facio-acoustic preganglion complex, brain, olfactory pit, and mandibular component of the first branchial arch. Microarray gene-expression analysis showed a signature pattern of gene-expression differences that distinguished the individuals with CHARGE syndrome with CHD7 mutation from the controls. We conclude that cardiovascular malformations, coloboma, and facial asymmetry are common findings in CHARGE syndrome caused by CHD7 mutation.

%B Am J Hum Genet %V 78 %P 303-14 %8 2006 Feb %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/16400610?dopt=Abstract %R 10.1086/500273 %0 Journal Article %J Hypertension %D 2005 %T Combined genealogical, mapping, and expression approaches to identify spontaneously hypertensive rat hypertension candidate genes. %A Hinojos, Cruz A %A Eric Boerwinkle %A Fornage, Myriam %A Doris, Peter A %K Animals %K Blood Pressure %K Chromosome Mapping %K Expressed Sequence Tags %K Gene Expression %K Genome %K Hypertension %K Kidney %K Oligonucleotide Array Sequence Analysis %K Pedigree %K Quantitative Trait Loci %K Rats %K Rats, Inbred SHR %K Rats, Inbred WKY %K Regression Analysis %K Species Specificity %X

Allelic expression in genes has become recognized as a heritable trait by which phenotypes are generated. We have examined gene expression in the rat kidney using genome-wide microarray technology (Affymetrix). Gene expression was determined across 4 rat strains, 3 hypertensive spontaneously hypertensive rat (SHR) substrains (SHR-A3, SHR-B2, and SHR-C), and a normotensive strain (Wistar-Kyoto [WKY]). Expression measurements were made in multiple animals from all strains at 4 time points (4 weeks, 8 weeks, 12 weeks, and 18 weeks of age), covering the prehypertensive period in SHR (4 weeks), and the period of rapidly rising blood pressure (8 and 12 weeks) and of sustained hypertension (18 weeks). Regression analysis revealed a close relationship across all strains during the first 3 time points, after which SHR-A3 became a substantial outlier. SHR-B2 and SHR-C demonstrated a very close relationship in gene expression at all times but also showed increased differences compared with the other strains at 18 weeks of age. We identified genes that were consistently different in expression, comparing all SHR substrains at each time point with WKY. The resulting list of genes was compared with blood pressure quantitative trait loci reported for SHR to refine a number of genes consistently differentially expressed between SHR substrains and WKY, persistently differentially expressed across multiple time points, and located in SHR blood pressure-determinative regions of the genome. Genealogical relationships and SHR substrain intercrosses suggest that genes responsible for heritable hypertension in SHR are shared across SHR substrains. The present approach identifies a number of genes that may influence blood pressure in SHR by virtue of allelic effects on gene expression.

%B Hypertension %V 45 %P 698-704 %8 2005 Apr %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/15710778?dopt=Abstract %R 10.1161/01.HYP.0000156498.78896.37 %0 Journal Article %J Am J Hum Genet %D 2004 %T Somatic and germline instability of the ATTCT repeat in spinocerebellar ataxia type 10. %A Matsuura, Tohru %A Fang, Ping %A Lin, Xi %A Khajavi, Mehrdad %A Tsuji, Kuniko %A Rasmussen, Astrid %A Grewal, Raji P %A Achari, Madhureeta %A Alonso, Maria E %A Pulst, Stefan M %A Zoghbi, Huda Y %A Nelson, David L %A Roa, Benjamin B %A Ashizawa, Tetsuo %K Age Distribution %K Cell Line %K Disease Transmission, Infectious %K DNA %K Female %K Genes, Dominant %K Germ Cells %K Humans %K Leukocytes %K Male %K Microsatellite Repeats %K Mouth Mucosa %K Pedigree %K Repetitive Sequences, Nucleic Acid %K Spermatozoa %K Spinocerebellar Ataxias %X

Spinocerebellar ataxia type 10 (SCA10) is an autosomal dominant disorder characterized by ataxia, seizures, and anticipation. It is caused by an expanded ATTCT pentanucleotide repeat in intron 9 of a novel gene, designated "SCA10." The ATTCT expansion in SCA10 represents a novel class of microsatellite repeat and is one of the largest found to cause human diseases. The expanded ATTCT repeat is unstably transmitted from generation to generation, and an inverse correlation has been observed between size of repeat and age at onset. In this multifamily study, we investigated the intergenerational instability, somatic and germline mosaicism, and age-dependent repeat-size changes of the expanded ATTCT repeat. Our results showed that (1) the expanded ATTCT repeats are highly unstable when paternally transmitted, whereas maternal transmission resulted in significantly smaller changes in repeat size; (2) blood leukocytes, lymphoblastoid cells, buccal cells, and sperm have a variable degree of mosaicism in ATTCT expansion; (3) the length of the expanded repeat was not observed to change in individuals over a 5-year period; and (4) clinically determined anticipation is sometimes associated with intergenerational contraction rather than expansion of the ATTCT repeat.

%B Am J Hum Genet %V 74 %P 1216-24 %8 2004 Jun %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/15127363?dopt=Abstract %R 10.1086/421526 %0 Journal Article %J Circulation %D 2003 %T Mapping a locus for familial thoracic aortic aneurysms and dissections (TAAD2) to 3p24-25. %A Hasham, Sumera N %A Willing, Marcia C %A Guo, Dong-chuan %A Muilenburg, Ann %A He, Rumin %A Tran, Van T %A Steven E Scherer %A Shete, Sanjay S %A Milewicz, Dianna M %K Adolescent %K Adult %K Aortic Aneurysm, Thoracic %K Aortic Dissection %K Calcium-Binding Proteins %K Child %K Chromosome Mapping %K Chromosomes, Human, Pair 3 %K Comorbidity %K DNA Mutational Analysis %K Echocardiography %K Extracellular Matrix Proteins %K Female %K Genes, Dominant %K Genetic Linkage %K Genetic Markers %K Genotype %K Germany %K Haplotypes %K Humans %K Lod Score %K Male %K Marfan Syndrome %K Middle Aged %K Pedigree %K Penetrance %K Switzerland %X

BACKGROUND: Familial thoracic aortic aneurysms and dissections (TAAD) occur as part of known syndromes such as Marfan syndrome but can also be inherited in families in an autosomal dominant manner as an isolated condition. Previous studies have mapped genes causing nonsyndromic familial TAAD to 5q13-15 (TAAD1) and 11q23.2-q24 (FAA1). Further genetic heterogeneity for the condition was evident by the presence of TAAD in some families not linked to these known loci.

METHODS AND RESULTS: A 4-generation family with dominant mode of inheritance of TAAD was studied. Affected status was determined by dilation of the ascending aorta, surgical repair of an aneurysm or dissection, or death as the result of aortic dissection. None of the family members evaluated met the diagnostic criteria for Marfan syndrome. After exclusion of known loci for familial TAAD, a genome-wide scan was carried out to map the defective gene causing the disease in the family. A locus was mapped to a 25-cM region on 3p24-25 with a maximum multipoint logarithm of the odds score of 4.28.

CONCLUSIONS: A third locus for nonsyndromic TAAD was mapped to 3p24-25 and termed the TAAD2 locus. This locus overlaps a previously mapped second locus for Marfan syndrome, termed the MFS2 locus. Future characterization of the TAAD2 gene will determine if TAAD2 is allelic to MFS2. In addition, identification of the TAAD2 gene will improve the presymptomatic diagnosis of individuals with this life-threatening genetic syndrome and provide information concerning the pathogenesis of the disease.

%B Circulation %V 107 %P 3184-90 %8 2003 Jul 01 %G eng %N 25 %1 https://www.ncbi.nlm.nih.gov/pubmed/12821554?dopt=Abstract %R 10.1161/01.CIR.0000078634.33124.95 %0 Journal Article %J Am J Hum Genet %D 2003 %T Polymorphisms at the G72/G30 gene locus, on 13q33, are associated with bipolar disorder in two independent pedigree series. %A Hattori, Eiji %A Liu, Chunyu %A Badner, Judith A %A Bonner, Tom I %A Christian, Susan L %A Maheshwari, Manjula %A Detera-Wadleigh, Sevilla D %A Gibbs, Richard A %A Gershon, Elliot S %K Alternative Splicing %K Bipolar Disorder %K Carrier Proteins %K Chromosomes, Human, Pair 13 %K DNA, Complementary %K Gene Frequency %K Genes %K Genetic Linkage %K Genetic Predisposition to Disease %K Haplotypes %K Humans %K Intracellular Signaling Peptides and Proteins %K Likelihood Functions %K Linkage Disequilibrium %K Molecular Sequence Data %K Pedigree %K Polymorphism, Single Nucleotide %K Sequence Analysis, DNA %X

Linkage evidence suggests that chromosome 13 (13q32-33) contains susceptibility genes for both bipolar disorder and schizophrenia. Recently, genes called "G72" and "G30" were identified, and polymorphisms of these overlapping genes were reported to be associated with schizophrenia. We studied two series of pedigrees with bipolar disorder: the Clinical Neurogenetics (CNG) pedigrees (in which linkage to illness had been previously reported at 13q32-33), with 83 samples from 22 multiplex families, and the National Institute of Mental Health (NIMH) Genetics Initiative pedigrees, with 474 samples from 152 families. Sixteen single-nucleotide polymorphisms (SNPs) were genotyped at and around the G72/G30 locus, which covered a 157-kb region encompassing the entire complementary DNA sequences of G72 and G30. We performed transmission/disequilibrium testing (TDT) and haplotype analysis, since a linkage-disequilibrium block was present at this gene locus. In the CNG and NIMH data sets, the results of global TDT of the entire haplotype set were significant and consistent (P=.0004 and P=.008, respectively). In the CNG series, the associated genotypes divided the families into those with linkage and those without linkage (partitioned by the linkage evidence). Analysis of the decay of haplotype sharing gave a location estimate that included G72/G30 in its 95% confidence interval. Although statistically significant association was not detected for individual SNPs in the NIMH data set, the same haplotype was consistently overtransmitted in both series. These data suggest that a susceptibility variant for bipolar illness exists in the vicinity of the G72/G30 genes. Taken together with the earlier report, this is the first demonstration of a novel gene(s), discovered through a positional approach, independently associated with both bipolar illness and schizophrenia.

%B Am J Hum Genet %V 72 %P 1131-40 %8 2003 May %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/12647258?dopt=Abstract %R 10.1086/374822 %0 Journal Article %J Genomics %D 2000 %T Construction of a high-resolution physical map of the chromosome 10q22-q23 dilated cardiomyopathy locus and analysis of candidate genes. %A Bowles, K R %A Abraham, S E %A Brugada, R %A Zintz, C %A Comeaux, J %A Sorajja, D %A Tsubata, S %A Li, H %A Brandon, L %A Richard A Gibbs %A Steven E Scherer %A Bowles, N E %A Towbin, J A %K Cardiomyopathy, Dilated %K Chromosomes, Bacterial %K Chromosomes, Human, Pair 10 %K DNA Mutational Analysis %K Expressed Sequence Tags %K Family Health %K Female %K Genetic Predisposition to Disease %K Genomic Library %K Humans %K Male %K Pedigree %K Phenotype %K Physical Chromosome Mapping %K Sequence Analysis, DNA %X

Dilated cardiomyopathy (DCM) is a major cause of morbidity and mortality and a leading cause of cardiac transplantation worldwide. Multiple loci and three genes encoding cardiac actin, desmin, and lamin A/C have been described for autosomal dominant DCM. Using recombination analysis, we have narrowed the 10q21-q23 locus to a region of approximately 4.1 cM. In addition, we have constructed a BAC contig, composed of 199 clones, which was used to develop a high-resolution physical map that contains the DCM critical region (approximately 3.9 Mb long). Seven genes, including ANX11, PPIF, DLG5, RPC155, RPS24, SFTPA1, and KCNMA1, have been mapped to the region of interest. RPC155, RPS24, SFTPA1, and KCNMA1 were excluded from further analysis based on their known functions and tissue-specific expression patterns. Mutational analysis of ANX11, DLG5, and PPIF revealed no disease-associated mutations. Multiple ESTs have also been mapped to the critical region.

%B Genomics %V 67 %P 109-27 %8 2000 Jul 15 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/10903836?dopt=Abstract %R 10.1006/geno.2000.6242 %0 Journal Article %J Nat Genet %D 2000 %T Large expansion of the ATTCT pentanucleotide repeat in spinocerebellar ataxia type 10. %A Matsuura, T %A Yamagata, T %A Burgess, D L %A Rasmussen, A %A Grewal, R P %A Watase, K %A Khajavi, M %A McCall, A E %A Davis, C F %A Zu, L %A Achari, M %A Pulst, S M %A Alonso, E %A Noebels, J L %A Nelson, D L %A Zoghbi, H Y %A Ashizawa, T %K Animals %K Asian People %K Brain %K Chromosome Mapping %K Chromosomes, Human, Pair 22 %K DNA %K Epilepsy %K Female %K Humans %K Male %K Mexican Americans %K Mice %K Mice, Inbred C57BL %K Molecular Sequence Data %K Pedigree %K Polymorphism, Genetic %K Repetitive Sequences, Nucleic Acid %K Spinocerebellar Ataxias %K United States %K White People %X

Spinocerebellar ataxia type 10 (SCA10; MIM 603516; refs 1,2) is an autosomal dominant disorder characterized by cerebellar ataxia and seizures. The gene SCA10 maps to a 3.8-cM interval on human chromosome 22q13-qter (refs 1,2). Because several other SCA subtypes show trinucleotide repeat expansions, we examined microsatellites in this region. We found an expansion of a pentanucleotide (ATTCT) repeat in intron 9 of SCA10 in all patients in five Mexican SCA10 families. There was an inverse correlation between the expansion size, up to 22.5 kb larger than the normal allele, and the age of onset (r2=0.34, P=0.018). Analysis of 562 chromosomes from unaffected individuals of various ethnic origins (including 242 chromosomes from Mexican persons) showed a range of 10 to 22 ATTCT repeats with no evidence of expansions. Our data indicate that the new SCA10 intronic ATTCT pentanucleotide repeat in SCA10 patients is unstable and represents the largest microsatellite expansion found so far in the human genome.

%B Nat Genet %V 26 %P 191-4 %8 2000 Oct %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/11017075?dopt=Abstract %R 10.1038/79911 %0 Journal Article %J Hum Mutat %D 1998 %T DNA deletion confined to the iduronate-2-sulfatase promoter abolishes IDS gene expression. %A Timms, K M %A Huckett, L E %A Belmont, J W %A Shapira, S K %A Richard A Gibbs %K Base Sequence %K Child, Preschool %K DNA Mutational Analysis %K Gene Expression Regulation %K Humans %K Iduronate Sulfatase %K Male %K Molecular Sequence Data %K Mucopolysaccharidosis II %K Pedigree %K Phenotype %K Promoter Regions, Genetic %K Sequence Analysis, DNA %K Sequence Deletion %X

Deficiency of the enzyme iduronate-2-sulfatase (IDS) results in Hunter syndrome, an X-linked recessive lysosomal storage disorder. In this study, analysis of a patient with features of moderate to severe Hunter syndrome identified a 178-bp deletion upstream of IDS exon 1 spanning a predicted promoter element. Sequencing of all nine IDS exons from this patient failed to identify any additional mutations within the coding regions or in intron-exon boundaries. The 178-bp deletion is flanked by two 13-bp direct repeats and potential DNA topoisomerase II recognition sites. These findings point toward nonhomologous recombination as a possible mechanism for this mutation. Expression studies on this patient do not detect any IDS transcripts, indicating that the deletion spans sequences essential for IDS expression. Complete lack of expression of IDS is consistent with the moderate to severe phenotype observed in this patient.

%B Hum Mutat %V 11 %P 121-6 %8 1998 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/9482575?dopt=Abstract %R 10.1002/(SICI)1098-1004(1998)11:2<121::AID-HUMU4>3.0.CO;2-M %0 Journal Article %J J Med Genet %D 1998 %T Reassessment of biochemically determined Hunter syndrome carrier status by DNA testing. %A Timms, K M %A Edwards, F J %A Belmont, J W %A Yates, J R %A Gibbs, R A %K DNA %K Female %K Heterozygote %K Humans %K Iduronate Sulfatase %K Male %K Mucopolysaccharidosis II %K Pedigree %X

Deficiency of iduronate-2-sulphatase (IDS) results in the X linked recessive lysosomal storage disorder Hunter syndrome. Determination of carrier status in families affected by this disorder has been performed using a variety of enzymatic tests. None of these tests has proved to be 100% effective at identifying carriers. The aim of this study was to perform carrier testing in a family affected by the disorder, where testing was complicated by the fact that no surviving affected subjects were available for study. Direct dye primer sequencing of PCR products was used to identify mixed bases in an obligate carrier. Two mixed bases were observed within exon VIII. The first base change (T-->A) at nucleotide position 1150 results in a missense mutation (H342Q), while the second base change (G-->T) at nucleotide position 1151 results in a nonsense mutation (G343X). Four additional female family members were screened for the same mutation. Using this approach it is possible to provide unambiguous information about a subject's carrier status and, unlike biochemical testing, this approach will be equally effective when applied to families with the mild form of this disorder.

%B J Med Genet %V 35 %P 646-9 %8 1998 Aug %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/9719370?dopt=Abstract %R 10.1136/jmg.35.8.646 %0 Journal Article %J Nat Genet %D 1997 %T Autosomal dominant cerebellar ataxia (SCA6) associated with small polyglutamine expansions in the alpha 1A-voltage-dependent calcium channel. %A Zhuchenko, O %A Bailey, J %A Bonnen, P %A Ashizawa, T %A Stockton, D W %A Amos, C %A Dobyns, W B %A Subramony, S H %A Zoghbi, H Y %A Lee, C C %K Alleles %K Amino Acid Sequence %K Animals %K Calcium Channels %K Cerebellar Ataxia %K Female %K Genes, Dominant %K Genotype %K Humans %K Male %K Molecular Sequence Data %K Mutation %K Nerve Tissue Proteins %K Pedigree %K Peptides %K Rabbits %K Sequence Homology, Amino Acid %K Trinucleotide Repeats %X

A polymorphic CAG repeat was identified in the human alpha 1A voltage-dependent calcium channel subunit. To test the hypothesis that expansion of this CAG repeat could be the cause of an inherited progressive ataxia, we genotyped a large number of unrelated controls and ataxia patients. Eight unrelated patients with late onset ataxia had alleles with larger repeat numbers (21-27) compared to the number of repeats (4-16) in 475 non-ataxia individuals. Analysis of the repeat length in families of the affected individuals revealed that the expansion segregated with the phenotype in every patient. We identified six isoforms of the human alpha 1A calcium channel subunit. The CAG repeat is within the open reading frame and is predicted to encode glutamine in three of the isoforms. We conclude that a small polyglutamine expansion in the human alpha 1A calcium channel is most likely the cause of a newly classified autosomal dominant spinocerebellar ataxia, SCA6.

%B Nat Genet %V 15 %P 62-9 %8 1997 Jan %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/8988170?dopt=Abstract %R 10.1038/ng0197-62 %0 Journal Article %J Calcif Tissue Int %D 1997 %T Beyond one gene-one disease: alternative strategies for deciphering genetic determinants of osteoporosis. %A Rogers, J %A Mahaney, M C %A Beamer, W G %A Donahue, L R %A Rosen, C J %K Animals %K Bone and Bones %K Bone Density %K Chromosome Mapping %K Disease Models, Animal %K Humans %K Osteoporosis %K Papio %K Pedigree %K Point Mutation %K Risk Factors %B Calcif Tissue Int %V 60 %P 225-8 %8 1997 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/9069155?dopt=Abstract %R 10.1007/s002239900218 %0 Journal Article %J Cytogenet Cell Genet %D 1996 %T Conservation of human chromosome 18 in baboons (Papio hamadryas): a linkage map of eight human microsatellites. %A Perelygin, A A %A Kammerer, C M %A Stowell, N C %A Rogers, J %K Animals %K Chromosomes, Human, Pair 18 %K Evolution, Molecular %K Female %K Hominidae %K Humans %K Lod Score %K Male %K Microsatellite Repeats %K Papio %K Pedigree %K Phylogeny %K Polymerase Chain Reaction %K Recombination, Genetic %K Species Specificity %X

A panel of 25 microsatellite loci known to map to human chromosome 18 was screened for length polymorphisms in a multigenerational pedigree of baboons (Papio hamadryas). Eight of these loci were polymorphic in the baboon pedigrees, with observed heterozygosity values ranging from 0.16 to 0.88. All eight loci show strong evidence of linkage. The most likely map order among the microsatellite loci for Papio is completely compatible with the locus order found in the human genome, and sex differences in recombination rates are also similar in the two species. We conclude that the organization of the chromosomal region defined by these loci is largely conserved between baboons and humans.

%B Cytogenet Cell Genet %V 75 %P 207-9 %8 1996 %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/9067425?dopt=Abstract %R 10.1159/000134484 %0 Journal Article %J Am J Med Genet %D 1995 %T Rapid molecular cytogenetic analysis of X-chromosomal microdeletions: fluorescence in situ hybridization (FISH) for complex glycerol kinase deficiency. %A Kim C Worley %A Lindsay, E A %A Bailey, W %A Wise, J %A McCabe, E R %A Baldini, A %K Chromosome Mapping %K Female %K Gene Deletion %K Glycerol Kinase %K Heterozygote %K Humans %K In Situ Hybridization, Fluorescence %K Infant, Newborn %K Male %K Pedigree %K X Chromosome %X

Diagnosis of X-chromosomal microdeletions has relied upon the traditional methods of Southern blotting and DNA amplification, with carrier identification requiring time-consuming and unreliable dosage calculations. In this report, we describe rapid molecular cytogenetic identification of deleted DNA in affected males with the Xp21 contiguous gene syndrome (complex glycerol kinase deficiency, CGKD) and female carriers for this disorder. CGKD deletions involve the genes for glycerol kinase, Duchenne muscular dystrophy, and/or adrenal hypoplasia congenita. We report an improved method for diagnosis of deletions in individuals with CGKD and for identification of female carriers within their families, using fluorescence in situ hybridization (FISH) with a cosmid marker (cosmid 35) within the glycerol kinase gene. When used in combination with an Xq control probe, affected males demonstrate a single signal from the control probe, while female carriers demonstrate a normal chromosome with two signals, as well as a deleted chromosome with a single signal from the control probe. FISH analysis for CGKD provides the advantages of speed and accuracy for evaluation of submicroscopic X-chromosomal deletions, particularly in identification of female carriers. In addition to improving carrier evaluation, FISH will make prenatal diagnosis of CGKD more readily available.

%B Am J Med Genet %V 57 %P 615-9 %8 1995 Jul 17 %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/7573140?dopt=Abstract %R 10.1002/ajmg.1320570420 %0 Journal Article %J Am J Hum Genet %D 1991 %T Carrier detection and prenatal diagnosis in Duchenne and Becker muscular dystrophy families, using dinucleotide repeat polymorphisms. %A Clemens, P R %A Fenwick, R G %A Chamberlain, J S %A Gibbs, R A %A de Andrade, M %A Chakraborty, R %A Caskey, C T %K Alleles %K Base Sequence %K Cells, Cultured %K Dystrophin %K Female %K Gene Frequency %K Genetic Carrier Screening %K Genetic Markers %K Humans %K Male %K Molecular Sequence Data %K Muscular Dystrophies %K Pedigree %K Polydeoxyribonucleotides %K Polymerase Chain Reaction %K Polymorphism, Genetic %K Pregnancy %K Prenatal Diagnosis %K Repetitive Sequences, Nucleic Acid %X

To improve carrier detection and prenatal diagnosis for Duchenne and Becker muscular dystrophy families, we determined allele frequencies and measures of variation for four (dC-dA)n.(dG-dT)n loci identified within a deletion-prone region of the human dystrophin gene. The loci are highly polymorphic, with predicted heterozygosities of 71.6%-93.3%. Direct DNA sequence analysis of the (dC-dA)n.(dG-dT)n locus in intron 49 revealed an additional length polymorphism which varies by single-basepair increments, is adjacent to the dinucleotide repeat block, and enhances the polymorphic content of this marker. The four (dC-dA)n.(dG-dT)n loci are each easily amplified by PCR in two diplex reactions. The variability of allele lengths at these loci makes them ideal for carrier detection and prenatal diagnosis, often providing diagnostic information when RFLP analysis is uninformative. These markers have aided in identification of deletion mutations, exclusion of maternal cell contamination of chorionic villus samples, confirmation of paternity, and mapping of gene recombinations. The allele identification of these loci can be performed either with a radiolabel or with an automated, nonradioactive, fluorescent gel detection system.

%B Am J Hum Genet %V 49 %P 951-60 %8 1991 Nov %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/1928100?dopt=Abstract %0 Journal Article %J Genomics %D 1990 %T Multiplex DNA deletion detection and exon sequencing of the hypoxanthine phosphoribosyltransferase gene in Lesch-Nyhan families. %A Richard A Gibbs %A Nguyen, P N %A Edwards, A %A Civitello, A B %A Caskey, C T %K Base Sequence %K Chromosome Deletion %K DNA %K Exons %K Female %K Genes %K Genetic Carrier Screening %K Humans %K Hypoxanthine Phosphoribosyltransferase %K Lesch-Nyhan Syndrome %K Male %K Molecular Sequence Data %K Pedigree %K Polymerase Chain Reaction %X

The Lesch-Nyhan (LN) syndrome is a genetically lethal human neurological disease that results from mutations that inactivate the hypoxanthine phosphoribosyltransferase (HPRT) gene. The elucidation of the complete DNA sequence of the human HPRT gene locus has enabled the construction of multiple oligonucleotide primer sets for the simultaneous in vitro amplification of all nine HPRT exons. The multiplex polymerase chain reaction provides a facile assay for the detection of HPRT exon deletions and the reaction products can be analyzed by direct automated fluorescent DNA sequencing to identify subtle alterations in the gene. Alterations have been identified in the HPRT genes from 15 independent LN cases, and 10 LN family studies were performed. The sequencing method uses solid supports and is sufficiently simple and sensitive to be a favored approach for LN diagnosis. LN heterozygotes can be diagnosed without reference to the affected male. In addition, these procedures will be useful for somatic mutagenesis studies.

%B Genomics %V 7 %P 235-44 %8 1990 Jun %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/2347587?dopt=Abstract %R 10.1016/0888-7543(90)90545-6 %0 Journal Article %J Trans Assoc Am Physicians %D 1989 %T Automated DNA sequencing methods for detection and analysis of mutations: applications to the Lesch-Nyhan syndrome. %A Edwards, A %A Richard A Gibbs %A Nguyen, P N %A Ansorge, W %A Caskey, C T %K Base Sequence %K Chromosome Deletion %K DNA %K Female %K Genetic Carrier Screening %K Humans %K Hypoxanthine Phosphoribosyltransferase %K Lesch-Nyhan Syndrome %K Male %K Mutation %K Pedigree %K Polymerase Chain Reaction %K Polymorphism, Genetic %K Pregnancy %K Prenatal Diagnosis %K Repetitive Sequences, Nucleic Acid %K Restriction Mapping %B Trans Assoc Am Physicians %V 102 %P 185-94 %8 1989 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/2638525?dopt=Abstract %0 Journal Article %J Proc Natl Acad Sci U S A %D 1989 %T Identification of mutations leading to the Lesch-Nyhan syndrome by automated direct DNA sequencing of in vitro amplified cDNA. %A Gibbs, R A %A Nguyen, P N %A McBride, L J %A Koepf, S M %A Caskey, C T %K Alleles %K Autoanalysis %K Base Sequence %K DNA %K DNA-Directed DNA Polymerase %K Gene Amplification %K Humans %K Hypoxanthine Phosphoribosyltransferase %K Lesch-Nyhan Syndrome %K Mutation %K Nucleic Acid Hybridization %K Oligonucleotide Probes %K Pedigree %K RNA Splicing %K Software %X

The Lesch-Nyhan (LN) syndrome is a severe X chromosome-linked disease that results from a deficiency of the purine salvage enzyme hypoxanthine phosphoribosyltransferase (HPRT). The mutations leading to the disease are heterogeneous and frequently arise as de novo events. We have identified nucleotide alterations in 15 independently arising HPRT-deficiency cases by direct DNA sequencing of in vitro amplified HPRT cDNA. We also demonstrate that the direct DNA sequence analysis can be automated, further simplifying the detection of new mutations at this locus. The mutations include DNA base substitutions, small DNA deletions, a single DNA base insertion, and errors in RNA splicing. The application of these procedures allows DNA diagnosis and carrier identification by the direct detection of the mutant alleles within individual families affected by LN.

%B Proc Natl Acad Sci U S A %V 86 %P 1919-23 %8 1989 Mar %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/2928313?dopt=Abstract %R 10.1073/pnas.86.6.1919