%0 Journal Article %J Genome Med %D 2022 %T Sequencing individual genomes with recurrent genomic disorder deletions: an approach to characterize genes for autosomal recessive rare disease traits. %A Bo Yuan %A Schulze, Katharina V %A Assia Batzir, Nurit %A Sinson, Jefferson %A Dai, Hongzheng %A Zhu, Wenmiao %A Bocanegra, Francia %A Fong, Chin-To %A Holder, Jimmy %A Nguyen, Joanne %A Schaaf, Christian P %A Yang, Yaping %A Bi, Weimin %A Eng, Christine %A Shaw, Chad %A James R Lupski %A Liu, Pengfei %K Base Sequence %K Genomics %K Homologous Recombination %K Humans %K Rare Diseases %K Retrospective Studies %X

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

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

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

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

%B Genome Med %V 14 %P 113 %8 2022 Sep 30 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/36180924?dopt=Abstract %R 10.1186/s13073-022-01113-y %0 Journal Article %J 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 Ann Neurol %D 2021 %T MED27 Variants Cause Developmental Delay, Dystonia, and Cerebellar Hypoplasia. %A Meng, Linyan %A Isohanni, Pirjo %A Shao, Yunru %A Graham, Brett H %A Hickey, Scott E %A Brooks, Stephanie %A Suomalainen, Anu %A Joset, Pascal %A Steindl, Katharina %A Rauch, Anita %A Hackenberg, Annette %A High, Frances A %A Armstrong-Javors, Amy %A Mencacci, Niccolò E %A Gonzàlez-Latapi, Paulina %A Kamel, Walaa A %A Al-Hashel, Jasem Y %A Bustos, Bernabé I %A Hernandez, Alejandro V %A Krainc, Dimitri %A Lubbe, Steven J %A Van Esch, Hilde %A De Luca, Chiara %A Ballon, Katleen %A Ravelli, Claudia %A Burglen, Lydie %A Qebibo, Leila %A Calame, Daniel G %A Mitani, Tadahiro %A Marafi, Dana %A Pehlivan, Davut %A Saadi, Nebal W %A Sahin, Yavuz %A Maroofian, Reza %A Efthymiou, Stephanie %A Houlden, Henry %A Maqbool, Shazia %A Rahman, Fatima %A Gu, Shen %A Posey, Jennifer E %A James R Lupski %A Hunter, Jill V %A Wangler, Michael F %A Carroll, Christopher J %A Yang, Yaping %K Adolescent %K Adult %K Amino Acid Sequence %K Cataract %K Cerebellum %K Child %K Child, Preschool %K Developmental Disabilities %K Dystonia %K Epilepsy %K Exome Sequencing %K Genetic Variation %K Humans %K Infant %K Mediator Complex %K Nervous System Malformations %K Phenotype %X

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

%B Ann Neurol %V 89 %P 828-833 %8 2021 Apr %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/33443317?dopt=Abstract %R 10.1002/ana.26019 %0 Journal Article %J Genet Med %D 2020 %T CNVs cause autosomal recessive genetic diseases with or without involvement of SNV/indels. %A Bo Yuan %A Wang, Lei %A Liu, Pengfei %A Shaw, Chad %A Dai, Hongzheng %A Cooper, Lance %A Zhu, Wenmiao %A Anderson, Stephanie A %A Meng, Linyan %A Wang, Xia %A Wang, Yue %A Xia, Fan %A Xiao, Rui %A Braxton, Alicia %A Peacock, Sandra %A Schmitt, Eric %A Ward, Patricia A %A Vetrini, Francesco %A He, Weimin %A Chiang, Theodore %A Donna M Muzny %A Richard A Gibbs %A Beaudet, Arthur L %A Breman, Amy M %A Smith, Janice %A Cheung, Sau Wai %A Bacino, Carlos A %A Eng, Christine M %A Yang, Yaping %A James R Lupski %A Bi, Weimin %K Child %K DNA Copy Number Variations %K Exome Sequencing %K Exons %K Humans %K INDEL Mutation %K Retrospective Studies %X

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

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

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

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

%B Genet Med %V 22 %P 1633-1641 %8 2020 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/32576985?dopt=Abstract %R 10.1038/s41436-020-0864-8 %0 Journal Article %J Genet Med %D 2020 %T Low-level parental somatic mosaic SNVs in exomes from a large cohort of trios with diverse suspected Mendelian conditions. %A Gambin, Tomasz %A Liu, Qian %A Karolak, Justyna A %A Grochowski, Christopher M %A Xie, Nina G %A Wu, Lucia R %A Yan, Yan Helen %A Cao, Ye %A Coban Akdemir, Zeynep H %A Wilson, Theresa A %A Jhangiani, Shalini N %A Chen, Ed %A Eng, Christine M %A Donna M Muzny %A Posey, Jennifer E %A Yang, Yaping %A Zhang, David Y %A Shaw, Chad %A Liu, Pengfei %A James R Lupski %A Stankiewicz, Paweł %K Exome %K Exome Sequencing %K High-Throughput Nucleotide Sequencing %K Humans %K Mosaicism %K Parents %X

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

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

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

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

%B Genet Med %V 22 %P 1768-1776 %8 2020 Nov %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/32655138?dopt=Abstract %R 10.1038/s41436-020-0897-z %0 Journal Article %J Am J Med Genet A %D 2020 %T Wolff-Parkinson-White syndrome: De novo variants and evidence for mutational burden in genes associated with atrial fibrillation. %A Coban-Akdemir, Zeynep H %A Charng, Wu-Lin %A Azamian, Mahshid %A Paine, Ingrid S %A Punetha, Jaya %A Grochowski, Christopher M %A Gambin, Tomasz %A Valdes, Santiago O %A Cannon, Bryan %A Zapata, Gladys %A Hernandez, Patricia P %A Jhangiani, Shalini %A Harshavardhan Doddapaneni %A Jianhong Hu %A Boricha, Fatima %A Donna M Muzny %A Eric Boerwinkle %A Yang, Yaping %A Richard A Gibbs %A Posey, Jennifer E %A Wehrens, Xander H T %A Belmont, John W %A Kim, Jeffrey J %A Miyake, Christina Y %A James R Lupski %A Lalani, Seema R %K Adolescent %K Adult %K AMP-Activated Protein Kinases %K Ankyrins %K Atrial Fibrillation %K Carrier Proteins %K Child %K Cohort Studies %K Cytoskeletal Proteins %K DNA-Binding Proteins %K Exome Sequencing %K Female %K Genetic Association Studies %K Genetic Predisposition to Disease %K Heart Atria %K Homeodomain Proteins %K Humans %K LIM Domain Proteins %K Male %K Mutation %K Transcription Factors %K Wolff-Parkinson-White Syndrome %K Young Adult %X

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

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

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

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

%B Am J Med Genet A %V 182 %P 1387-1399 %8 2020 Jun %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/32233023?dopt=Abstract %R 10.1002/ajmg.a.61571 %0 Journal Article %J Genet Med %D 2019 %T Atlas-CNV: a validated approach to call single-exon CNVs in the eMERGESeq gene panel. %A Chiang, Theodore %A Liu, Xiuping %A Wu, Tsung-Jung %A Jianhong Hu %A Fritz J Sedlazeck %A White, Simon %A Schaid, Daniel %A Andrade, Mariza de %A Jarvik, Gail P %A Crosslin, David %A Stanaway, Ian %A Carrell, David S %A Connolly, John J %A Hakonarson, Hakon %A Groopman, Emily E %A Gharavi, Ali G %A Fedotov, Alexander %A Bi, Weimin %A Leduc, Magalie S %A David R Murdock %A Jiang, Yunyun %A Meng, Linyan %A Eng, Christine M %A Wen, Shu %A Yang, Yaping %A Donna M Muzny %A Eric Boerwinkle %A Salerno, William %A Eric Venner %A Richard A Gibbs %K DNA Copy Number Variations %K Exons %K Genome, Human %K High-Throughput Nucleotide Sequencing %K Humans %K Sequence Analysis, DNA %K Software %X

PURPOSE: To provide a validated method to confidently identify exon-containing copy-number variants (CNVs), with a low false discovery rate (FDR), in targeted sequencing data from a clinical laboratory with particular focus on single-exon CNVs.

METHODS: DNA sequence coverage data are normalized within each sample and subsequently exonic CNVs are identified in a batch of samples, when the target log ratio of the sample to the batch median exceeds defined thresholds. The quality of exonic CNV calls is assessed by C-scores (Z-like scores) using thresholds derived from gold standard samples and simulation studies. We integrate an ExonQC threshold to lower FDR and compare performance with alternate software (VisCap).

RESULTS: Thirteen CNVs were used as a truth set to validate Atlas-CNV and compared with VisCap. We demonstrated FDR reduction in validation, simulation, and 10,926 eMERGESeq samples without sensitivity loss. Sixty-four multiexon and 29 single-exon CNVs with high C-scores were assessed by Multiplex Ligation-dependent Probe Amplification (MLPA).

CONCLUSION: Atlas-CNV is validated as a method to identify exonic CNVs in targeted sequencing data generated in the clinical laboratory. The ExonQC and C-score assignment can reduce FDR (identification of targets with high variance) and improve calling accuracy of single-exon CNVs respectively. We propose guidelines and criteria to identify high confidence single-exon CNVs.

%B Genet Med %V 21 %P 2135-2144 %8 2019 Sep %G eng %N 9 %1 https://www.ncbi.nlm.nih.gov/pubmed/30890783?dopt=Abstract %R 10.1038/s41436-019-0475-4 %0 Journal Article %J Genet Med %D 2019 %T Clinical exome sequencing reveals locus heterogeneity and phenotypic variability of cohesinopathies. %A Bo Yuan %A Neira, Juanita %A Pehlivan, Davut %A Santiago-Sim, Teresa %A Song, Xiaofei %A Rosenfeld, Jill %A Posey, Jennifer E %A Patel, Vipulkumar %A Jin, Weihong %A Adam, Margaret P %A Baple, Emma L %A Dean, John %A Fong, Chin-To %A Hickey, Scott E %A Hudgins, Louanne %A Leon, Eyby %A Madan-Khetarpal, Suneeta %A Rawlins, Lettie %A Rustad, Cecilie F %A Stray-Pedersen, Asbjørg %A Tveten, Kristian %A Wenger, Olivia %A Diaz, Jullianne %A Jenkins, Laura %A Martin, Laura %A McGuire, Marianne %A Pietryga, Marguerite %A Ramsdell, Linda %A Slattery, Leah %A Abid, Farida %A Bertuch, Alison A %A Grange, Dorothy %A Immken, Ladonna %A Schaaf, Christian P %A Van Esch, Hilde %A Bi, Weimin %A Cheung, Sau Wai %A Breman, Amy M %A Smith, Janice L %A Shaw, Chad %A Crosby, Andrew H %A Christine M Eng %A Yang, Yaping %A James R Lupski %A Xiao, Rui %A Liu, Pengfei %K Adolescent %K Alleles %K Antigens, Nuclear %K Biological Variation, Population %K Carrier Proteins %K Cell Cycle Proteins %K Child %K Child, Preschool %K Chromosomal Proteins, Non-Histone %K Cohort Studies %K De Lange Syndrome %K Exome %K Female %K Gene Frequency %K Genetic Heterogeneity %K Humans %K INDEL Mutation %K Male %K Mutation %K Nuclear Proteins %K Phenotype %K Polymorphism, Single Nucleotide %K Proto-Oncogene Proteins %K Retrospective Studies %K Whole Exome Sequencing %X

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

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

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

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

%B Genet Med %V 21 %P 663-675 %8 2019 03 %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/30158690?dopt=Abstract %R 10.1038/s41436-018-0085-6 %0 Journal Article %J Genome Med %D 2019 %T Copy number variant and runs of homozygosity detection by microarrays enabled more precise molecular diagnoses in 11,020 clinical exome cases. %A Dharmadhikari, Avinash V %A Ghosh, Rajarshi %A Bo Yuan %A Liu, Pengfei %A Dai, Hongzheng %A Al Masri, Sami %A Scull, Jennifer %A Posey, Jennifer E %A Jiang, Allen H %A He, Weimin %A Vetrini, Francesco %A Braxton, Alicia A %A Ward, Patricia %A Chiang, Theodore %A Qu, Chunjing %A Gu, Shen %A Shaw, Chad A %A Smith, Janice L %A Lalani, Seema %A Stankiewicz, Pawel %A Cheung, Sau-Wai %A Bacino, Carlos A %A Patel, Ankita %A Breman, Amy M %A Wang, Xia %A Meng, Linyan %A Xiao, Rui %A Xia, Fan %A Donna M Muzny %A Richard A Gibbs %A Beaudet, Arthur L %A Eng, Christine M %A James R Lupski %A Yang, Yaping %A Bi, Weimin %K Chromosome Aberrations %K DNA Copy Number Variations %K Exome Sequencing %K Female %K Genetic Testing %K Homozygote %K Humans %K Limit of Detection %K Male %K Microarray Analysis %X

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

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

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

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

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

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

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

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

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

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

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

%B Genome Med %V 11 %P 12 %8 2019 Feb 28 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/30819258?dopt=Abstract %R 10.1186/s13073-019-0623-0 %0 Journal Article %J 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 Missense Variants in the Histone Acetyltransferase Complex Component Gene TRRAP Cause Autism and Syndromic Intellectual Disability. %A Cogné, Benjamin %A Ehresmann, Sophie %A Beauregard-Lacroix, Eliane %A Rousseau, Justine %A Besnard, Thomas %A Garcia, Thomas %A Petrovski, Slavé %A Avni, Shiri %A McWalter, Kirsty %A Blackburn, Patrick R %A Sanders, Stephan J %A Uguen, Kévin %A Harris, Jacqueline %A Cohen, Julie S %A Blyth, Moira %A Lehman, Anna %A Berg, Jonathan %A Li, Mindy H %A Kini, Usha %A Joss, Shelagh %A von der Lippe, Charlotte %A Gordon, Christopher T %A Humberson, Jennifer B %A Robak, Laurie %A Scott, Daryl A %A Sutton, Vernon R %A Skraban, Cara M %A Johnston, Jennifer J %A Poduri, Annapurna %A Nordenskjöld, Magnus %A Shashi, Vandana %A Gerkes, Erica H %A Bongers, Ernie M H F %A Gilissen, Christian %A Zarate, Yuri A %A Kvarnung, Malin %A Lally, Kevin P %A Kulch, Peggy A %A Daniels, Brina %A Hernandez-Garcia, Andres %A Stong, Nicholas %A McGaughran, Julie %A Retterer, Kyle %A Tveten, Kristian %A Sullivan, Jennifer %A Geisheker, Madeleine R %A Stray-Pedersen, Asbjorg %A Tarpinian, Jennifer M %A Klee, Eric W %A Sapp, Julie C %A Zyskind, Jacob %A Holla, Øystein L %A Bedoukian, Emma %A Filippini, Francesca %A Guimier, Anne %A Picard, Arnaud %A Busk, Øyvind L %A Punetha, Jaya %A Pfundt, Rolph %A Lindstrand, Anna %A Nordgren, Ann %A Kalb, Fayth %A Desai, Megha %A Ebanks, Ashley Harmon %A Jhangiani, Shalini N %A Dewan, Tammie %A Coban Akdemir, Zeynep H %A Telegrafi, Aida %A Zackai, Elaine H %A Begtrup, Amber %A Song, Xiaofei %A Toutain, Annick %A Wentzensen, Ingrid M %A Odent, Sylvie %A Bonneau, Dominique %A Latypova, Xénia %A Deb, Wallid %A Redon, Sylvia %A Bilan, Frédéric %A Legendre, Marine %A Troyer, Caitlin %A Whitlock, Kerri %A Caluseriu, Oana %A Murphree, Marine I %A Pichurin, Pavel N %A Agre, Katherine %A Gavrilova, Ralitza %A Rinne, Tuula %A Park, Meredith %A Shain, Catherine %A Heinzen, Erin L %A Xiao, Rui %A Amiel, Jeanne %A Lyonnet, Stanislas %A Isidor, Bertrand %A Biesecker, Leslie G %A Lowenstein, Dan %A Posey, Jennifer E %A Denommé-Pichon, Anne-Sophie %A Férec, Claude %A Yang, Xiang-Jiao %A Rosenfeld, Jill A %A Gilbert-Dussardier, Brigitte %A Audebert-Bellanger, Séverine %A Redon, Richard %A Stessman, Holly A F %A Nellaker, Christoffer %A Yang, Yaping %A James R Lupski %A Goldstein, David B %A Eichler, Evan E %A Bolduc, Francois %A Bézieau, Stéphane %A Küry, Sébastien %A Campeau, Philippe M %K Adaptor Proteins, Signal Transducing %K Adolescent %K Adult %K Amino Acid Sequence %K Autistic Disorder %K Child %K Child, Preschool %K Female %K Genetic Association Studies %K Humans %K Infant %K Intellectual Disability %K Male %K Mutation, Missense %K Nuclear Proteins %K Prognosis %K Sequence Homology %K Syndrome %K Young Adult %X

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

%B Am J Hum Genet %V 104 %P 530-541 %8 2019 Mar 07 %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/30827496?dopt=Abstract %R 10.1016/j.ajhg.2019.01.010 %0 Journal Article %J N Engl J Med %D 2019 %T Reanalysis of Clinical Exome Sequencing Data. %A Liu, Pengfei %A Meng, Linyan %A Normand, Elizabeth A %A Xia, Fan %A Song, Xiaofei %A Ghazi, Andrew %A Rosenfeld, Jill %A Magoulas, Pilar L %A Braxton, Alicia %A Ward, Patricia %A Dai, Hongzheng %A Bo Yuan %A Bi, Weimin %A Xiao, Rui %A Wang, Xia %A Chiang, Theodore %A Vetrini, Francesco %A He, Weimin %A Cheng, Hanyin %A Dong, Jie %A Gijavanekar, Charul %A Benke, Paul J %A Bernstein, Jonathan A %A Eble, Tanya %A Eroglu, Yasemen %A Erwin, Deanna %A Escobar, Luis %A Gibson, James B %A Gripp, Karen %A Kleppe, Soledad %A Koenig, Mary K %A Lewis, Andrea M %A Natowicz, Marvin %A Mancias, Pedro %A Minor, LaKeesha %A Scaglia, Fernando %A Schaaf, Christian P %A Streff, Haley %A Vernon, Hilary %A Uhles, Crescenda L %A Zackai, Elaine H %A Wu, Nan %A Sutton, V Reid %A Beaudet, Arthur L %A Donna M Muzny %A Richard A Gibbs %A Posey, Jennifer E %A Lalani, Seema %A Shaw, Chad %A Christine M Eng %A James R Lupski %A Yang, Yaping %K Exome %K Genetic Diseases, Inborn %K Genetic Testing %K Humans %K Mutation %K Phenotype %K Sequence Analysis, DNA %K Whole Exome Sequencing %B N Engl J Med %V 380 %P 2478-2480 %8 2019 06 20 %G eng %N 25 %1 https://www.ncbi.nlm.nih.gov/pubmed/31216405?dopt=Abstract %R 10.1056/NEJMc1812033 %0 Journal Article %J Genome Med %D 2018 %T Clinical exome sequencing for fetuses with ultrasound abnormalities and a suspected Mendelian disorder. %A Normand, Elizabeth A %A Braxton, Alicia %A Nassef, Salma %A Ward, Patricia A %A Vetrini, Francesco %A He, Weimin %A Patel, Vipulkumar %A Qu, Chunjing %A Westerfield, Lauren E %A Stover, Samantha %A Dharmadhikari, Avinash V %A Donna M Muzny %A Richard A Gibbs %A Dai, Hongzheng %A Meng, Linyan %A Wang, Xia %A Xiao, Rui %A Liu, Pengfei %A Bi, Weimin %A Xia, Fan %A Walkiewicz, Magdalena %A Van den Veyver, Ignatia B %A Eng, Christine M %A Yang, Yaping %K Exome Sequencing %K Family %K Fetus %K Genetic Diseases, Inborn %K Humans %K Inheritance Patterns %K Phenotype %K Ultrasonography, Prenatal %X

BACKGROUND: Exome sequencing is now being incorporated into clinical care for pediatric and adult populations, but its integration into prenatal diagnosis has been more limited. One reason for this is the paucity of information about the clinical utility of exome sequencing in the prenatal setting.

METHODS: We retrospectively reviewed indications, results, time to results (turnaround time, TAT), and impact of exome results for 146 consecutive "fetal exomes" performed in a clinical diagnostic laboratory between March 2012 and November 2017. We define a fetal exome as one performed on a sample obtained from a fetus or a product of conception with at least one structural anomaly detected by prenatal imaging or autopsy. Statistical comparisons were performed using Fisher's exact test.

RESULTS: Prenatal exome yielded an overall molecular diagnostic rate of 32% (n = 46/146). Of the 46 molecular diagnoses, 50% were autosomal dominant disorders (n = 23/46), 41% were autosomal recessive disorders (n = 19/46), and 9% were X-linked disorders (n = 4/46). The molecular diagnostic rate was highest for fetuses with anomalies affecting multiple organ systems and for fetuses with craniofacial anomalies. Out of 146 cases, a prenatal trio exome option designed for ongoing pregnancies was performed on 62 fetal specimens, resulting in a diagnostic yield of 35% with an average TAT of 14 days for initial reporting (excluding tissue culture time). The molecular diagnoses led to refined recurrence risk estimates, altered medical management, and informed reproductive planning for families.

CONCLUSION: Exome sequencing is a useful diagnostic tool when fetal structural anomalies suggest a genetic etiology, but other standard prenatal genetic tests did not provide a diagnosis.

%B Genome Med %V 10 %P 74 %8 2018 Sep 28 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/30266093?dopt=Abstract %R 10.1186/s13073-018-0582-x %0 Journal Article %J Ann Clin Transl Neurol %D 2018 %T Phenotypic expansion in - a common cause of intellectual disability in females. %A Wang, Xia %A Posey, Jennifer E %A Rosenfeld, Jill A %A Bacino, Carlos A %A Scaglia, Fernando %A Immken, Ladonna %A Harris, Jill M %A Hickey, Scott E %A Mosher, Theresa M %A Slavotinek, Anne %A Zhang, Jing %A Beuten, Joke %A Leduc, Magalie S %A He, Weimin %A Vetrini, Francesco %A Walkiewicz, Magdalena A %A Bi, Weimin %A Xiao, Rui %A Liu, Pengfei %A Shao, Yunru %A Gezdirici, Alper %A Gulec, Elif Y %A Jiang, Yunyun %A Darilek, Sandra A %A Hansen, Adam W %A Khayat, Michael M %A Pehlivan, Davut %A Piard, Juliette %A Donna M Muzny %A Hanchard, Neil %A Belmont, John W %A Van Maldergem, Lionel %A Richard A Gibbs %A Eldomery, Mohammad K %A Akdemir, Zeynep C %A Adesina, Adekunle M %A Chen, Shan %A Lee, Yi-Chien %A Lee, Brendan %A James R Lupski %A Eng, Christine M %A Xia, Fan %A Yang, Yaping %A Graham, Brett H %A Moretti, Paolo %X

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

%B Ann Clin Transl Neurol %V 5 %P 1277-1285 %8 2018 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/30349862?dopt=Abstract %R 10.1002/acn3.622 %0 Journal Article %J Am J 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 Med Genet %D 2017 %T Congenital heart defects and left ventricular non-compaction in males with loss-of-function variants in NONO. %A Scott, Daryl A %A Hernandez-Garcia, Andres %A Azamian, Mahshid S %A Jordan, Valerie K %A Kim, Bum Jun %A Starkovich, Molly %A Zhang, Jinglan %A Wong, Lee-Jun %A Darilek, Sandra A %A Breman, Amy M %A Yang, Yaping %A Lupski, James R %A Jiwani, Amyn K %A Das, Bibhuti %A Lalani, Seema R %A Iglesias, Alejandro D %A Rosenfeld, Jill A %A Xia, Fan %K Child %K Child, Preschool %K Developmental Disabilities %K DNA-Binding Proteins %K Exome %K Heart Defects, Congenital %K Heart Ventricles %K Humans %K Infant %K Male %K Nuclear Matrix-Associated Proteins %K Octamer Transcription Factors %K RNA-Binding Proteins %X

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

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

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

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

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

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

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

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

%B Am J Hum Genet %V 101 %P 716-724 %8 2017 Nov 02 %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/29100085?dopt=Abstract %R 10.1016/j.ajhg.2017.09.014 %0 Journal Article %J Hum Genet %D 2017 %T Erratum to: Haploinsufficiency of the E3 ubiquitin-protein ligase gene TRIP12 causes intellectual disability with or without autism spectrum disorders, speech delay, and dysmorphic features. %A Zhang, Jing %A Gambin, Tomasz %A Bo Yuan %A Szafranski, Przemyslaw %A Rosenfeld, Jill A %A Balwi, Mohammed Al %A Alswaid, Abdulrahman %A Al-Gazali, Lihadh %A Shamsi, Aisha M Al %A Komara, Makanko %A Ali, Bassam R %A Roeder, Elizabeth %A McAuley, Laura %A Roy, Daniel S %A Manchester, David K %A Magoulas, Pilar %A King, Lauren E %A Hannig, Vickie %A Bonneau, Dominique %A Denommé-Pichon, Anne-Sophie %A Charif, Majida %A Besnard, Thomas %A Bézieau, Stéphane %A Cogné, Benjamin %A Andrieux, Joris %A Zhu, Wenmiao %A He, Weimin %A Vetrini, Francesco %A Ward, Patricia A %A Cheung, Sau Wai %A Bi, Weimin %A Eng, Christine M %A Lupski, James R %A Yang, Yaping %A Patel, Ankita %A Lalani, Seema R %A Xia, Fan %A Stankiewicz, Paweł %B Hum Genet %V 136 %P 1009-1011 %8 2017 Aug %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/28660352?dopt=Abstract %R 10.1007/s00439-017-1828-1 %0 Journal Article %J Nat Genet %D 2017 %T Germline mutations in ABL1 cause an autosomal dominant syndrome characterized by congenital heart defects and skeletal malformations. %A Wang, Xia %A Charng, Wu-Lin %A Chen, Chun-An %A Rosenfeld, Jill A %A Al Shamsi, Aisha %A Al-Gazali, Lihadh %A McGuire, Marianne %A Mew, Nicholas Ah %A Arnold, Georgianne L %A Qu, Chunjing %A Ding, Yan %A Muzny, Donna M %A Gibbs, Richard A %A Eng, Christine M %A Walkiewicz, Magdalena %A Xia, Fan %A Plon, Sharon E %A Lupski, James R %A Schaaf, Christian P %A Yang, Yaping %K Abnormalities, Multiple %K Animals %K Bone Diseases, Developmental %K Cell Line %K Chromosome Disorders %K Craniofacial Abnormalities %K Feeding and Eating Disorders %K Female %K Fusion Proteins, bcr-abl %K Germ-Line Mutation %K Heart Defects, Congenital %K HEK293 Cells %K Humans %K Leukemia, Myelogenous, Chronic, BCR-ABL Positive %K Limb Deformities, Congenital %K Male %K Mice %K Mice, Knockout %K Philadelphia Chromosome %K Phosphorylation %K Proto-Oncogene Mas %K Signal Transduction %X

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

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

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

%B Hum Genet %V 136 %P 377-386 %8 2017 Apr %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/28251352?dopt=Abstract %R 10.1007/s00439-017-1763-1 %0 Journal Article %J Hum Mutat %D 2017 %T Heterozygous variants in ACTL6A, encoding a component of the BAF complex, are associated with intellectual disability. %A Marom, Ronit %A Jain, Mahim %A Burrage, Lindsay C %A Song, I-Wen %A Graham, Brett H %A Brown, Chester W %A Stevens, Servi J C %A Stegmann, Alexander P A %A Gunter, Andrew T %A Kaplan, Julie D %A Gavrilova, Ralitza H %A Shinawi, Marwan %A Rosenfeld, Jill A %A Bae, Yangjin %A Tran, Alyssa A %A Chen, Yuqing %A Lu, James T %A Gibbs, Richard A %A Eng, Christine %A Yang, Yaping %A Rousseau, Justine %A de Vries, Bert B A %A Campeau, Philippe M %A Lee, Brendan %K Actins %K Adolescent %K Child %K Chromatin Assembly and Disassembly %K Chromosomal Proteins, Non-Histone %K DNA Helicases %K DNA-Binding Proteins %K Exome %K Face %K Female %K Hand Deformities, Congenital %K Heterozygote %K Humans %K Intellectual Disability %K Male %K Micrognathism %K Multiprotein Complexes %K Mutation, Missense %K Nuclear Proteins %K Protein Binding %K Transcription Factors %X

Pathogenic variants in genes encoding components of the BRG1-associated factor (BAF) chromatin remodeling complex have been associated with intellectual disability syndromes. We identified heterozygous, novel variants in ACTL6A, a gene encoding a component of the BAF complex, in three subjects with varying degrees of intellectual disability. Two subjects have missense variants affecting highly conserved amino acid residues within the actin-like domain. Missense mutations in the homologous region in yeast actin were previously reported to be dominant lethal and were associated with impaired binding of the human ACTL6A to β-actin and BRG1. A third subject has a splicing variant that creates an in-frame deletion. Our findings suggest that the variants identified in our subjects may have a deleterious effect on the function of the protein by disturbing the integrity of the BAF complex. Thus, ACTL6A gene mutation analysis should be considered in patients with intellectual disability, learning disabilities, or developmental language disorder.

%B Hum Mutat %V 38 %P 1365-1371 %8 2017 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/28649782?dopt=Abstract %R 10.1002/humu.23282 %0 Journal Article %J Genome Med %D 2017 %T Identification of novel candidate disease genes from de novo exonic copy number variants. %A Gambin, Tomasz %A Bo Yuan %A Bi, Weimin %A Liu, Pengfei %A Rosenfeld, Jill A %A Coban-Akdemir, Zeynep %A Pursley, Amber N %A Nagamani, Sandesh C S %A Marom, Ronit %A Golla, Sailaja %A Dengle, Lauren %A Petrie, Heather G %A Matalon, Reuben %A Emrick, Lisa %A Proud, Monica B %A Treadwell-Deering, Diane %A Chao, Hsiao-Tuan %A Koillinen, Hannele %A Brown, Chester %A Urraca, Nora %A Mostafavi, Roya %A Bernes, Saunder %A Roeder, Elizabeth R %A Nugent, Kimberly M %A Bader, Patricia I %A Bellus, Gary %A Cummings, Michael %A Northrup, Hope %A Ashfaq, Myla %A Westman, Rachel %A Wildin, Robert %A Beck, Anita E %A Immken, Ladonna %A Elton, Lindsay %A Varghese, Shaun %A Buchanan, Edward %A Faivre, Laurence %A Lefebvre, Mathilde %A Schaaf, Christian P %A Walkiewicz, Magdalena %A Yang, Yaping %A Kang, Sung-Hae L %A Lalani, Seema R %A Bacino, Carlos A %A Beaudet, Arthur L %A Breman, Amy M %A Smith, Janice L %A Cheung, Sau Wai %A James R Lupski %A Patel, Ankita %A Shaw, Chad A %A Stankiewicz, Paweł %K Cohort Studies %K DNA Copy Number Variations %K Exons %K Genetic Diseases, Inborn %K Genome, Human %K Homeodomain Proteins %K Humans %K Intracellular Signaling Peptides and Proteins %K Membrane Proteins %K Neurodevelopmental Disorders %K Protein Serine-Threonine Kinases %K Retrospective Studies %K Serine-Threonine Kinase 3 %K Transcription Factors %K Whole Genome Sequencing %X

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

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

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

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

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

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

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

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

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

%B Genome Med %V 9 %P 26 %8 2017 Mar 21 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/28327206?dopt=Abstract %R 10.1186/s13073-017-0412-6 %0 Journal Article %J Genet Med %D 2017 %T The next generation of population-based spinal muscular atrophy carrier screening: comprehensive pan-ethnic SMN1 copy-number and sequence variant analysis by massively parallel sequencing. %A Feng, Yanming %A Ge, Xiaoyan %A Meng, Linyan %A Scull, Jennifer %A Li, Jianli %A Tian, Xia %A Zhang, Tao %A Jin, Weihong %A Cheng, Hanyin %A Wang, Xia %A Tokita, Mari %A Liu, Pengfei %A Mei, Hui %A Wang, Yue %A Li, Fangyuan %A Schmitt, Eric S %A Zhang, Wei V %A Donna M Muzny %A Wen, Shu %A Chen, Zhao %A Yang, Yaping %A Beaudet, Arthur L %A Liu, Xiaoming %A Eng, Christine M %A Xia, Fan %A Wong, Lee-Jun %A Zhang, Jinglan %K Gene Dosage %K Genetic Carrier Screening %K High-Throughput Nucleotide Sequencing %K Humans %K Muscular Atrophy, Spinal %K Polymorphism, Single Nucleotide %K Reproducibility of Results %K Sensitivity and Specificity %K Survival of Motor Neuron 1 Protein %K Survival of Motor Neuron 2 Protein %X

PURPOSE: To investigate pan-ethnic SMN1 copy-number and sequence variation by hybridization-based target enrichment coupled with massively parallel sequencing or next-generation sequencing (NGS).

METHODS: NGS reads aligned to SMN1 and SMN2 exon 7 were quantified to determine the total combined copy number of SMN1 and SMN2. The ratio of SMN1 to SMN2 was calculated based on a single-nucleotide difference that distinguishes the two genes. SMN1 copy-number results were compared between the NGS and quantitative polymerase chain reaction and/or multiplex ligation-dependent probe amplification. The NGS data set was also queried for the g.27134T>G single-nucleotide polymorphism (SNP) and other SMN1 sequence pathogenic variants.

RESULTS: The sensitivity of the test to detect spinal muscular atrophy (SMA) carriers with one copy of SMN1 was 100% (95% confidence interval (CI): 95.9-100%; n = 90) and specificity was 99.6% (95% CI: 99.4-99.7%; n = 6,648). Detection of the g.27134T>G SNP by NGS was 100% concordant with an restriction fragment-length polymorphism method (n = 493). Ten single-nucleotide variants in SMN1 were detectable by NGS and confirmed by gene-specific amplicon-based sequencing. This comprehensive approach yielded SMA carrier detection rates of 90.3-95.0% in five ethnic groups studied.

CONCLUSION: We have developed a novel, comprehensive SMN1 copy-number and sequence variant analysis method by NGS that demonstrated improved SMA carrier detection rates across the entire population examined.Genet Med advance online publication 19 January 2017.

%B Genet Med %V 19 %P 936-944 %8 2017 Aug %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/28125085?dopt=Abstract %R 10.1038/gim.2016.215 %0 Journal Article %J Genome Med %D 2017 %T Phenotypic and molecular characterisation of CDK13-related congenital heart defects, dysmorphic facial features and intellectual developmental disorders. %A Bostwick, Bret L %A McLean, Scott %A Posey, Jennifer E %A Streff, Haley E %A Gripp, Karen W %A Blesson, Alyssa %A Powell-Hamilton, Nina %A Tusi, Jessica %A Stevenson, David A %A Farrelly, Ellyn %A Hudgins, Louanne %A Yang, Yaping %A Xia, Fan %A Wang, Xia %A Liu, Pengfei %A Walkiewicz, Magdalena %A McGuire, Marianne %A Grange, Dorothy K %A Andrews, Marisa V %A Hummel, Marybeth %A Madan-Khetarpal, Suneeta %A Infante, Elena %A Coban-Akdemir, Zeynep %A Miszalski-Jamka, Karol %A Jefferies, John L %A Rosenfeld, Jill A %A Emrick, Lisa %A Nugent, Kimberly M %A Lupski, James R %A Belmont, John W %A Lee, Brendan %A Lalani, Seema R %K Adolescent %K Adult %K CDC2 Protein Kinase %K Child %K Child, Preschool %K Face %K Female %K Heart Defects, Congenital %K Humans %K Infant %K Intellectual Disability %K Male %K Mutation %K Phenotype %K Syndrome %X

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

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

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

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

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

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

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

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

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

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

%B J Allergy Clin Immunol %V 139 %P 232-245 %8 2017 Jan %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/27577878?dopt=Abstract %R 10.1016/j.jaci.2016.05.042 %0 Journal Article %J 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 Pediatr Blood Cancer %D 2017 %T Renal cell carcinoma harboring somatic TSC2 mutations in a child with methylmalonic acidemia. %A Potter, Samara L %A Venkatramani, Rajkumar %A Wenderfer, Scott %A Graham, Brett H %A Vasudevan, Sanjeev A %A Sher, Andrew %A Wu, Hao %A Wheeler, David A %A Yang, Yaping %A Eng, Christine M %A Gibbs, Richard A %A Roy, Angshumoy %A Plon, Sharon E %A Parsons, D Williams %K Amino Acid Metabolism, Inborn Errors %K Antineoplastic Agents %K Carcinoma, Renal Cell %K Child %K Everolimus %K Female %K Humans %K Kidney Neoplasms %K Sirolimus %K TOR Serine-Threonine Kinases %K Tuberous Sclerosis Complex 2 Protein %K Tumor Suppressor Proteins %X

Pediatric renal cell carcinoma (RCC) is a rare cancer that can be associated with inherited diseases including tuberous sclerosis complex (TSC) caused by germline mutations in TSC1 or TSC2. Somatic mutations in TSC1 and TSC2 have also been reported in adult RCC, which predict response to mTOR inhibitors. Here, we present the first case of RCC in a child with methylmalonic acidemia (MMA). Clinical whole exome sequencing of blood and tumor samples confirmed the diagnosis of MMA and revealed two somatic inactivating mutations in TSC2, suggesting the potential consideration of an mTOR inhibitor in the event of tumor recurrence.

%B Pediatr Blood Cancer %V 64 %8 2017 May %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/27748010?dopt=Abstract %R 10.1002/pbc.26286 %0 Journal Article %J N Engl J Med %D 2017 %T Resolution of Disease Phenotypes Resulting from Multilocus Genomic Variation. %A Posey, Jennifer E %A Harel, Tamar %A Liu, Pengfei %A Rosenfeld, Jill A %A James, Regis A %A Coban Akdemir, Zeynep H %A Walkiewicz, Magdalena %A Bi, Weimin %A Xiao, Rui %A Ding, Yan %A Xia, Fan %A Beaudet, Arthur L %A Muzny, Donna M %A Gibbs, Richard A %A Boerwinkle, Eric %A Eng, Christine M %A Sutton, V Reid %A Shaw, Chad A %A Plon, Sharon E %A Yang, Yaping %A Lupski, James R %K Exome %K Genetic Diseases, Inborn %K Genetic Variation %K Genotyping Techniques %K High-Throughput Nucleotide Sequencing %K Humans %K Phenotype %K Retrospective Studies %K Sequence Analysis, DNA %X

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

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

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

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

%B N Engl J Med %V 376 %P 21-31 %8 2017 Jan 05 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/27959697?dopt=Abstract %R 10.1056/NEJMoa1516767 %0 Journal Article %J JAMA Pediatr %D 2017 %T Use of Exome Sequencing for Infants in Intensive Care Units: Ascertainment of Severe Single-Gene Disorders and Effect on Medical Management. %A Meng, Linyan %A Pammi, Mohan %A Saronwala, Anirudh %A Magoulas, Pilar %A Ghazi, Andrew Ray %A Vetrini, Francesco %A Zhang, Jing %A He, Weimin %A Dharmadhikari, Avinash V %A Qu, Chunjing %A Ward, Patricia %A Braxton, Alicia %A Narayanan, Swetha %A Ge, Xiaoyan %A Tokita, Mari J %A Santiago-Sim, Teresa %A Dai, Hongzheng %A Chiang, Theodore %A Smith, Hadley %A Azamian, Mahshid S %A Robak, Laurie %A Bostwick, Bret L %A Schaaf, Christian P %A Potocki, Lorraine %A Scaglia, Fernando %A Bacino, Carlos A %A Hanchard, Neil A %A Wangler, Michael F %A Scott, Daryl %A Brown, Chester %A Hu, Jianhong %A Belmont, John W %A Burrage, Lindsay C %A Graham, Brett H %A Sutton, Vernon Reid %A Craigen, William J %A Plon, Sharon E %A Lupski, James R %A Beaudet, Arthur L %A Gibbs, Richard A %A Muzny, Donna M %A Miller, Marcus J %A Wang, Xia %A Leduc, Magalie S %A Xiao, Rui %A Liu, Pengfei %A Shaw, Chad %A Walkiewicz, Magdalena %A Bi, Weimin %A Xia, Fan %A Lee, Brendan %A Eng, Christine M %A Yang, Yaping %A Lalani, Seema R %K Adult %K Critical Care %K Disease Management %K Exome %K Exome Sequencing %K Genetic Counseling %K Genetic Diseases, Inborn %K Humans %K Infant %K Infant Care %K Infant, Newborn %K Intensive Care Units, Pediatric %K Length of Stay %K Retrospective Studies %K Texas %X

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

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

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

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

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

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

%B JAMA Pediatr %V 171 %P e173438 %8 2017 Dec 04 %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/28973083?dopt=Abstract %R 10.1001/jamapediatrics.2017.3438 %0 Journal Article %J 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 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 JAMA Oncol %D 2016 %T Diagnostic Yield of Clinical Tumor and Germline Whole-Exome Sequencing for Children With Solid Tumors. %A Parsons, D Williams %A Roy, Angshumoy %A Yang, Yaping %A Wang, Tao %A Scollon, Sarah %A Bergstrom, Katie %A Kerstein, Robin A %A Gutierrez, Stephanie %A Petersen, Andrea K %A Bavle, Abhishek %A Lin, Frank Y %A López-Terrada, Dolores H %A Monzon, Federico A %A Hicks, M John %A Eldin, Karen W %A Quintanilla, Norma M %A Adesina, Adekunle M %A Mohila, Carrie A %A Whitehead, William %A Jea, Andrew %A Vasudevan, Sanjeev A %A Nuchtern, Jed G %A Ramamurthy, Uma %A McGuire, Amy L %A Hilsenbeck, Susan G %A Reid, Jeffrey G %A Muzny, Donna M %A Wheeler, David A %A Berg, Stacey L %A Chintagumpala, Murali M %A Eng, Christine M %A Gibbs, Richard A %A Plon, Sharon E %X

IMPORTANCE: Whole-exome sequencing (WES) has the potential to reveal tumor and germline mutations of clinical relevance, but the diagnostic yield for pediatric patients with solid tumors is unknown.

OBJECTIVE: To characterize the diagnostic yield of combined tumor and germline WES for children with solid tumors.

DESIGN: Unselected children with newly diagnosed and previously untreated central nervous system (CNS) and non-CNS solid tumors were prospectively enrolled in the BASIC3 study at a large academic children's hospital during a 23-month period from August 2012 through June 2014. Blood and tumor samples underwent WES in a certified clinical laboratory with genetic results categorized on the basis of perceived clinical relevance and entered in the electronic health record.

MAIN OUTCOMES AND MEASURES: Clinical categorization of somatic mutations; frequencies of deleterious germline mutations related to patient phenotype and incidental medically-actionable mutations.

RESULTS: Of the first 150 participants (80 boys and 70 girls, mean age, 7.4 years), tumor samples adequate for WES were available from 121 patients (81%). Somatic mutations of established clinical utility (category I) were reported in 4 (3%) of 121 patients, with mutations of potential utility (category II) detected in an additional 29 (24%) of 121 patients. CTNNB1 was the gene most frequently mutated, with recurrent mutations in KIT, TSC2, and MAPK pathway genes (BRAF, KRAS, and NRAS) also identified. Mutations in consensus cancer genes (category III) were found in an additional 24 (20%) of 121 tumors. Fewer than half of somatic mutations identified were in genes known to be recurrently mutated in the tumor type tested. Diagnostic germline findings related to patient phenotype were discovered in 15 (10%) of 150 cases: 13 pathogenic or likely pathogenic dominant mutations in adult and pediatric cancer susceptibility genes (including 2 each in TP53, VHL, and BRCA1), 1 recessive liver disorder with hepatocellular carcinoma (TJP2), and 1 renal diagnosis (CLCN5). Incidental findings were reported in 8 (5%) of 150 patients. Most patients harbored germline uncertain variants in cancer genes (98%), pharmacogenetic variants (89%), and recessive carrier mutations (85%).

CONCLUSIONS AND RELEVANCE: Tumor and germline WES revealed mutations in a broad spectrum of genes previously implicated in both adult and pediatric cancers. Combined reporting of tumor and germline WES identified diagnostic and/or potentially actionable findings in nearly 40% of newly diagnosed pediatric patients with solid tumors.

%B JAMA Oncol %V 2 %P 616-624 %8 2016 May 01 %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/26822237?dopt=Abstract %R 10.1001/jamaoncol.2015.5699 %0 Journal Article %J BMC Med Genomics %D 2016 %T Exome sequencing in mostly consanguineous Arab families with neurologic disease provides a high potential molecular diagnosis rate. %A Charng, Wu-Lin %A Karaca, Ender %A Coban Akdemir, Zeynep %A Gambin, Tomasz %A Atik, Mehmed M %A Gu, Shen %A Posey, Jennifer E %A Jhangiani, Shalini N %A Muzny, Donna M %A Doddapaneni, Harsha %A Hu, Jianhong %A Boerwinkle, Eric %A Gibbs, Richard A %A Rosenfeld, Jill A %A Cui, Hong %A Xia, Fan %A Manickam, Kandamurugu %A Yang, Yaping %A Faqeih, Eissa A %A Al Asmari, Ali %A Saleh, Mohammed A M %A El-Hattab, Ayman W %A Lupski, James R %K Arabs %K Cohort Studies %K Consanguinity %K Data Mining %K Databases, Genetic %K DNA Copy Number Variations %K Exome %K Female %K High-Throughput Nucleotide Sequencing %K Humans %K Male %K Molecular Diagnostic Techniques %K Nervous System Diseases %K Pedigree %K Phenotype %K Polymorphism, Single Nucleotide %K Sequence Analysis, DNA %X

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

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

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

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

TRIAL REGISTRATION: Not applicable.

%B BMC Med Genomics %V 9 %P 42 %8 2016 Jul 19 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/27435318?dopt=Abstract %R 10.1186/s12920-016-0208-3 %0 Journal Article %J Genome Med %D 2016 %T MIPEP recessive variants cause a syndrome of left ventricular non-compaction, hypotonia, and infantile death. %A Eldomery, Mohammad K %A Akdemir, Zeynep C %A Vögtle, F-Nora %A Charng, Wu-Lin %A Mulica, Patrycja %A Rosenfeld, Jill A %A Gambin, Tomasz %A Gu, Shen %A Burrage, Lindsay C %A Al Shamsi, Aisha %A Penney, Samantha %A Jhangiani, Shalini N %A Zimmerman, Holly H %A Muzny, Donna M %A Wang, Xia %A Tang, Jia %A Medikonda, Ravi %A Ramachandran, Prasanna V %A Wong, Lee-Jun %A Boerwinkle, Eric %A Gibbs, Richard A %A Eng, Christine M %A Lalani, Seema R %A Hertecant, Jozef %A Rodenburg, Richard J %A Abdul-Rahman, Omar A %A Yang, Yaping %A Xia, Fan %A Wang, Meng C %A Lupski, James R %A Meisinger, Chris %A Sutton, V Reid %K Adult %K Amino Acid Sequence %K Female %K Genes, Recessive %K Heart Defects, Congenital %K Humans %K Infant %K Infant, Newborn %K Male %K Metalloendopeptidases %K Muscle Hypotonia %K Pedigree %K Phenotype %K Sequence Homology, Amino Acid %K Sudden Infant Death %K Syndrome %X

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

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

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

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

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

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

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

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

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

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

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

%B Am J Hum Genet %V 98 %P 562-570 %8 2016 Mar 03 %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/26942288?dopt=Abstract %R 10.1016/j.ajhg.2016.01.011 %0 Journal Article %J Nat Commun %D 2016 %T Mutations in the nuclear bile acid receptor FXR cause progressive familial intrahepatic cholestasis. %A Gomez-Ospina, Natalia %A Potter, Carol J %A Xiao, Rui %A Manickam, Kandamurugu %A Kim, Mi-Sun %A Kim, Kang Ho %A Shneider, Benjamin L %A Picarsic, Jennifer L %A Jacobson, Theodora A %A Zhang, Jing %A He, Weimin %A Liu, Pengfei %A Knisely, A S %A Finegold, Milton J %A Muzny, Donna M %A Boerwinkle, Eric %A Lupski, James R %A Plon, Sharon E %A Gibbs, Richard A %A Eng, Christine M %A Yang, Yaping %A Washington, Gabriel C %A Porteus, Matthew H %A Berquist, William E %A Kambham, Neeraja %A Singh, Ravinder J %A Xia, Fan %A Enns, Gregory M %A Moore, David D %K ATP Binding Cassette Transporter, Subfamily B, Member 11 %K ATP-Binding Cassette Transporters %K Bile Acids and Salts %K Cholestasis, Intrahepatic %K Female %K Humans %K Male %K Mutation %K Receptors, Cytoplasmic and Nuclear %K Young Adult %X

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

%B Nat Commun %V 7 %P 10713 %8 2016 Feb 18 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/26888176?dopt=Abstract %R 10.1038/ncomms10713 %0 Journal Article %J Genome Med %D 2016 %T POGZ truncating alleles cause syndromic intellectual disability. %A White, Janson %A Beck, Christine R %A Harel, Tamar %A Posey, Jennifer E %A Jhangiani, Shalini N %A Tang, Sha %A Farwell, Kelly D %A Powis, Zöe %A Mendelsohn, Nancy J %A Baker, Janice A %A Pollack, Lynda %A Mason, Kati J %A Wierenga, Klaas J %A Arrington, Daniel K %A Hall, Melissa %A Psychogios, Apostolos %A Fairbrother, Laura %A Walkiewicz, Magdalena %A Person, Richard E %A Niu, Zhiyv %A Zhang, Jing %A Rosenfeld, Jill A %A Muzny, Donna M %A Eng, Christine %A Beaudet, Arthur L %A Lupski, James R %A Boerwinkle, Eric %A Gibbs, Richard A %A Yang, Yaping %A Xia, Fan %A Sutton, V Reid %K Adolescent %K Adult %K Alleles %K Child, Preschool %K Exome %K Female %K Heterozygote %K Humans %K Infant %K Intellectual Disability %K Male %K Mutation %K Sequence Analysis, DNA %K Transposases %X

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

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

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

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

%B Genome Med %V 8 %P 3 %8 2016 Jan 06 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/26739615?dopt=Abstract %R 10.1186/s13073-015-0253-0 %0 Journal Article %J Am J Hum Genet %D 2016 %T Recurrent De Novo and Biallelic Variation of ATAD3A, Encoding a Mitochondrial Membrane Protein, Results in Distinct Neurological Syndromes. %A Harel, Tamar %A Yoon, Wan Hee %A Garone, Caterina %A Gu, Shen %A Coban-Akdemir, Zeynep %A Eldomery, Mohammad K %A Posey, Jennifer E %A Jhangiani, Shalini N %A Rosenfeld, Jill A %A Cho, Megan T %A Fox, Stephanie %A Withers, Marjorie %A Brooks, Stephanie M %A Chiang, Theodore %A Duraine, Lita %A Erdin, Serkan %A Yuan, Bo %A Shao, Yunru %A Moussallem, Elie %A Lamperti, Costanza %A Donati, Maria A %A Smith, Joshua D %A McLaughlin, Heather M %A Eng, Christine M %A Walkiewicz, Magdalena %A Xia, Fan %A Pippucci, Tommaso %A Magini, Pamela %A Seri, Marco %A Zeviani, Massimo %A Hirano, Michio %A Hunter, Jill V %A Srour, Myriam %A Zanigni, Stefano %A Lewis, Richard Alan %A Muzny, Donna M %A Lotze, Timothy E %A Boerwinkle, Eric %A Gibbs, Richard A %A Hickey, Scott E %A Graham, Brett H %A Yang, Yaping %A Buhas, Daniela %A Martin, Donna M %A Potocki, Lorraine %A Graziano, Claudio %A Bellen, Hugo J %A Lupski, James R %K Adenosine Triphosphatases %K Adult %K Alleles %K Animals %K ATPases Associated with Diverse Cellular Activities %K Axons %K Cardiomyopathies %K Child %K Child, Preschool %K Developmental Disabilities %K DNA Copy Number Variations %K Drosophila melanogaster %K Female %K Fibroblasts %K Homozygote %K Humans %K Infant %K Infant, Newborn %K Male %K Membrane Proteins %K Mitochondria %K Mitochondrial Proteins %K Muscle Hypotonia %K Muscles %K Mutation %K Nervous System Diseases %K Neurons %K Optic Atrophy %K Phenotype %K Polymorphism, Single Nucleotide %K Syndrome %K Young Adult %X

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

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

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

%B Am J Hum Genet %V 98 %P 347-57 %8 2016 Feb 04 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/26805781?dopt=Abstract %R 10.1016/j.ajhg.2015.12.008 %0 Journal Article %J Genome Med %D 2016 %T A visual and curatorial approach to clinical variant prioritization and disease gene discovery in genome-wide diagnostics. %A James, Regis A %A Campbell, Ian M %A Chen, Edward S %A Boone, Philip M %A Rao, Mitchell A %A Bainbridge, Matthew N %A Lupski, James R %A Yang, Yaping %A Eng, Christine M %A Posey, Jennifer E %A Shaw, Chad A %K Computational Biology %K Diagnosis, Differential %K Disease %K Genetic Variation %K Genome-Wide Association Study %K Humans %K Phenotype %K Pilot Projects %K Retrospective Studies %K Software %X

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

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

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

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

%B Genome Med %V 8 %P 13 %8 2016 Feb 02 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/26838676?dopt=Abstract %R 10.1186/s13073-016-0261-8 %0 Journal Article %J 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 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 Am J Hum Genet %D 2014 %T De novo truncating mutations in AHDC1 in individuals with syndromic expressive language delay, hypotonia, and sleep apnea. %A Xia, Fan %A Bainbridge, Matthew N %A Tan, Tiong Yang %A Wangler, Michael F %A Scheuerle, Angela E %A Zackai, Elaine H %A Harr, Margaret H %A Sutton, V Reid %A Nalam, Roopa L %A Zhu, Wenmiao %A Nash, Margot %A Ryan, Monique M %A Yaplito-Lee, Joy %A Hunter, Jill V %A Deardorff, Matthew A %A Penney, Samantha J %A Beaudet, Arthur L %A Plon, Sharon E %A Boerwinkle, Eric A %A Lupski, James R %A Eng, Christine M %A Muzny, Donna M %A Yang, Yaping %A Gibbs, Richard A %K Child %K Child, Preschool %K DNA-Binding Proteins %K Exome %K Female %K Humans %K Infant %K Intellectual Disability %K Language Development Disorders %K Male %K Muscle Hypotonia %K Mutation %K Sleep Apnea Syndromes %K Syndrome %X

Clinical whole-exome sequencing (WES) for identification of mutations leading to Mendelian disease has been offered to the medical community since 2011. Clinically undiagnosed neurological disorders are the most frequent basis for test referral, and currently, approximately 25% of such cases are diagnosed at the molecular level. To date, there are approximately 4,000 "known" disease-associated loci, and many are associated with striking dysmorphic features, making genotype-phenotype correlations relatively straightforward. A significant fraction of cases, however, lack characteristic dysmorphism or clinical pathognomonic traits and are dependent upon molecular tests for definitive diagnoses. Further, many molecular diagnoses are guided by recent gene-disease association discoveries. Hence, there is a critical interplay between clinical testing and research leading to gene-disease association discovery. Here, we describe four probands, all of whom presented with hypotonia, intellectual disability, global developmental delay, and mildly dysmorphic facial features. Three of the four also had sleep apnea. Each was a simplex case without a remarkable family history. Using WES, we identified AHDC1 de novo truncating mutations that most likely cause this genetic syndrome.

%B Am J Hum Genet %V 94 %P 784-9 %8 2014 May 01 %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/24791903?dopt=Abstract %R 10.1016/j.ajhg.2014.04.006 %0 Journal Article %J PLoS Genet %D 2014 %T Heterozygous de novo and inherited mutations in the smooth muscle actin (ACTG2) gene underlie megacystis-microcolon-intestinal hypoperistalsis syndrome. %A Wangler, Michael F %A Gonzaga-Jauregui, Claudia %A Gambin, Tomasz %A Penney, Samantha %A Moss, Timothy %A Chopra, Atul %A Probst, Frank J %A Xia, Fan %A Yang, Yaping %A Werlin, Steven %A Eglite, Ieva %A Kornejeva, Liene %A Bacino, Carlos A %A Baldridge, Dustin %A Neul, Jeff %A Lehman, Efrat Lev %A Larson, Austin %A Beuten, Joke %A Muzny, Donna M %A Jhangiani, Shalini %A Gibbs, Richard A %A Lupski, James R %A Beaudet, Arthur %K Abnormalities, Multiple %K Actins %K Adolescent %K Adult %K Child %K Child, Preschool %K Colon %K Exome %K Female %K Heterozygote %K Humans %K Intestinal Pseudo-Obstruction %K Male %K Muscle, Smooth %K Mutation %K Urinary Bladder %X

Megacystis-microcolon-intestinal hypoperistalsis syndrome (MMIHS) is a rare disorder of enteric smooth muscle function affecting the intestine and bladder. Patients with this severe phenotype are dependent on total parenteral nutrition and urinary catheterization. The cause of this syndrome has remained a mystery since Berdon's initial description in 1976. No genes have been clearly linked to MMIHS. We used whole-exome sequencing for gene discovery followed by targeted Sanger sequencing in a cohort of patients with MMIHS and intestinal pseudo-obstruction. We identified heterozygous ACTG2 missense variants in 15 unrelated subjects, ten being apparent de novo mutations. Ten unique variants were detected, of which six affected CpG dinucleotides and resulted in missense mutations at arginine residues, perhaps related to biased usage of CpG containing codons within actin genes. We also found some of the same heterozygous mutations that we observed as apparent de novo mutations in MMIHS segregating in families with intestinal pseudo-obstruction, suggesting that ACTG2 is responsible for a spectrum of smooth muscle disease. ACTG2 encodes γ2 enteric actin and is the first gene to be clearly associated with MMIHS, suggesting an important role for contractile proteins in enteric smooth muscle disease.

%B PLoS Genet %V 10 %P e1004258 %8 2014 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/24676022?dopt=Abstract %R 10.1371/journal.pgen.1004258 %0 Journal Article %J JAMA %D 2014 %T Molecular findings among patients referred for clinical whole-exome sequencing. %A Yang, Yaping %A Muzny, Donna M %A Xia, Fan %A Niu, Zhiyv %A Person, Richard %A Ding, Yan %A Ward, Patricia %A Braxton, Alicia %A Wang, Min %A Buhay, Christian %A Veeraraghavan, Narayanan %A Hawes, Alicia %A Chiang, Theodore %A Leduc, Magalie %A Beuten, Joke %A Zhang, Jing %A He, Weimin %A Scull, Jennifer %A Willis, Alecia %A Landsverk, Megan %A Craigen, William J %A Bekheirnia, Mir Reza %A Stray-Pedersen, Asbjorg %A Liu, Pengfei %A Wen, Shu %A Alcaraz, Wendy %A Cui, Hong %A Walkiewicz, Magdalena %A Reid, Jeffrey %A Bainbridge, Matthew %A Patel, Ankita %A Boerwinkle, Eric %A Beaudet, Arthur L %A Lupski, James R %A Plon, Sharon E %A Gibbs, Richard A %A Eng, Christine M %K Adolescent %K Adult %K Child %K Child, Preschool %K Exome %K Female %K Fetus %K Genetic Diseases, Inborn %K Genetic Testing %K Genomics %K Humans %K Incidental Findings %K Infant %K Infant, Newborn %K Male %K Molecular Diagnostic Techniques %K Mutation %K Phenotype %K Referral and Consultation %K Sequence Analysis, DNA %X

IMPORTANCE: Clinical whole-exome sequencing is increasingly used for diagnostic evaluation of patients with suspected genetic disorders.

OBJECTIVE: To perform clinical whole-exome sequencing and report (1) the rate of molecular diagnosis among phenotypic groups, (2) the spectrum of genetic alterations contributing to disease, and (3) the prevalence of medically actionable incidental findings such as FBN1 mutations causing Marfan syndrome.

DESIGN, SETTING, AND PATIENTS: Observational study of 2000 consecutive patients with clinical whole-exome sequencing analyzed between June 2012 and August 2014. Whole-exome sequencing tests were performed at a clinical genetics laboratory in the United States. Results were reported by clinical molecular geneticists certified by the American Board of Medical Genetics and Genomics. Tests were ordered by the patient's physician. The patients were primarily pediatric (1756 [88%]; mean age, 6 years; 888 females [44%], 1101 males [55%], and 11 fetuses [1% gender unknown]), demonstrating diverse clinical manifestations most often including nervous system dysfunction such as developmental delay.

MAIN OUTCOMES AND MEASURES: Whole-exome sequencing diagnosis rate overall and by phenotypic category, mode of inheritance, spectrum of genetic events, and reporting of incidental findings.

RESULTS: A molecular diagnosis was reported for 504 patients (25.2%) with 58% of the diagnostic mutations not previously reported. Molecular diagnosis rates for each phenotypic category were 143/526 (27.2%; 95% CI, 23.5%-31.2%) for the neurological group, 282/1147 (24.6%; 95% CI, 22.1%-27.2%) for the neurological plus other organ systems group, 30/83 (36.1%; 95% CI, 26.1%-47.5%) for the specific neurological group, and 49/244 (20.1%; 95% CI, 15.6%-25.8%) for the nonneurological group. The Mendelian disease patterns of the 527 molecular diagnoses included 280 (53.1%) autosomal dominant, 181 (34.3%) autosomal recessive (including 5 with uniparental disomy), 65 (12.3%) X-linked, and 1 (0.2%) mitochondrial. Of 504 patients with a molecular diagnosis, 23 (4.6%) had blended phenotypes resulting from 2 single gene defects. About 30% of the positive cases harbored mutations in disease genes reported since 2011. There were 95 medically actionable incidental findings in genes unrelated to the phenotype but with immediate implications for management in 92 patients (4.6%), including 59 patients (3%) with mutations in genes recommended for reporting by the American College of Medical Genetics and Genomics.

CONCLUSIONS AND RELEVANCE: Whole-exome sequencing provided a potential molecular diagnosis for 25% of a large cohort of patients referred for evaluation of suspected genetic conditions, including detection of rare genetic events and new mutations contributing to disease. The yield of whole-exome sequencing may offer advantages over traditional molecular diagnostic approaches in certain patients.

%B JAMA %V 312 %P 1870-9 %8 2014 Nov 12 %G eng %N 18 %1 https://www.ncbi.nlm.nih.gov/pubmed/25326635?dopt=Abstract %R 10.1001/jama.2014.14601 %0 Journal Article %J Am J Hum Genet %D 2014 %T Mutations in PURA cause profound neonatal hypotonia, seizures, and encephalopathy in 5q31.3 microdeletion syndrome. %A Lalani, Seema R %A Zhang, Jing %A Schaaf, Christian P %A Brown, Chester W %A Magoulas, Pilar %A Tsai, Anne Chun-Hui %A El-Gharbawy, Areeg %A Wierenga, Klaas J %A Bartholomew, Dennis %A Fong, Chin-To %A Barbaro-Dieber, Tina %A Kukolich, Mary K %A Burrage, Lindsay C %A Austin, Elise %A Keller, Kory %A Pastore, Matthew %A Fernandez, Fabio %A Lotze, Timothy %A Wilfong, Angus %A Purcarin, Gabriela %A Zhu, Wenmiao %A Craigen, William J %A McGuire, Marianne %A Jain, Mahim %A Cooney, Erin %A Azamian, Mahshid %A Bainbridge, Matthew N %A Muzny, Donna M %A Boerwinkle, Eric %A Person, Richard E %A Niu, Zhiyv %A Eng, Christine M %A Lupski, James R %A Gibbs, Richard A %A Beaudet, Arthur L %A Yang, Yaping %A Wang, Meng C %A Xia, Fan %K Abnormalities, Multiple %K Amino Acid Sequence %K Animals %K Base Sequence %K Caenorhabditis elegans %K Chromosome Deletion %K Chromosome Mapping %K Chromosomes, Human, Pair 5 %K DNA-Binding Proteins %K Humans %K Molecular Sequence Data %K Muscle Hypotonia %K Mutation %K Seizures %K Sequence Analysis, DNA %K Syndrome %K Transcription Factors %X

5q31.3 microdeletion syndrome is characterized by neonatal hypotonia, encephalopathy with or without epilepsy, and severe developmental delay, and the minimal critical deletion interval harbors three genes. We describe 11 individuals with clinical features of 5q31.3 microdeletion syndrome and de novo mutations in PURA, encoding transcriptional activator protein Pur-α, within the critical region. These data implicate causative PURA mutations responsible for the severe neurological phenotypes observed in this syndrome.

%B Am J Hum Genet %V 95 %P 579-83 %8 2014 Nov 06 %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/25439098?dopt=Abstract %R 10.1016/j.ajhg.2014.09.014 %0 Journal Article %J Genome Med %D 2013 %T De novo truncating mutations in ASXL3 are associated with a novel clinical phenotype with similarities to Bohring-Opitz syndrome. %A Bainbridge, Matthew N %A Hu, Hao %A Muzny, Donna M %A Musante, Luciana %A Lupski, James R %A Graham, Brett H %A Chen, Wei %A Gripp, Karen W %A Jenny, Kim %A Wienker, Thomas F %A Yang, Yaping %A Sutton, V Reid %A Gibbs, Richard A %A Ropers, H Hilger %X

BACKGROUND: Molecular diagnostics can resolve locus heterogeneity underlying clinical phenotypes that may otherwise be co-assigned as a specific syndrome based on shared clinical features, and can associate phenotypically diverse diseases to a single locus through allelic affinity. Here we describe an apparently novel syndrome, likely caused by de novo truncating mutations in ASXL3, which shares characteristics with Bohring-Opitz syndrome, a disease associated with de novo truncating mutations in ASXL1.

METHODS: We used whole-genome and whole-exome sequencing to interrogate the genomes of four subjects with an undiagnosed syndrome.

RESULTS: Using genome-wide sequencing, we identified heterozygous, de novo truncating mutations in ASXL3, a transcriptional repressor related to ASXL1, in four unrelated probands. We found that these probands shared similar phenotypes, including severe feeding difficulties, failure to thrive, and neurologic abnormalities with significant developmental delay. Further, they showed less phenotypic overlap with patients who had de novo truncating mutations in ASXL1.

CONCLUSION: We have identified truncating mutations in ASXL3 as the likely cause of a novel syndrome with phenotypic overlap with Bohring-Opitz syndrome.

%B Genome Med %V 5 %P 11 %8 2013 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/23383720?dopt=Abstract %R 10.1186/gm415 %0 Journal Article %J Genome Med %D 2013 %T Exome sequencing resolves apparent incidental findings and reveals further complexity of SH3TC2 variant alleles causing Charcot-Marie-Tooth neuropathy. %A Lupski, James R %A Gonzaga-Jauregui, Claudia %A Yang, Yaping %A Bainbridge, Matthew N %A Jhangiani, Shalini %A Buhay, Christian J %A Kovar, Christie L %A Wang, Min %A Hawes, Alicia C %A Reid, Jeffrey G %A Eng, Christine %A Muzny, Donna M %A Gibbs, Richard A %X

BACKGROUND: The debate regarding the relative merits of whole genome sequencing (WGS) versus exome sequencing (ES) centers around comparative cost, average depth of coverage for each interrogated base, and their relative efficiency in the identification of medically actionable variants from the myriad of variants identified by each approach. Nevertheless, few genomes have been subjected to both WGS and ES, using multiple next generation sequencing platforms. In addition, no personal genome has been so extensively analyzed using DNA derived from peripheral blood as opposed to DNA from transformed cell lines that may either accumulate mutations during propagation or clonally expand mosaic variants during cell transformation and propagation.

METHODS: We investigated a genome that was studied previously by SOLiD chemistry using both ES and WGS, and now perform six independent ES assays (Illumina GAII (x2), Illumina HiSeq (x2), Life Technologies' Personal Genome Machine (PGM) and Proton), and one additional WGS (Illumina HiSeq).

RESULTS: We compared the variants identified by the different methods and provide insights into the differences among variants identified between ES runs in the same technology platform and among different sequencing technologies. We resolved the true genotypes of medically actionable variants identified in the proband through orthogonal experimental approaches. Furthermore, ES identified an additional SH3TC2 variant (p.M1?) that likely contributes to the phenotype in the proband.

CONCLUSIONS: ES identified additional medically actionable variant calls and helped resolve ambiguous single nucleotide variants (SNV) documenting the power of increased depth of coverage of the captured targeted regions. Comparative analyses of WGS and ES reveal that pseudogenes and segmental duplications may explain some instances of apparent disease mutations in unaffected individuals.

%B Genome Med %V 5 %P 57 %8 2013 %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/23806086?dopt=Abstract %R 10.1186/gm461