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Eric Vallabh Minikel, Daniel G MacArthur
It has recently been reported that an NR1H3 missense variant, R415Q, causes a novel familial form of multiple sclerosis (Wang et al., 2016a). This claim is at odds with publicly available data from the Exome Aggregation Consortium (ExAC; The allele frequency of R415Q is not significantly higher in cases (0.024%-0.049%) than in ExAC population controls (0.031%), whereas if R415Q conferred even 50% lifetime risk of developing MS, it would be hundreds of times more common in cases than in controls...
October 19, 2016: Neuron
S Birla, R Khadgawat, V P Jyotsna, V Jain, M K Garg, A S Bhalla, A Sharma
Growth hormone deficiency (GHD) results from variations affecting the production and release of growth hormone (GH) and is of 2 types: isolated growth hormone deficiency (IGHD) and combined pituitary hormone deficiency (CPHD). IGHD results from mutations in GH1 and GHRHR while CPHD is associated with defects in transcription factor genes PROP1, POU1F1, and HESX1. The present study reports on screening of POU1F1, PROP1, and HESX1 in CPHD patients and the novel variations identified. Fifty-one CPHD patients from 49 unrelated families clinically diagnosed on the basis of biochemical and imaging investigations along with 100 controls were enrolled...
October 18, 2016: Hormone and Metabolic Research, Hormon- und Stoffwechselforschung, Hormones et Métabolisme
Amélie Pinard, David Salgado, Jean-Pierre Desvignes, Ghadi Rai, Nadine Hanna, Pauline Arnaud, Céline Guien, Maria Martinez, Laurence Faivre, Guillaume Jondeau, Catherine Boileau, Stéphane Zaffran, Christophe Béroud, Gwenaëlle Collod-Béroud
High-throughput next-generation sequencing such as whole-exome and whole-genome sequencing are being rapidly integrated into clinical practice. The use of these techniques leads to the identification of secondary variants for which decisions about the reporting or not to the patient need to be made. The American College of Medical Genetics and Genomics recently published recommendations for the reporting of these variants in clinical practice for 56 "actionable" genes. Among these, seven are involved in Marfan Syndrome And Related Disorders (MSARD) resulting from mutations of the FBN1, TGFBR1 and 2, ACTA2, SMAD3, MYH11 and MYLK genes...
September 20, 2016: Human Mutation
Orli G Bahcall
No abstract text is available yet for this article.
September 15, 2016: Nature Reviews. Genetics
Diana L Cousminer, Alexandre Arkader, Benjamin F Voight, Maurizio Pacifici, Struan F A Grant
Hereditary multiple exostoses (HME) is a rare childhood-onset skeletal disease linked to mutations in exostosin glycosyltransferase 1 (EXT1) or 2 (EXT2). Patients are heterozygous for either an EXT1 or EXT2 mutation, and it is widely assumed that exostosis formation and associated defects, such as growth retardation and skeletal deformities, require loss-of-heterozygosity or a second hit in affected cells. However, the relevance and phenotypic impact of many presumed pathogenic EXT variants remain uncertain...
November 2016: Bone
David E Sleat, Erika Gedvilaite, Yeting Zhang, Peter Lobel, Jinchuan Xing
The neuronal ceroid lipofuscinoses (NCLs) are a group of fatal, mostly recessive neurodegenerative lysosomal storage diseases. While clinically similar, they are genetically distinct and result from mutations in at least twelve different genes. Estimates of NCL incidence range from 0.6 to 14 per 100,000 live births but vary widely between populations and are influenced by whether patients are classified based upon clinical or genetic criteria. We investigated mutations in twelve NCL genes in ~61,000 individuals represented in the Exome Aggregation Consortium (ExAC) whole exome sequencing database...
November 30, 2016: Gene
C Paludan-Müller, G Ahlberg, J Ghouse, C Herfelt, J H Svendsen, S Haunsø, J K Kanters, M S Olesen
Catecholaminergic Polymorphic Ventricular Tachycardia (CPVT) is a highly lethal cardiac arrhythmia disease occurring during exercise or psychological stress. CPVT has an estimated prevalence of 1:10,000 and has mainly been associated with variants in calcium-regulating genes. Identification of potential false-positive pathogenic variants was conducted by searching the Exome Aggregation Consortium (ExAC) database (n = 60,706) for variants reported to be associated with CPVT. The pathogenicity of the interrogated variants was assessed using guidelines from the American College of Medical Genetics and Genomics (ACMG) and in silico prediction tools...
August 19, 2016: Clinical Genetics
Monkol Lek, Konrad J Karczewski, Eric V Minikel, Kaitlin E Samocha, Eric Banks, Timothy Fennell, Anne H O'Donnell-Luria, James S Ware, Andrew J Hill, Beryl B Cummings, Taru Tukiainen, Daniel P Birnbaum, Jack A Kosmicki, Laramie E Duncan, Karol Estrada, Fengmei Zhao, James Zou, Emma Pierce-Hoffman, Joanne Berghout, David N Cooper, Nicole Deflaux, Mark DePristo, Ron Do, Jason Flannick, Menachem Fromer, Laura Gauthier, Jackie Goldstein, Namrata Gupta, Daniel Howrigan, Adam Kiezun, Mitja I Kurki, Ami Levy Moonshine, Pradeep Natarajan, Lorena Orozco, Gina M Peloso, Ryan Poplin, Manuel A Rivas, Valentin Ruano-Rubio, Samuel A Rose, Douglas M Ruderfer, Khalid Shakir, Peter D Stenson, Christine Stevens, Brett P Thomas, Grace Tiao, Maria T Tusie-Luna, Ben Weisburd, Hong-Hee Won, Dongmei Yu, David M Altshuler, Diego Ardissino, Michael Boehnke, John Danesh, Stacey Donnelly, Roberto Elosua, Jose C Florez, Stacey B Gabriel, Gad Getz, Stephen J Glatt, Christina M Hultman, Sekar Kathiresan, Markku Laakso, Steven McCarroll, Mark I McCarthy, Dermot McGovern, Ruth McPherson, Benjamin M Neale, Aarno Palotie, Shaun M Purcell, Danish Saleheen, Jeremiah M Scharf, Pamela Sklar, Patrick F Sullivan, Jaakko Tuomilehto, Ming T Tsuang, Hugh C Watkins, James G Wilson, Mark J Daly, Daniel G MacArthur
Large-scale reference data sets of human genetic variation are critical for the medical and functional interpretation of DNA sequence changes. Here we describe the aggregation and analysis of high-quality exome (protein-coding region) DNA sequence data for 60,706 individuals of diverse ancestries generated as part of the Exome Aggregation Consortium (ExAC). This catalogue of human genetic diversity contains an average of one variant every eight bases of the exome, and provides direct evidence for the presence of widespread mutational recurrence...
August 17, 2016: Nature
(no author information available yet)
No abstract text is available yet for this article.
August 18, 2016: Nature
Douglas M Ruderfer, Tymor Hamamsy, Monkol Lek, Konrad J Karczewski, David Kavanagh, Kaitlin E Samocha, Mark J Daly, Daniel G MacArthur, Menachem Fromer, Shaun M Purcell
Copy number variation (CNV) affecting protein-coding genes contributes substantially to human diversity and disease. Here we characterized the rates and properties of rare genic CNVs (<0.5% frequency) in exome sequencing data from nearly 60,000 individuals in the Exome Aggregation Consortium (ExAC) database. On average, individuals possessed 0.81 deleted and 1.75 duplicated genes, and most (70%) carried at least one rare genic CNV. For every gene, we empirically estimated an index of relative intolerance to CNVs that demonstrated moderate correlation with measures of genic constraint based on single-nucleotide variation (SNV) and was independently correlated with measures of evolutionary conservation...
October 2016: Nature Genetics
Roddy Walsh, Kate L Thomson, James S Ware, Birgit H Funke, Jessica Woodley, Karen J McGuire, Francesco Mazzarotto, Edward Blair, Anneke Seller, Jenny C Taylor, Eric V Minikel, Exome Aggregation Consortium, Daniel G MacArthur, Martin Farrall, Stuart A Cook, Hugh Watkins
PURPOSE: The accurate interpretation of variation in Mendelian disease genes has lagged behind data generation as sequencing has become increasingly accessible. Ongoing large sequencing efforts present huge interpretive challenges, but they also provide an invaluable opportunity to characterize the spectrum and importance of rare variation. METHODS: We analyzed sequence data from 7,855 clinical cardiomyopathy cases and 60,706 Exome Aggregation Consortium (ExAC) reference samples to obtain a better understanding of genetic variation in a representative autosomal dominant disorder...
August 17, 2016: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Asta Försti, Abhishek Kumar, Nagarajan Paramasivam, Matthias Schlesner, Calogerina Catalano, Dagmara Dymerska, Jan Lubinski, Roland Eils, Kari Hemminki
BACKGROUND: In the course of our whole-genome sequencing efforts, we have developed a pipeline for analyzing germline genomes from Mendelian types of cancer pedigrees (familial cancer variant prioritization pipeline, FCVPP). RESULTS: The variant calling step distinguishes two types of genomic variants: single nucleotide variants (SNVs) and indels, which undergo technical quality control. Mendelian types of variants are assumed to be rare and variants with frequencies higher that 0...
2016: Hereditary Cancer in Clinical Practice
Cheng Xue, Hua Chen, Fuli Yu
Understanding the evolution of disease-associated mutations is fundamental to analyze pathogenetics of diseases. Mutation, recombination (by GC-biased gene conversion, gBGC), and selection have been known to shape the evolution of disease-associated mutations, but how these evolutionary forces work together is still an open question. In this study, we analyzed several human large-scale datasets (1000 Genomes, ESP6500, ExAC and ClinVar), and found that base-biased mutagenesis generates more GC→AT than AT→GC mutations, while gBGC promotes the fixation of AT→GC mutations to balance the impact of base-biased mutation on genome...
November 2016: Human Mutation
Andreas Rump, Anna Benet-Pages, Steffen Schubert, Jan Dominik Kuhlmann, Ramūnas Janavičius, Eva Macháčková, Lenka Foretová, Zdenek Kleibl, Filip Lhota, Petra Zemankova, Elitza Betcheva-Krajcir, Luisa Mackenroth, Karl Hackmann, Janin Lehmann, Anke Nissen, Nataliya DiDonato, Romy Opitz, Holger Thiele, Karin Kast, Pauline Wimberger, Elke Holinski-Feder, Steffen Emmert, Evelin Schröck, Barbara Klink
The increasing application of gene panels for familial cancer susceptibility disorders will probably lead to an increased proposal of susceptibility gene candidates. Using ERCC2 DNA repair gene as an example, we show that proof of a possible role in cancer susceptibility requires a detailed dissection and characterization of the underlying mutations for genes with diverse cellular functions (in this case mainly DNA repair and basic cellular transcription). In case of ERCC2, panel sequencing of 1345 index cases from 587 German, 405 Lithuanian and 353 Czech families with breast and ovarian cancer (BC/OC) predisposition revealed 25 mutations (3 frameshift, 2 splice-affecting, 20 missense), all absent or very rare in the ExAC database...
August 2016: PLoS Genetics
Samuel D Quaynor, Maggie E Bosley, Christina G Duckworth, Kelsey R Porter, Soo-Hyun Kim, Hyung-Goo Kim, Lynn P Chorich, Megan E Sullivan, Jeong-Hyeon Choi, Richard S Cameron, Lawrence C Layman
The genetic basis is unknown for ∼60% of normosmic hypogonadotropic hypogonadism (nHH)/Kallmann syndrome (KS). DNAs from (17 male and 31 female) nHH/KS patients were analyzed by targeted next generation sequencing (NGS) of 261 genes involved in hypothalamic, pituitary, and/or olfactory pathways, or suggested by chromosome rearrangements. Selected variants were subjected to Sanger DNA sequencing, the gold standard. The frequency of Sanger-confirmed variants was determined using the ExAC database. Variants were classified as likely pathogenic (frameshift, nonsense, and splice site) or predicted pathogenic (nonsynonymous missense)...
December 5, 2016: Molecular and Cellular Endocrinology
Louise Cheryl Gregory, Kyriaki Sandy Alatzoglou, Mark James McCabe, Peter Christopher Hindmarsh, Jose William Saldanha, Nicola Romano, Paul Le Tissier, Mehul Tulsidas Dattani
OBJECTIVE: Recessive mutations in GHRHR are associated with severe isolated growth hormone deficiency (IGHD), with a final height in untreated patients of 130 cm ± 10 cm (-7.2 ± 1.6 SDS; males) and 114 ± 0.7 cm (-8.3 ± 0.1 SDS; females). DESIGN: We hypothesized that a consanguineous Pakistani family with IGHD in three siblings (two males, one female) would have mutations in GH1 or GHRHR. RESULTS: Two novel homozygous missense variants [c...
October 2016: Journal of Clinical Endocrinology and Metabolism
Laxmi Kirola, Madhuri Behari, Chandan Shishir, B K Thelma
BACKGROUND: A novel homozygous missense mutation (c.773G > A, p.Arg258Gln) in Synaptojanin 1 (SYNJ1, 21q22.2) has recently been reported in two Italian and one Iranian consanguineous families with autosomal recessive juvenile Parkinsonism (ARJP). Contribution of this synaptic gene related to Parkinsonism phenotypes in other populations still remains unidentified. METHODS: An ARJP family with two affected siblings characterized by frequent tremor with bradykinesia and rigidity was recruited in this study...
October 2016: Parkinsonism & related Disorders
Michael Zech, Angela Jochim, Sylvia Boesch, Sandrina Weber, Tobias Meindl, Annette Peters, Christian Gieger, Joerg Mueller, Michael Messner, Andres Ceballos-Baumann, Werner Poewe, Bernhard Haslinger, Juliane Winkelmann
BACKGROUND: An increasing number of rare, functionally relevant non-c.907_909delGAG (non-ΔGAG) variants in TOR1A have been recognized, associated with phenotypic expressions different from classic DYT1 childhood-onset generalized dystonia. Only recently, DYT1 genotype-phenotype correlations have been proposed, awaiting further elucidation in independent cohorts. METHODS: We screened the entire coding sequence and the 5'-UTR region of TOR1A for rare non-ΔGAG sequence variants in a large series of 940 individuals with various forms of isolated dystonia as well as in 376 ancestry-matched controls...
October 2016: Parkinsonism & related Disorders
Julia N Bailey, Christopher Patterson, Laurence de Nijs, Reyna M Durón, Viet-Huong Nguyen, Miyabi Tanaka, Marco T Medina, Aurelio Jara-Prado, Iris E Martínez-Juárez, Adriana Ochoa, Yolli Molina, Toshimitsu Suzuki, María E Alonso, Jenny E Wight, Yu-Chen Lin, Laura Guilhoto, Elza Marcia Targas Yacubian, Jesús Machado-Salas, Andrea Daga, Kazuhiro Yamakawa, Thierry M Grisar, Bernard Lakaye, Antonio V Delgado-Escueta
PURPOSE: EFHC1 variants are the most common mutations in inherited myoclonic and grand mal clonic-tonic-clonic (CTC) convulsions of juvenile myoclonic epilepsy (JME). We reanalyzed 54 EFHC1 variants associated with epilepsy from 17 cohorts based on National Human Genome Research Institute (NHGRI) and American College of Medical Genetics and Genomics (ACMG) guidelines for interpretation of sequence variants. METHODS: We calculated Bayesian LOD scores for variants in coinheritance, unconditional exact tests and odds ratios (OR) in case-control associations, allele frequencies in genome databases, and predictions for conservation/pathogenicity...
July 28, 2016: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Andrea Garofalo, Lynette Sholl, Brendan Reardon, Amaro Taylor-Weiner, Ali Amin-Mansour, Diana Miao, David Liu, Nelly Oliver, Laura MacConaill, Matthew Ducar, Vanesa Rojas-Rudilla, Marios Giannakis, Arezou Ghazani, Stacy Gray, Pasi Janne, Judy Garber, Steve Joffe, Neal Lindeman, Nikhil Wagle, Levi A Garraway, Eliezer M Van Allen
BACKGROUND: The diversity of clinical tumor profiling approaches (small panels to whole exomes with matched or unmatched germline analysis) may engender uncertainty about their benefits and liabilities, particularly in light of reported germline false positives in tumor-only profiling and use of global mutational and/or neoantigen data. The goal of this study was to determine the impact of genomic analysis strategies on error rates and data interpretation across contexts and ancestries...
2016: Genome Medicine
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