Analysis of protein-coding genetic variation in 60,706 humans View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2016-08-17

AUTHORS

, 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

ABSTRACT

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. We have used this catalogue to calculate objective metrics of pathogenicity for sequence variants, and to identify genes subject to strong selection against various classes of mutation; identifying 3,230 genes with near-complete depletion of predicted protein-truncating variants, with 72% of these genes having no currently established human disease phenotype. Finally, we demonstrate that these data can be used for the efficient filtering of candidate disease-causing variants, and for the discovery of human 'knockout' variants in protein-coding genes. More... »

PAGES

285-291

References to SciGraph publications

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  • Journal

    TITLE

    Nature

    ISSUE

    7616

    VOLUME

    536

    Author Affiliations

  • Institute for Neuroscience and Muscle Research, Childrens Hospital at Westmead, Sydney, NSW, Australia
  • Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
  • Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
  • Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
  • MRC Clinical Sciences Centre, Imperial College London, London, UK
  • Genome Sciences, University of Washington, Seattle, WA, USA
  • Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, USA
  • Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
  • Center for Biomedical Informatics and Biostatistics, University of Arizona, Tucson, AZ, USA
  • Institute of Medical Genetics, Cardiff University, Cardiff, UK
  • Google Inc, Mountain View, CA, USA
  • Broad Institute of MIT and Harvard, Cambridge, MA, USA
  • The Center for Statistical Genetics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
  • Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
  • Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
  • Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
  • Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
  • Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Gen—mica, Mexico City, Mexico
  • Molecular Biology and Genomic Medicine Unit, Instituto Nacional de Ciencias M_dicas y Nutrici—n, Mexico City, Mexico
  • Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University,Samsung Medical Center, Seoul, Republic of Korea
  • Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
  • Vertex Pharmaceuticals, Boston, MA, USA
  • Department of Cardiology, University Hospital, Parma, Italy
  • Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
  • Department of Public Health and Primary Care, Strangeways Research Laboratory, Cambridge, UK
  • Cardiovascular Epidemiology and Genetics, Hospital del Mar Medical Research Institute, Barcelona, Spain
  • Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA
  • Department of Pathology and Cancer Center, Massachusetts General Hospital, Boston, MA, USA
  • Department of Neuroscience and Physiology, State University of New York,Upstate Medical University, Syracuse, NY, USA
  • Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
  • Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
  • Department of Genetics, Harvard Medical School, Boston, MA, USA
  • Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Foundation Trust, Oxford, UK
  • Inflammatory Bowel Disease and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
  • Atherogenomics Laboratory, University of Ottawa Heart Institute, Ottawa, ON, Canada
  • Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
  • Center for Non-Communicable Diseases, Karachi, Pakistan
  • Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
  • Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
  • Department of Public Health, University of Helsinki, Helsinki, Finland
  • Department of Psychiatry, University of California, San Diego, CA, USA
  • Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
  • Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/nature19057

    DOI

    http://dx.doi.org/10.1038/nature19057

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1022281897

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/27535533


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