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

2015; Cold Spring Harbor Laboratory; Linguagem: Inglês

10.1101/030338

Monkol Lek, Konrad J. Karczewski, Eric Vallabh Minikel, Kaitlin E. Samocha, Eric Banks, Timothy R. Fennell, Anne O’Donnell‐Luria, James S. Ware, Andrew 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, D.N. Cooper, Nicole Deflaux, Mark A. DePristo, Ron Do, Jason Flannick, Menachem Fromer, Laura D. Gauthier, Jackie Goldstein, Namrata Gupta, Daniel P. Howrigan, Adam Kieżun, Mitja Kurki, Ami Levy Moonshine, Pradeep Natarajan, Lorena Orozco, Gina M. Peloso, Ryan Poplin, Manuel A. Rivas, Valentín Ruano-Rubio, Samuel A. Rose, Douglas M. Ruderfer, Khalid Shakir, Peter D. Stenson, Christine Stevens, Brett Thomas, Grace Tiao, Maria T. Tusie-Luna, Ben Weisburd, Hong‐Hee Won, Dongmei Yu, David Altshuler, Diego Ardissino, Michael Boehnke, John Danesh, Stacey Donnelly, Roberto Elosúa, José C. Florez, Stacey Gabriel, Gad Getz, Stephen J. Glatt, Christina M. Hultman, Sekar Kathiresan, Markku Laakso, Steven A. McCarroll, Mark I. McCarthy, Dermot McGovern, Ruth McPherson, Benjamin M. Neale, Aarno Palotie, Shaun Purcell, Danish Saleheen, Jeremiah M. Scharf, Pamela Sklar, Patrick F. Sullivan, Jaakko Tuomilehto, Ming T. Tsuang, Hugh Watkins, James G. Wilson, Mark J. Daly, Daniel G. MacArthur,

Genomic variations and chromosomal abnormalities

Summary 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) sequence data for 60,706 individuals of diverse ethnicities generated as part of the Exome Aggregation Consortium (ExAC). The resulting 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 show that this catalogue can be used to calculate objective metrics of pathogenicity for sequence variants, and to identify genes subject to strong selection against various classes of mutation; we identify 3,230 genes with near-complete depletion of truncating variants, 72% of which have 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.