The mutational constraint spectrum quantified from variation in 141,456 humans.

TitleThe mutational constraint spectrum quantified from variation in 141,456 humans.
Publication TypeJournal Article
Year of Publication2020
AuthorsKarczewski, KJ, Francioli, LC, Tiao, G, Cummings, BB, Alföldi, J, Wang, Q, Collins, RL, Laricchia, KM, Ganna, A, Birnbaum, DP, Gauthier, LD, Brand, H, Solomonson, M, Watts, NA, Rhodes, D, Singer-Berk, M, England, EM, Seaby, EG, Kosmicki, JA, Walters, RK, Tashman, K, Farjoun, Y, Banks, E, Poterba, T, Wang, A, Seed, C, Whiffin, N, Chong, JX, Samocha, KE, Pierce-Hoffman, E, Zappala, Z, O'Donnell-Luria, AH, Minikel, EVallabh, Weisburd, B, Lek, M, Ware, JS, Vittal, C, Armean, IM, Bergelson, L, Cibulskis, K, Connolly, KM, Covarrubias, M, Donnelly, S, Ferriera, S, Gabriel, S, Gentry, J, Gupta, N, Jeandet, T, Kaplan, D, Llanwarne, C, Munshi, R, Novod, S, Petrillo, N, Roazen, D, Ruano-Rubio, V, Saltzman, A, Schleicher, M, Soto, J, Tibbetts, K, Tolonen, C, Wade, G, Talkowski, ME, Neale, BM, Daly, MJ, MacArthur, DG
Corporate AuthorsGenome Aggregation Database Consortium
JournalNature
Volume581
Issue7809
Pagination434-443
Date Published2020 05
ISSN1476-4687
KeywordsAdult, Brain, Cardiovascular Diseases, Cohort Studies, Databases, Genetic, Exome, Female, Genes, Essential, Genetic Predisposition to Disease, Genetic Variation, Genome, Human, Genome-Wide Association Study, Humans, Loss of Function Mutation, Male, Mutation Rate, Proprotein Convertase 9, Reproducibility of Results, RNA, Messenger, Whole Exome Sequencing, Whole Genome Sequencing
Abstract

Genetic variants that inactivate protein-coding genes are a powerful source of information about the phenotypic consequences of gene disruption: genes that are crucial for the function of an organism will be depleted of such variants in natural populations, whereas non-essential genes will tolerate their accumulation. However, predicted loss-of-function variants are enriched for annotation errors, and tend to be found at extremely low frequencies, so their analysis requires careful variant annotation and very large sample sizes. Here we describe the aggregation of 125,748 exomes and 15,708 genomes from human sequencing studies into the Genome Aggregation Database (gnomAD). We identify 443,769 high-confidence predicted loss-of-function variants in this cohort after filtering for artefacts caused by sequencing and annotation errors. Using an improved model of human mutation rates, we classify human protein-coding genes along a spectrum that represents tolerance to inactivation, validate this classification using data from model organisms and engineered human cells, and show that it can be used to improve the power of gene discovery for both common and rare diseases.

DOI10.1038/s41586-020-2308-7
Alternate JournalNature
PubMed ID32461654
PubMed Central IDPMC7334197
Grant ListUM1 HG008900 / HG / NHGRI NIH HHS / United States
R01 MH115957 / MH / NIMH NIH HHS / United States
MH115957 / MH / NIMH NIH HHS / United States
R01 HD081256 / HD / NICHD NIH HHS / United States
R56 MH115957 / MH / NIMH NIH HHS / United States
R01 GM104371 / GM / NIGMS NIH HHS / United States
HD081256 / HD / NICHD NIH HHS / United States
U54 DK105566 / DK / NIDDK NIH HHS / United States
UM1 HG006493 / HG / NHGRI NIH HHS / United States
U24 HG008956 / HG / NHGRI NIH HHS / United States
F32 GM115208 / GM / NIGMS NIH HHS / United States