Analysis of Protein-coding Genetic Variation in 60,706 Humans

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.

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References

Jeong H, Mason S, Barabasi A, Oltvai Z . Lethality and centrality in protein networks. Nature. 2001; 411(6833):41-2. DOI: 10.1038/35075138. View

Chagnon P, Michaud J, Mitchell G, Mercier J, Marion J, Drouin E . A missense mutation (R565W) in cirhin (FLJ14728) in North American Indian childhood cirrhosis. Am J Hum Genet. 2002; 71(6):1443-9. PMC: 378590. DOI: 10.1086/344580. View

Vicoso B, Charlesworth B . Evolution on the X chromosome: unusual patterns and processes. Nat Rev Genet. 2006; 7(8):645-53. DOI: 10.1038/nrg1914. View

Goh K, Cusick M, Valle D, Childs B, Vidal M, Barabasi A . The human disease network. Proc Natl Acad Sci U S A. 2007; 104(21):8685-90. PMC: 1885563. DOI: 10.1073/pnas.0701361104. View

Blekhman R, Man O, Herrmann L, Boyko A, Indap A, Kosiol C . Natural selection on genes that underlie human disease susceptibility. Curr Biol. 2008; 18(12):883-9. PMC: 2474766. DOI: 10.1016/j.cub.2008.04.074. View

Bell C, Dinwiddie D, Miller N, Hateley S, Ganusova E, Mudge J . Carrier testing for severe childhood recessive diseases by next-generation sequencing. Sci Transl Med. 2011; 3(65):65ra4. PMC: 3740116. DOI: 10.1126/scitranslmed.3001756. View

DePristo M, Banks E, Poplin R, Garimella K, Maguire J, Hartl C . A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011; 43(5):491-8. PMC: 3083463. DOI: 10.1038/ng.806. View

Li H, Durbin R . Inference of human population history from individual whole-genome sequences. Nature. 2011; 475(7357):493-6. PMC: 3154645. DOI: 10.1038/nature10231. View

Stoneking M, Krause J . Learning about human population history from ancient and modern genomes. Nat Rev Genet. 2011; 12(9):603-14. DOI: 10.1038/nrg3029. View

10.

Bamshad M, Ng S, Bigham A, Tabor H, Emond M, Nickerson D . Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet. 2011; 12(11):745-55. DOI: 10.1038/nrg3031. View

11.

MacArthur D, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K . A systematic survey of loss-of-function variants in human protein-coding genes. Science. 2012; 335(6070):823-8. PMC: 3299548. DOI: 10.1126/science.1215040. View

12.

Tennessen J, Bigham A, OConnor T, Fu W, Kenny E, Gravel S . Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science. 2012; 337(6090):64-9. PMC: 3708544. DOI: 10.1126/science.1219240. View

13.

Voight B, Kang H, Ding J, Palmer C, Sidore C, Chines P . The metabochip, a custom genotyping array for genetic studies of metabolic, cardiovascular, and anthropometric traits. PLoS Genet. 2012; 8(8):e1002793. PMC: 3410907. DOI: 10.1371/journal.pgen.1002793. View

14.

Fu W, OConnor T, Jun G, Kang H, Abecasis G, Leal S . Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants. Nature. 2012; 493(7431):216-20. PMC: 3676746. DOI: 10.1038/nature11690. View

15.

Xue Y, Chen Y, Ayub Q, Huang N, Ball E, Mort M . Deleterious- and disease-allele prevalence in healthy individuals: insights from current predictions, mutation databases, and population-scale resequencing. Am J Hum Genet. 2012; 91(6):1022-32. PMC: 3516590. DOI: 10.1016/j.ajhg.2012.10.015. View

16.

Piton A, Redin C, Mandel J . XLID-causing mutations and associated genes challenged in light of data from large-scale human exome sequencing. Am J Hum Genet. 2013; 93(2):368-83. PMC: 3738825. DOI: 10.1016/j.ajhg.2013.06.013. View

17.

Petrovski S, Wang Q, Heinzen E, Allen A, Goldstein D . Genic intolerance to functional variation and the interpretation of personal genomes. PLoS Genet. 2013; 9(8):e1003709. PMC: 3749936. DOI: 10.1371/journal.pgen.1003709. View

18.

Stenson P, Mort M, Ball E, Shaw K, Phillips A, Cooper D . The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine. Hum Genet. 2013; 133(1):1-9. PMC: 3898141. DOI: 10.1007/s00439-013-1358-4. View

19.

Fromer M, Pocklington A, Kavanagh D, Williams H, Dwyer S, Gormley P . De novo mutations in schizophrenia implicate synaptic networks. Nature. 2014; 506(7487):179-84. PMC: 4237002. DOI: 10.1038/nature12929. View

20.

Zook J, Chapman B, Wang J, Mittelman D, Hofmann O, Hide W . Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls. Nat Biotechnol. 2014; 32(3):246-51. DOI: 10.1038/nbt.2835. View