Europeans have a higher proportion of high-frequency deleterious variants than Africans

Human Genetics

Volumn 135, Issue 1, 2016, Pages 1-7

  Subramanian, Sankar ^a  

^a GRIFFITH UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID;

ARTICLE; COMPARATIVE STUDY; CONTROLLED STUDY; EUROPEAN; EUROPEAN AMERICAN; EXOME; GENE FREQUENCY; GENE MUTATION; GENETIC ASSOCIATION; GENETIC DISORDER; GENETIC VARIABILITY; GENOME ANALYSIS; HUMAN; HUMAN GENOME; INTRON; PRIORITY JOURNAL; BLACK PERSON; CAUCASIAN; GENETICS; MUTATION;

AFRICAN CONTINENTAL ANCESTRY GROUP; EUROPEAN CONTINENTAL ANCESTRY GROUP; EXOME; HUMANS; MUTATION;

EID: 84952714752     PISSN: 03406717     EISSN: 14321203     Source Type: Journal    
DOI: 10.1007/s00439-015-1604-z     Document Type: Article

References (26)

1. Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA (2010) A map of human genome variation from population-scale sequencing. Nature 467:1061–1073. doi:10.1038/nature09534
2. Blekhman R, Man O, Herrmann L, Boyko AR, Indap A, Kosiol C, Bustamante CD, Teshima KM, Przeworski M (2008) Natural selection on genes that underlie human disease susceptibility. Curr Biol 18:883–889. doi:10.1016/j.cub.2008.04.074
3. Cooper GM, Stone EA, Asimenos G, Program NCS, Green ED, Batzoglou S, Sidow A (2005) Distribution and intensity of constraint in mammalian genomic sequence. Genome Res 15:901–913. doi:10.1101/gr.3577405
4. Coventry A, Bull-Otterson LM, Liu X, Clark AG, Maxwell TJ, Crosby J, Hixson JE, Rea TJ, Muzny DM, Lewis LR, Wheeler DA, Sabo A, Lusk C, Weiss KG, Akbar H, Cree A, Hawes AC, Newsham I, Varghese RT, Villasana D, Gross S, Joshi V, Santibanez J, Morgan M, Chang K, Iv WH, Templeton AR, Boerwinkle E, Gibbs R, Sing CF (2010) Deep resequencing reveals excess rare recent variants consistent with explosive population growth. Nat Commun 1:131. doi:10.1038/ncomms1130
5. Do R, Balick D, Li H, Adzhubei I, Sunyaev S, Reich D (2015) No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans. Nat Genet 47:126–131. doi:10.1038/ng.3186
6. Fu W, O’Connor TD, Jun G, Kang HM, Abecasis G, Leal SM, Gabriel S, Rieder MJ, Altshuler D, Shendure J, Nickerson DA, Bamshad MJ, Project NES, Akey JM (2013) Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants. Nature 493:216–220. doi:10.1038/nature11690
7. Griffiths RC, Tavare S (1998) The age of a mutation in a general coalescent tree. Commun Stat Stoch Models 14: 273–295
8. Keinan A, Clark AG (2012) Recent explosive human population growth has resulted in an excess of rare genetic variants. Science 336:740–743. doi:10.1126/science.1217283
9. Keinan A, Mullikin JC, Patterson N, Reich D (2007) Measurement of the human allele frequency spectrum demonstrates greater genetic drift in East Asians than in Europeans. Nat Genet 39:1251–1255. doi:10.1038/ng2116
10. Kiezun A, Pulit SL, Francioli LC, van Dijk F, Swertz M, Boomsma DI, van Duijn CM, Slagboom PE, van Ommen GJ, Wijmenga C, Genome of the Netherlands C, de Bakker PI, Sunyaev SR (2013) Deleterious alleles in the human genome are on average younger than neutral alleles of the same frequency. PLoS Genet 9:e1003301. doi:10.1371/journal.pgen.1003301
11. Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge
12. Kimura M, Ohta T (1973) The age of a neutral mutant persisting in a finite population. Genetics 75:199–212
13. Kircher M, Witten DM, Jain P, O’Roak BJ, Cooper GM, Shendure J (2014) A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet 46:310–315. doi:10.1038/ng.2892
14. Kumar S, Sanderford M, Gray VE, Ye J, Liu L (2012) Evolutionary diagnosis method for variants in personal exomes. Nat Methods 9:855–856. doi:10.1038/nmeth.2147
15. Li H, Durbin R (2011) Inference of human population history from individual whole-genome sequences. Nature 475:493–496. doi:10.1038/nature10231
16. Li Y, Vinckenbosch N, Tian G, Huerta-Sanchez E, Jiang T, Jiang H, Albrechtsen A, Andersen G, Cao H, Korneliussen T, Grarup N, Guo Y, Hellman I, Jin X, Li Q, Liu J, Liu X, Sparso T, Tang M, Wu H, Wu R, Yu C, Zheng H, Astrup A, Bolund L, Holmkvist J, Jorgensen T, Kristiansen K, Schmitz O, Schwartz TW, Zhang X, Li R, Yang H, Wang J, Hansen T, Pedersen O, Nielsen R, Wang J (2010) Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nat Genet 42:969–972. doi:10.1038/ng.680
17. Lohmueller KE, Indap AR, Schmidt S, Boyko AR, Hernandez RD, Hubisz MJ, Sninsky JJ, White TJ, Sunyaev SR, Nielsen R, Clark AG, Bustamante CD (2008) Proportionally more deleterious genetic variation in European than in African populations. Nature 451:994–997. doi:10.1038/nature06611
18. Marth GT, Czabarka E, Murvai J, Sherry ST (2004) The allele frequency spectrum in genome-wide human variation data reveals signals of differential demographic history in three large world populations. Genetics 166:351–372
19. Nelson MR, Wegmann D, Ehm MG, Kessner D, St Jean P, Verzilli C, Shen J, Tang Z, Bacanu SA, Fraser D, Warren L, Aponte J, Zawistowski M, Liu X, Zhang H, Zhang Y, Li J, Li Y, Li L, Woollard P, Topp S, Hall MD, Nangle K, Wang J, Abecasis G, Cardon LR, Zollner S, Whittaker JC, Chissoe SL, Novembre J, Mooser V (2012) An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science 337:100–104. doi:10.1126/science.1217876
20. O’Fallon BD, Fehren-Schmitz L (2011) Native Americans experienced a strong population bottleneck coincident with European contact. Proc Natl Acad Sci 108:20444–20448. doi:10.1073/pnas.1112563108
21. Racimo F, Schraiber JG (2014) Approximation to the distribution of fitness effects across functional categories in human segregating polymorphisms. PLoS Genet 10:e1004697. doi:10.1371/journal.pgen.1004697
22. Sajantila A, Salem AH, Savolainen P, Bauer K, Gierig C, Paabo S (1996) Paternal and maternal DNA lineages reveal a bottleneck in the founding of the Finnish population. Proc Natl Acad Sci 93:12035–12039
23. Schwarz JM, Cooper DN, Schuelke M, Seelow D (2014) MutationTaster2: mutation prediction for the deep-sequencing age. Nat Methods 11:361–362. doi:10.1038/nmeth.2890
24. Simons YB, Turchin MC, Pritchard JK, Sella G (2014) The deleterious mutation load is insensitive to recent population history. Nat Genet 46:220–224. doi:10.1038/ng.2896
25. Subramanian S (2009) Temporal trails of natural selection in human mitogenomes. Mol Biol Evol 26:715–717. doi:10.1093/molbev/msp005
26. Tennessen JA, Bigham AW, O’Connor TD, Fu W, Kenny EE, Gravel S, McGee S, Do R, Liu X, Jun G, Kang HM, Jordan D, Leal SM, Gabriel S, Rieder MJ, Abecasis G, Altshuler D, Nickerson DA, Boerwinkle E, Sunyaev S, Bustamante CD, Bamshad MJ, Akey JM, Broad GO, Seattle GO, Project NES (2012) Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science 337:64–69. doi:10.1126/science.1219240