Genome-wide comparison of African-ancestry populations from CARe and other cohorts reveals signals of natural selection

American Journal of Human Genetics

Volumn 89, Issue 3, 2011, Pages 368-381

  Bhatia, Gaurav ^a   Patterson, Nick ^a   Pasaniuc, Bogdan ^a,b   Zaitlen, Noah ^a,b   Genovese, Giulio ^c   Pollack, Samuela ^a,b   Mallick, Swapan ^a,c   Myers, Simon ^d   Tandon, Arti ^a,c   Spencer, Chris ^e   Palmer, Cameron D ^a,f   Adeyemo, Adebowale A ^g   Akylbekova, Ermeg L ^h   Cupples, L Adrienne ⁱ   Divers, Jasmin ^j   Fornage, Myriam ^k   Kao, W H Linda ^l,m   Lange, Leslie ⁿ   Li, Mingyao ^o   Musani, Solomon ^p   Mychaleckyj, Josyf C ^q   Ogunniyi, Adesola ^r   Papanicolaou, George ^s   Rotimi, Charles N ^g   Rotter, Jerome I ^t   Ruczinski, Ingo ^l   Salako, Babatunde ^r   Siscovick, David S ^u,v   Tayo, Bamidele O ^w   Yang, Qiong ⁱ   McCarroll, Steve ^a,c   Sabeti, Pardis ^x   Lettre, Guillaume ^y,z   De Jager, Phil ^a,aa,ab   Hirschhorn, Joel ^a,f   Zhu, Xiaofeng ^ac   Cooper, Richard ^w   Reich, David ^a,c   Wilson, James G ^p   Price, Alkes L ^a,b   more..

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

^d UNIVERSITY OF OXFORD   (United Kingdom)

^e UNIVERSITY OF OXFORD   (United Kingdom)

^f BOSTON CHILDREN S HOSPITAL   (United States)

^g NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^h JACKSON STATE UNIVERSITY   (United States)

ⁱ BOSTON UNIVERSITY   (United States)

^j WAKE FOREST SCHOOL OF MEDICINE   (United States)

^k UNIVERSITY OF TEXAS SCHOOL OF PUBLIC HEALTH   (United States)

^l JOHNS HOPKINS UNIVERSITY   (United States)

^m JOHNS HOPKINS UNIVERSITY   (United States)

ⁿ UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^o UNIVERSITY OF PENNSYLVANIA   (United States)

^p UNIVERSITY OF MISSISSIPPI MEDICAL CENTER   (United States)

^q UNIVERSITY OF VIRGINIA   (United States)

^r UNIVERSITY OF IBADAN   (Nigeria)

^s NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

^t CEDARS SINAI MEDICAL CENTER   (United States)

^u UNIVERSITY OF WASHINGTON   (United States)

^v UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^w LOYOLA UNIVERSITY CHICAGO   (United States)

^x HARVARD UNIVERSITY   (United States)

^y MONTREAL HEART INSTITUTE   (Canada)

^z UNIVERSITÉ DE MONTRÉAL   (Canada)

^aa BRIGHAM AND WOMEN S HOSPITAL   (United States)

^ab LABORATORY FOR MOLECULAR MEDICINE   (United States)

^ac CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

CD36 ANTIGEN; HLA ANTIGEN; PROSTATE STEM CELL ANTIGEN;

ADULT; AFRICAN AMERICAN; ARTICLE; ASIA; BLADDER CANCER; CHROMOSOME 6; DISEASE ASSOCIATION; FEMALE; GAMBIA; GENE FREQUENCY; GENE LOCUS; GENETIC ASSOCIATION; GENETIC VARIABILITY; HUMAN; INFECTION; MAJOR CLINICAL STUDY; MALE; NATURAL SELECTION; NIGERIA; POPULATION DIFFERENTIATION; POPULATION STRUCTURE; PRIORITY JOURNAL; STOMACH CANCER;

AFRICAN AMERICANS; AFRICAN CONTINENTAL ANCESTRY GROUP; ANTIGENS, CD36; ANTIGENS, NEOPLASM; GAMBIA; GENE FREQUENCY; GENETIC VARIATION; GENETICS, POPULATION; GENOME, HUMAN; GENOTYPE; GPI-LINKED PROTEINS; HLA ANTIGENS; HUMANS; MODELS, GENETIC; NEOPLASM PROTEINS; NIGERIA; SELECTION, GENETIC; UNITED STATES;

EID: 80052749307     PISSN: 00029297     EISSN: 15376605     Source Type: Journal    
DOI: 10.1016/j.ajhg.2011.07.025     Document Type: Article

References (61)

1. P.C. Sabeti, D.E. Reich, J.M. Higgins, H.Z. Levine, D.J. Richter, S.F. Schaffner, S.B. Gabriel, J.V. Platko, N.J. Patterson, and G.J. McDonald Detecting recent positive selection in the human genome from haplotype structure Nature 419 2002 832 837 (Pubitemid 35238568)
2. International HapMap Consortium A haplotype map of the human genome Nature 437 2005 1299 1320
3. W.Y. Ko, K.A. Kaercher, E. Giombini, P. Marcatili, A. Froment, M. Ibrahim, G. Lema, T.B. Nyambo, S.A. Omar, and C. Wambebe Effects of natural selection and gene conversion on the evolution of human glycophorins coding for MNS blood polymorphisms in malaria-endemic African populations Am. J. Hum. Genet. 88 2011 741 754
4. M.T. Hamblin, and A. Di Rienzo Detection of the signature of natural selection in humans: evidence from the Duffy blood group locus Am. J. Hum. Genet. 66 2000 1669 1679 (Pubitemid 30463085)
5. P.C. Sabeti, P. Varilly, B. Fry, J. Lohmueller, E. Hostetter, C. Cotsapas, X. Xie, E.H. Byrne, S.A. McCarroll, R. Gaudet International HapMap Consortium Genome-wide detection and characterization of positive selection in human populations Nature 449 2007 913 918 (Pubitemid 47598625)
6. G. Genovese, D.J. Friedman, M.D. Ross, L. Lecordier, P. Uzureau, B.I. Freedman, D.W. Bowden, C.D. Langefeld, T.K. Oleksyk, and A.L. Uscinski Knob Association of trypanolytic ApoL1 variants with kidney disease in African Americans Science 329 2010 841 845
7. P.I. de Bakker, G. McVean, P.C. Sabeti, M.M. Miretti, T. Green, J. Marchini, X. Ke, A.J. Monsuur, P. Whittaker, and M. Delgado A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC Nat. Genet. 38 2006 1166 1172 (Pubitemid 44470362)
8. D.A. Lewinsohn, E. Winata, G.M. Swarbrick, K.E. Tanner, M.S. Cook, M.D. Null, M.E. Cansler, A. Sette, J. Sidney, and D.M. Lewinsohn Immunodominant tuberculosis CD8 antigens preferentially restricted by HLA-B PLoS Pathog. 3 2007 1240 1249 (Pubitemid 47510277)
9. J. Fellay, K.V. Shianna, D. Ge, S. Colombo, B. Ledergerber, M. Weale, K. Zhang, C. Gumbs, A. Castagna, and A. Cossarizza A whole-genome association study of major determinants for host control of HIV-1 Science 317 2007 944 947 (Pubitemid 47301321)
10. D.P. Kwiatkowski How malaria has affected the human genome and what human genetics can teach us about malaria Am. J. Hum. Genet. 77 2005 171 192 (Pubitemid 41022702)
11. R. Nielsen, I. Hellmann, M. Hubisz, C. Bustamante, and A.G. Clark Recent and ongoing selection in the human genome Nat. Rev. Genet. 8 2007 857 868 (Pubitemid 47609088)
12. P.C. Sabeti, S.F. Schaffner, B. Fry, J. Lohmueller, P. Varilly, O. Shamovsky, A. Palma, T.S. Mikkelsen, D. Altshuler, and E.S. Lander Positive natural selection in the human lineage Science 312 2006 1614 1620 (Pubitemid 43902654)
13. A. Bigham, M. Bauchet, D. Pinto, X. Mao, J.M. Akey, R. Mei, S.W. Scherer, C.G. Julian, M.J. Wilson, and D. López Herráez Identifying signatures of natural selection in Tibetan and Andean populations using dense genome scan data PLoS Genet. 6 2010 e1001116
14. X. Yi, Y. Liang, E. Huerta-Sanchez, X. Jin, Z.X. Cuo, J.E. Pool, X. Xu, H. Jiang, N. Vinckenbosch, and T.S. Korneliussen Sequencing of 50 human exomes reveals adaptation to high altitude Science 329 2010 75 78
15. T.S. Simonson, Y. Yang, C.D. Huff, H. Yun, G. Qin, D.J. Witherspoon, Z. Bai, F.R. Lorenzo, J. Xing, and L.B. Jorde Genetic evidence for high-altitude adaptation in Tibet Science 329 2010 72 75
16. J. Novembre, and A. Di Rienzo Spatial patterns of variation due to natural selection in humans Nat. Rev. Genet. 10 2009 745 755
17. K.A. Frazer, D.G. Ballinger, D.R. Cox, D.A. Hinds, L.L. Stuve, R.A. Gibbs, J.W. Belmont, A. Boudreau, P. Hardenbol, S.M. Leal International HapMap Consortium A second generation human haplotype map of over 3.1 million SNPs Nature 449 2007 851 861 (Pubitemid 47598626)
18. C.D. Campbell, N. Sampas, A. Tsalenko, P.H. Sudmant, J.M. Kidd, M. Malig, T.H. Vu, L. Vives, P. Tsang, L. Bruhn, and E.E. Eichler Population-genetic properties of differentiated human copy-number polymorphisms Am. J. Hum. Genet. 88 2011 317 332
19. J.M. Akey, G. Zhang, K. Zhang, L. Jin, and M.D. Shriver Interrogating a high-density SNP map for signatures of natural selection Genome Res. 12 2002 1805 1814 (Pubitemid 35469929)
20. K.E. Holsinger, and B.S. Weir Genetics in geographically structured populations: defining, estimating and interpreting F(ST) Nat. Rev. Genet. 10 2009 639 650
21. S.A. Tishkoff, F.A. Reed, F.R. Friedlaender, C. Ehret, A. Ranciaro, A. Froment, J.B. Hirbo, A.A. Awomoyi, J.M. Bodo, and O. Doumbo The genetic structure and history of Africans and African Americans Science 324 2009 1035 1044
22. A.L. Price, A. Helgason, S. Palsson, H. Stefansson, D. St Clair, O.A. Andreassen, D. Reich, A. Kong, and K. Stefansson The impact of divergence time on the nature of population structure: an example from Iceland PLoS Genet. 5 2009 e1000505
23. S. Xu, X. Yin, S. Li, W. Jin, H. Lou, L. Yang, X. Gong, H. Wang, Y. Shen, and X. Pan Genomic dissection of population substructure of Han Chinese and its implication in association studies Am. J. Hum. Genet. 85 2009 762 774
24. G. Ayodo, A.L. Price, A. Keinan, A. Ajwang, M.F. Otieno, A.S. Orago, N. Patterson, and D. Reich Combining evidence of natural selection with association analysis increases power to detect malaria-resistance variants Am. J. Hum. Genet. 81 2007 234 242 (Pubitemid 47236072)
25. N. Patterson, N. Hattangadi, B. Lane, K.E. Lohmueller, D.A. Hafler, J.R. Oksenberg, S.L. Hauser, M.W. Smith, S.J. O'Brien, and D. Altshuler Methods for high-density admixture mapping of disease genes Am. J. Hum. Genet. 74 2004 979 1000 (Pubitemid 38578397)
26. M. Jallow, Y.Y. Teo, K.S. Small, K.A. Rockett, P. Deloukas, T.G. Clark, K. Kivinen, K.A. Bojang, D.J. Conway, M. Pinder Wellcome Trust Case Control Consortium Malaria Genomic Epidemiology Network Genome-wide and fine-resolution association analysis of malaria in West Africa Nat. Genet. 41 2009 657 665
27. T. Thye, F.O. Vannberg, S.H. Wong, E. Owusu-Dabo, I. Osei, J. Gyapong, G. Sirugo, F. Sisay-Joof, A. Enimil, M.A. Chinbuah African TB Genetics Consortium Wellcome Trust Case Control Consortium Genome-wide association analyses identifies a susceptibility locus for tuberculosis on chromosome 18q11.2 Nat. Genet. 42 2010 739 741
28. D.M. Altshuler, R.A. Gibbs, L. Peltonen, D.M. Altshuler, R.A. Gibbs, L. Peltonen, E. Dermitzakis, S.F. Schaffner, F. Yu, L. Peltonen International HapMap 3 Consortium Integrating common and rare genetic variation in diverse human populations Nature 467 2010 52 58
29. M.D. Shriver, G.C. Kennedy, E.J. Parra, H.A. Lawson, V. Sonpar, J. Huang, J.M. Akey, and K.W. Jones The genomic distribution of population substructure in four populations using 8,525 autosomal SNPs Hum. Genomics 1 2004 274 286
30. J.M. Akey Constructing genomic maps of positive selection in humans: where do we go from here? Genome Res. 19 2009 711 722
31. A.E. Fry, A. Ghansa, K.S. Small, A. Palma, S. Auburn, M. Diakite, A. Green, S. Campino, Y.Y. Teo, and T.G. Clark Positive selection of a CD36 nonsense variant in sub-Saharan Africa, but no association with severe malaria phenotypes Hum. Mol. Genet. 18 2009 2683 2692
32. M. Currat, G. Trabuchet, D. Rees, P. Perrin, R.M. Harding, J.B. Clegg, A. Langaney, and L. Excoffier Molecular analysis of the beta-globin gene cluster in the Niokholo Mandenka population reveals a recent origin of the beta(S) Senegal mutation Am. J. Hum. Genet. 70 2002 207 223 (Pubitemid 34031709)
33. P.W. Hedrick Population genetics of malaria resistance in humans Heredity 2011 in press. Published online March 23, 2011
34. P.W. Hedrick, and G. Thomson Evidence for balancing selection at HLA Genetics 104 1983 449 456 (Pubitemid 13011682)
35. K. Cao, A.M. Moormann, K.E. Lyke, C. Masaberg, O.P. Sumba, O.K. Doumbo, D. Koech, A. Lancaster, M. Nelson, and D. Meyer Differentiation between African populations is evidenced by the diversity of alleles and haplotypes of HLA class I loci Tissue Antigens 63 2004 293 325 (Pubitemid 38406692)
36. H. Sakamoto, K. Yoshimura, N. Saeki, H. Katai, T. Shimoda, Y. Matsuno, D. Saito, H. Sugimura, F. Tanioka, S. Kato Study Group of Millennium Genome Project for Cancer Genetic variation in PSCA is associated with susceptibility to diffuse-type gastric cancer Nat. Genet. 40 2008 730 740 (Pubitemid 351748870)
37. X. Wu, Y. Ye, L.A. Kiemeney, P. Sulem, T. Rafnar, G. Matullo, D. Seminara, T. Yoshida, N. Saeki, and A.S. Andrew Genetic variation in the prostate stem cell antigen gene PSCA confers susceptibility to urinary bladder cancer Nat. Genet. 41 2009 991 995
38. B. Pasaniuc, N. Zaitlen, G. Lettre, G.K. Chen, A. Tandon, W.H.L. Kao, I. Ruczinski, M. Fornage, D.S. Siscovick, and X. Zhu Enhanced statistical tests for GWAS in admixed populations: assessment using African Americans from CARe and a Breast Cancer Consortium PLoS Genet. 7 2011 e1001371
39. G. Lettre, C.D. Palmer, T. Young, K.G. Ejebe, H. Allayee, E.J. Benjamin, F. Bennett, D.W. Bowden, A. Chakravarti, and A. Dreisbach Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe Project PLoS Genet. 7 2011 e1001300
40. H.M. Cann, C. de Toma, L. Cazes, M.-F. Legrand, V. Morel, L. Piouffre, J. Bodmer, W.F. Bodmer, B. Bonne-Tamir, and A. Cambon-Thomsen A human genome diversity cell line panel Science 296 2002 261 262 (Pubitemid 34303653)
41. D.G. Clayton, N.M. Walker, D.J. Smyth, R. Pask, J.D. Cooper, L.M. Maier, L.J. Smink, A.C. Lam, N.R. Ovington, and H.E. Stevens Population structure, differential bias and genomic control in a large-scale, case-control association study Nat. Genet. 37 2005 1243 1246 (Pubitemid 41568707)
42. G. Nicholson, A.V. Smith, F. Jonsson, A. Gustafsson, K. Stefansson, and P. Donnelly Assessing population differentiation and isolation from single-nucleotide polymorphism data J. R. Stat. Soc. Series B Stat. Methodol. 64 2002 695 715
43. Wellcome Trust Case Control Consortium Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls Nature 447 2007 661 678
44. L.L. Cavalli-Sforza, and A.W. Edwards Phylogenetic analysis. Models and estimation procedures Am. J. Hum. Genet. 19 1967 233 257
45. A.L. Price, A. Tandon, N. Patterson, K.C. Barnes, N. Rafaels, I. Ruczinski, T.H. Beaty, R. Mathias, D. Reich, and S. Myers Sensitive detection of chromosomal segments of distinct ancestry in admixed populations PLoS Genet. 5 2009 e1000519
46. L.B. Barreiro, G. Laval, H. Quach, E. Patin, and L. Quintana-Murci Natural selection has driven population differentiation in modern humans Nat. Genet. 40 2008 340 345 (Pubitemid 351311765)
47. G. McVicker, D. Gordon, C. Davis, and P. Green Widespread genomic signatures of natural selection in hominid evolution PLoS Genet. 5 2009 e1000471
48. Y. Li, C.J. Willer, J. Ding, P. Scheet, and G.R. Abecasis MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes Genet. Epidemiol. 34 2010 816 834
49. N. Patterson, A.L. Price, and D. Reich Population structure and eigenanalysis PLoS Genet. 2 2006 e190
50. J.S. Wainscoat, A.V.S. Hill, A.L. Boyce, J. Flint, M. Hernandez, S.L. Thein, J.M. Old, J.R. Lynch, A.G. Falusi, and D.J. Weatherall Evolutionary relationships of human populations from an analysis of nuclear DNA polymorphisms Nature 319 1986 491 493 (Pubitemid 16212926)
51. B.F. Voight, S. Kudaravalli, X. Wen, and J.K. Pritchard A map of recent positive selection in the human genome PLoS Biol. 4 2006 e72
52. V. Mattiangeli, A.W. Ryan, R. McManus, and D.G. Bradley A genome-wide approach to identify genetic loci with a signature of natural selection in the Irish population Genome Biol. 7 2006 R74
53. H.L. Norton, R.A. Kittles, E. Parra, P. McKeigue, X. Mao, K. Cheng, V.A. Canfield, D.G. Bradley, B. McEvoy, and M.D. Shriver Genetic evidence for the convergent evolution of light skin in Europeans and East Asians Mol. Biol. Evol. 24 2007 710 722 (Pubitemid 46355799)
54. B. McEvoy, S. Beleza, and M.D. Shriver The genetic architecture of normal variation in human pigmentation: an evolutionary perspective and model Hum. Mol. Genet. 15 Spec No 2 2006 R176 R181
55. M. Edwards, A. Bigham, J. Tan, S. Li, A. Gozdzik, K. Ross, L. Jin, and E.J. Parra Association of the OCA2 polymorphism His615Arg with melanin content in east Asian populations: further evidence of convergent evolution of skin pigmentation PLoS Genet. 6 2010 e1000867
56. S.E. Medland, D.R. Nyholt, J.N. Painter, B.P. McEvoy, A.F. McRae, G. Zhu, S.D. Gordon, M.A.R. Ferreira, M.J. Wright, and A.K. Henders Common variants in the trichohyalin gene are associated with straight hair in Europeans Am. J. Hum. Genet. 85 2009 750 755
57. T. Bersaglieri, P.C. Sabeti, N. Patterson, T. Vanderploeg, S.F. Schaffner, J.A. Drake, M. Rhodes, D.E. Reich, and J.N. Hirschhorn Genetic signatures of strong recent positive selection at the lactase gene Am. J. Hum. Genet. 74 2004 1111 1120 (Pubitemid 38669310)
58. S.H. Williamson, M.J. Hubisz, A.G. Clark, B.A. Payseur, C.D. Bustamante, and R. Nielsen Localizing recent adaptive evolution in the human genome PLoS Genet. 3 2007 e90
59. R.D. Hernandez, J.L. Kelley, E. Elyashiv, S.C. Melton, A. Auton, G. McVean, G. Sella, M. Przeworski 1000 Genomes Project Classic selective sweeps were rare in recent human evolution Science 331 2011 920 924
60. B.S. Weir, L.R. Cardon, A.D. Anderson, D.M. Nielsen, and W.G. Hill Measures of human population structure show heterogeneity among genomic regions Genome Res. 15 2005 1468 1476 (Pubitemid 41545000)
61. A.M. Hancock, D.B. Witonsky, A.S. Gordon, G. Eshel, J.K. Pritchard, G. Coop, and A. Di Rienzo Adaptations to climate in candidate genes for common metabolic disorders PLoS Genet. 4 2008 e32