Article: Genome-wide detection and characterization of positive selection in human populations

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TitleGenome-wide detection and characterization of positive selection in human populations
AuthorsSabeti, PC3
Varilly, P3
Fry, B3
Lohmueller, J3
Hostetter, E3
Cotsapas, C1 3
Xie, X3
Byrne, EH3
McCarroll, SA1 3
Gaudet, R26
Schaffner, SF3
Lander, ES3 15 19
Frazer, KA33
Ballinger, DG21
Cox, DR21
Hinds, DA21
Stuve, LL21
Gibbs, RA6
Belmont, JW6
Boudreau, A52
Hardenbol, P8
Leal, SM6
Pasternak, S11
Wheeler, DA6
Willis, TD52
Yu, F3
Yang, H37
Zeng, C37
Gao, Y37
Hu, H37
Hu, W37
Li, C37
Lin, W37
Liu, S37
Pan, H37
Tang, X37
Wang, J37
Wang, W37
Yu, J37
Zhang, B37
Zhang, Q37
Zhao, H37
Zhao, H37
Zhou, J37
Gabriel, SB3
Barry, R3
Blumenstiel, B3
Camargo, A3
Defelice, M3
Faggart, M3
Goyette, M3
Gupta, S3
Moore, J3
Nguyen, H3
Onofrio, RC3
Parkin, M3
Roy, J3
Stahl, E3
Winchester, E3
Ziaugra, L3
Altshuler, D1 3
Shen, Y24
Yao, Z24
Huang, W24
Chu, X24
He, Y24
Jin, L43
Liu, Y24
Shen, Y24
Sun, W24
Wang, H24
Wang, Y24
Wang, Y24
Xiong, X24
Xu, L24
Waye, MMY62
Tsui, SKW62
Xue, H51
Wong, JTF51
Galver, LM59
Fan, JB59
Gunderson, K59
Murray, SS33
Oliphant, AR22
Chee, MS35
Montpetit, A65
Chagnon, F65
Ferretti, V65
Leboeuf, M65
Olivier, JF52
Phillips, MS65
Roumy, S59
Sallée, C61
Verner, A65
Hudson, TJ28
Kwok, PY2
Cai, D2
Koboldt, DC10
Miller, RD10
Pawlikowska, L2
TaillonMiller, P10
Xiao, M2
Tsui, LC27
Mak, W27
You, QS27
Tam, PKH27
Nakamura, Y34 53
Kawaguchi, T34
Kitamoto, T34
Morizono, T34
Nagashima, A34
Ohnishi, Y34
Sekine, A34
Tanaka, T34
Tsunoda, T34
Deloukas, P32
Bird, CP32
Delgado, M32
Dermitzakis, ET32
Gwilliam, R32
Hunt, S32
Morrison, J45
Powell, D32
Stranger, BE32
Whittaker, P32
Bentley, DR49
Daly, MJ1 3
De Bakker, PIW1 3
Barrett, J1 3
Chretien, YR3
Maller, J1 3
McCarroll, S1 3
Patterson, N3
Pe'Er, I25
Price, A3
Purcell, S1
Richter, DJ3
Saxena, R1 3
Sham, PC27
Stein, LD11
Krishnan, L11
Smith, AV11
TelloRuiz, MK11
Thorisson, GA56
Chakravarti, A58
Chen, PE58
Cutler, DJ58
Kashuk, CS58
Lin, S58
Abecasis, GR64
Guan, W64
Li, Y64
Munro, HM36
Qin, ZS64
Thomas, DJ55
McVean, G54
Auton, A54
Bottolo, L54
Cardin, N54
Eyheramendy, S54
Freeman, C54
Marchini, J54
Myers, S54
Spencer, C3
Stephens, M44
Donnelly, P54
Cardon, LR39
Clarke, G54
Evans, DM54
Morris, AP54
Weir, BS5
Johnson, TA34
Mullikin, JC12
Sherry, ST38
Feolo, M38
Skol, A44
Zhang, H4
Matsuda, I40
Fukushima, Y57
MacEr, DR48
Suda, E14
Rotimi, CN30
Adebamowo, CA29
Ajayi, I29
Aniagwu, T29
Marshall, PA46
Nkwodimmah, C29
Royal, CDM30
Leppert, MF47
Dixon, M47
Peiffer, A47
Qiu, R7
Kent, A9
Kato, K42
Niikawa, N23
Adewole, IF29
Knoppers, BM61
Foster, MW17
Clayton, EW60
Watkin, J13
Muzny, D6
Nazareth, L6
Sodergren, E6
Weinstock, GM6
Yakub, I6
Birren, BW3
Wilson, RK10
Fulton, LL10
Rogers, J32
Burton, J32
Carter, NP32
Clee, CM32
Griffiths, M32
Jones, MC32
McLay, K32
Plumb, RW32
Ross, MT32
Sims, SK32
Willey, DL32
Chen, Z37
Han, H37
Kang, L37
Godbout, M50
Wallenburg, JC65
L'Archevêque, P
Bellemare, G
Saeki, K16
Wang, H31
An, D31
Fu, H31
Li, Q31
Wang, Z31
Wang, R20
Holden, AL59
Brooks, LD12
McEwen, JE12
Guyer, MS12
Wang, VO12 63
Peterson, JL12
Shi, M41
Spiegel, J63
Sung, LM18
Zacharia, LF12
Collins, FS12
Kennedy, K50
Jamieson, R13
Stewart, J13
KeywordsRegional Index: Eurasia
Europe
Issue Date2007
PublisherNature Publishing Group. The Journal's web site is located at http://www.nature.com/nature
CitationNature, 2007, v. 449 n. 7164, p. 913-918 [How to Cite?]
DOI: http://dx.doi.org/10.1038/nature06250
AbstractWith the advent of dense maps of human genetic variation, it is now possible to detect positive natural selection across the human genome. Here we report an analysis of over 3 million polymorphisms from the International HapMap Project Phase 2 (HapMap2). We used 'long-range haplotype' methods, which were developed to identify alleles segregating in a population that have undergone recent selection, and we also developed new methods that are based on cross-population comparisons to discover alleles that have swept to near-fixation within a population. The analysis reveals more than 300 strong candidate regions. Focusing on the strongest 22 regions, we develop a heuristic for scrutinizing these regions to identify candidate targets of selection. In a complementary analysis, we identify 26 non-synonymous, coding, single nucleotide polymorphisms showing regional evidence of positive selection. Examination of these candidates highlights three cases in which two genes in a common biological process have apparently undergone positive selection in the same population:LARGE and DMD, both related to infection by the Lassa virus, in West Africa;SLC24A5 and SLC45A2, both involved in skin pigmentation, in Europe; and EDAR and EDA2R, both involved in development of hair follicles, in Asia. ©2007 Nature Publishing Group.
ISSN0028-0836
2011 Impact Factor: 36.28
2011 SCImago Journal Rankings: 7.767
DOIhttp://dx.doi.org/10.1038/nature06250
ISI Accession Number IDWOS:000250230600049
PubMed Central IDPMC2687721
ReferencesReferences in Scopus
DC Field
Value
dc.contributor.authorSabeti, PC
dc.contributor.authorVarilly, P
dc.contributor.authorFry, B
dc.contributor.authorLohmueller, J
dc.contributor.authorHostetter, E
dc.contributor.authorCotsapas, C
dc.contributor.authorXie, X
dc.contributor.authorByrne, EH
dc.contributor.authorMcCarroll, SA
dc.contributor.authorGaudet, R
dc.contributor.authorSchaffner, SF
dc.contributor.authorLander, ES
dc.contributor.authorFrazer, KA
dc.contributor.authorBallinger, DG
dc.contributor.authorCox, DR
dc.contributor.authorHinds, DA
dc.contributor.authorStuve, LL
dc.contributor.authorGibbs, RA
dc.contributor.authorBelmont, JW
dc.contributor.authorBoudreau, A
dc.contributor.authorHardenbol, P
dc.contributor.authorLeal, SM
dc.contributor.authorPasternak, S
dc.contributor.authorWheeler, DA
dc.contributor.authorWillis, TD
dc.contributor.authorYu, F
dc.contributor.authorYang, H
dc.contributor.authorZeng, C
dc.contributor.authorGao, Y
dc.contributor.authorHu, H
dc.contributor.authorHu, W
dc.contributor.authorLi, C
dc.contributor.authorLin, W
dc.contributor.authorLiu, S
dc.contributor.authorPan, H
dc.contributor.authorTang, X
dc.contributor.authorWang, J
dc.contributor.authorWang, W
dc.contributor.authorYu, J
dc.contributor.authorZhang, B
dc.contributor.authorZhang, Q
dc.contributor.authorZhao, H
dc.contributor.authorZhao, H
dc.contributor.authorZhou, J
dc.contributor.authorGabriel, SB
dc.contributor.authorBarry, R
dc.contributor.authorBlumenstiel, B
dc.contributor.authorCamargo, A
dc.contributor.authorDefelice, M
dc.contributor.authorFaggart, M
dc.contributor.authorGoyette, M
dc.contributor.authorGupta, S
dc.contributor.authorMoore, J
dc.contributor.authorNguyen, H
dc.contributor.authorOnofrio, RC
dc.contributor.authorParkin, M
dc.contributor.authorRoy, J
dc.contributor.authorStahl, E
dc.contributor.authorWinchester, E
dc.contributor.authorZiaugra, L
dc.contributor.authorAltshuler, D
dc.contributor.authorShen, Y
dc.contributor.authorYao, Z
dc.contributor.authorHuang, W
dc.contributor.authorChu, X
dc.contributor.authorHe, Y
dc.contributor.authorJin, L
dc.contributor.authorLiu, Y
dc.contributor.authorShen, Y
dc.contributor.authorSun, W
dc.contributor.authorWang, H
dc.contributor.authorWang, Y
dc.contributor.authorWang, Y
dc.contributor.authorXiong, X
dc.contributor.authorXu, L
dc.contributor.authorWaye, MMY
dc.contributor.authorTsui, SKW
dc.contributor.authorXue, H
dc.contributor.authorWong, JTF
dc.contributor.authorGalver, LM
dc.contributor.authorFan, JB
dc.contributor.authorGunderson, K
dc.contributor.authorMurray, SS
dc.contributor.authorOliphant, AR
dc.contributor.authorChee, MS
dc.contributor.authorMontpetit, A
dc.contributor.authorChagnon, F
dc.contributor.authorFerretti, V
dc.contributor.authorLeboeuf, M
dc.contributor.authorOlivier, JF
dc.contributor.authorPhillips, MS
dc.contributor.authorRoumy, S
dc.contributor.authorSallée, C
dc.contributor.authorVerner, A
dc.contributor.authorHudson, TJ
dc.contributor.authorKwok, PY
dc.contributor.authorCai, D
dc.contributor.authorKoboldt, DC
dc.contributor.authorMiller, RD
dc.contributor.authorPawlikowska, L
dc.contributor.authorTaillonMiller, P
dc.contributor.authorXiao, M
dc.contributor.authorTsui, LC
dc.contributor.authorMak, W
dc.contributor.authorYou, QS
dc.contributor.authorTam, PKH
dc.contributor.authorNakamura, Y
dc.contributor.authorKawaguchi, T
dc.contributor.authorKitamoto, T
dc.contributor.authorMorizono, T
dc.contributor.authorNagashima, A
dc.contributor.authorOhnishi, Y
dc.contributor.authorSekine, A
dc.contributor.authorTanaka, T
dc.contributor.authorTsunoda, T
dc.contributor.authorDeloukas, P
dc.contributor.authorBird, CP
dc.contributor.authorDelgado, M
dc.contributor.authorDermitzakis, ET
dc.contributor.authorGwilliam, R
dc.contributor.authorHunt, S
dc.contributor.authorMorrison, J
dc.contributor.authorPowell, D
dc.contributor.authorStranger, BE
dc.contributor.authorWhittaker, P
dc.contributor.authorBentley, DR
dc.contributor.authorDaly, MJ
dc.contributor.authorDe Bakker, PIW
dc.contributor.authorBarrett, J
dc.contributor.authorChretien, YR
dc.contributor.authorMaller, J
dc.contributor.authorMcCarroll, S
dc.contributor.authorPatterson, N
dc.contributor.authorPe'Er, I
dc.contributor.authorPrice, A
dc.contributor.authorPurcell, S
dc.contributor.authorRichter, DJ
dc.contributor.authorSaxena, R
dc.contributor.authorSham, PC
dc.contributor.authorStein, LD
dc.contributor.authorKrishnan, L
dc.contributor.authorSmith, AV
dc.contributor.authorTelloRuiz, MK
dc.contributor.authorThorisson, GA
dc.contributor.authorChakravarti, A
dc.contributor.authorChen, PE
dc.contributor.authorCutler, DJ
dc.contributor.authorKashuk, CS
dc.contributor.authorLin, S
dc.contributor.authorAbecasis, GR
dc.contributor.authorGuan, W
dc.contributor.authorLi, Y
dc.contributor.authorMunro, HM
dc.contributor.authorQin, ZS
dc.contributor.authorThomas, DJ
dc.contributor.authorMcVean, G
dc.contributor.authorAuton, A
dc.contributor.authorBottolo, L
dc.contributor.authorCardin, N
dc.contributor.authorEyheramendy, S
dc.contributor.authorFreeman, C
dc.contributor.authorMarchini, J
dc.contributor.authorMyers, S
dc.contributor.authorSpencer, C
dc.contributor.authorStephens, M
dc.contributor.authorDonnelly, P
dc.contributor.authorCardon, LR
dc.contributor.authorClarke, G
dc.contributor.authorEvans, DM
dc.contributor.authorMorris, AP
dc.contributor.authorWeir, BS
dc.contributor.authorJohnson, TA
dc.contributor.authorMullikin, JC
dc.contributor.authorSherry, ST
dc.contributor.authorFeolo, M
dc.contributor.authorSkol, A
dc.contributor.authorZhang, H
dc.contributor.authorMatsuda, I
dc.contributor.authorFukushima, Y
dc.contributor.authorMacEr, DR
dc.contributor.authorSuda, E
dc.contributor.authorRotimi, CN
dc.contributor.authorAdebamowo, CA
dc.contributor.authorAjayi, I
dc.contributor.authorAniagwu, T
dc.contributor.authorMarshall, PA
dc.contributor.authorNkwodimmah, C
dc.contributor.authorRoyal, CDM
dc.contributor.authorLeppert, MF
dc.contributor.authorDixon, M
dc.contributor.authorPeiffer, A
dc.contributor.authorQiu, R
dc.contributor.authorKent, A
dc.contributor.authorKato, K
dc.contributor.authorNiikawa, N
dc.contributor.authorAdewole, IF
dc.contributor.authorKnoppers, BM
dc.contributor.authorFoster, MW
dc.contributor.authorClayton, EW
dc.contributor.authorWatkin, J
dc.contributor.authorMuzny, D
dc.contributor.authorNazareth, L
dc.contributor.authorSodergren, E
dc.contributor.authorWeinstock, GM
dc.contributor.authorYakub, I
dc.contributor.authorBirren, BW
dc.contributor.authorWilson, RK
dc.contributor.authorFulton, LL
dc.contributor.authorRogers, J
dc.contributor.authorBurton, J
dc.contributor.authorCarter, NP
dc.contributor.authorClee, CM
dc.contributor.authorGriffiths, M
dc.contributor.authorJones, MC
dc.contributor.authorMcLay, K
dc.contributor.authorPlumb, RW
dc.contributor.authorRoss, MT
dc.contributor.authorSims, SK
dc.contributor.authorWilley, DL
dc.contributor.authorChen, Z
dc.contributor.authorHan, H
dc.contributor.authorKang, L
dc.contributor.authorGodbout, M
dc.contributor.authorWallenburg, JC
dc.contributor.authorL'Archevêque, P
dc.contributor.authorBellemare, G
dc.contributor.authorSaeki, K
dc.contributor.authorWang, H
dc.contributor.authorAn, D
dc.contributor.authorFu, H
dc.contributor.authorLi, Q
dc.contributor.authorWang, Z
dc.contributor.authorWang, R
dc.contributor.authorHolden, AL
dc.contributor.authorBrooks, LD
dc.contributor.authorMcEwen, JE
dc.contributor.authorGuyer, MS
dc.contributor.authorWang, VO
dc.contributor.authorPeterson, JL
dc.contributor.authorShi, M
dc.contributor.authorSpiegel, J
dc.contributor.authorSung, LM
dc.contributor.authorZacharia, LF
dc.contributor.authorCollins, FS
dc.contributor.authorKennedy, K
dc.contributor.authorJamieson, R
dc.contributor.authorStewart, J
dc.date.accessioned2010-09-06T08:53:56Z
dc.date.available2010-09-06T08:53:56Z
dc.date.issued2007
dc.description.abstractWith the advent of dense maps of human genetic variation, it is now possible to detect positive natural selection across the human genome. Here we report an analysis of over 3 million polymorphisms from the International HapMap Project Phase 2 (HapMap2). We used 'long-range haplotype' methods, which were developed to identify alleles segregating in a population that have undergone recent selection, and we also developed new methods that are based on cross-population comparisons to discover alleles that have swept to near-fixation within a population. The analysis reveals more than 300 strong candidate regions. Focusing on the strongest 22 regions, we develop a heuristic for scrutinizing these regions to identify candidate targets of selection. In a complementary analysis, we identify 26 non-synonymous, coding, single nucleotide polymorphisms showing regional evidence of positive selection. Examination of these candidates highlights three cases in which two genes in a common biological process have apparently undergone positive selection in the same population:LARGE and DMD, both related to infection by the Lassa virus, in West Africa;SLC24A5 and SLC45A2, both involved in skin pigmentation, in Europe; and EDAR and EDA2R, both involved in development of hair follicles, in Asia. ©2007 Nature Publishing Group.
dc.description.naturelink_to_OA_fulltext
dc.identifier.citationNature, 2007, v. 449 n. 7164, p. 913-918 [How to Cite?]
DOI: http://dx.doi.org/10.1038/nature06250
dc.identifier.citeulike1780777
dc.identifier.doihttp://dx.doi.org/10.1038/nature06250
dc.identifier.epage918
dc.identifier.hkuros139460
dc.identifier.isiWOS:000250230600049
dc.identifier.issn0028-0836
2011 Impact Factor: 36.28
2011 SCImago Journal Rankings: 7.767
dc.identifier.issue7164
dc.identifier.openurl
dc.identifier.pmcidPMC2687721
dc.identifier.pmid17943131
dc.identifier.scopuseid_2-s2.0-35349012592
dc.identifier.spage913
dc.identifier.urihttp://hdl.handle.net/10722/84522
dc.identifier.volume449
dc.languageeng
dc.publisherNature Publishing Group. The Journal's web site is located at http://www.nature.com/nature
dc.publisher.placeUnited Kingdom
dc.relation.ispartofNature
dc.relation.referencesReferences in Scopus
dc.subjectRegional Index: Eurasia
dc.subjectEurope
dc.titleGenome-wide detection and characterization of positive selection in human populations
dc.typeArticle
Author Affiliations
  1. Massachusetts General Hospital
  2. University of California, San Francisco
  3. Massachusetts Institute of Technology
  4. Beijing Normal University
  5. University of Washington
  6. Baylor College of Medicine
  7. Chinese Academy of Social Sciences
  8. Pacific Biosciences
  9. Genetic Interest Group
  10. University of Washington School of Medicine
  11. Cold Spring Harbor Laboratory
  12. National Human Genome Research Institute
  13. Wellcome Trust
  14. University of Tsukuba
  15. Whitehead Institute for Biomedical Research
  16. Japan Ministry of Education, Culture, Sports, Science and Technology
  17. University of Oklahoma
  18. University of Maryland School of Law
  19. Harvard Medical School
  20. Human Genetic Resource Administration of China
  21. Perlegen Sciences, Inc.
  22. Complete Genomics Inc.
  23. Nagasaki University
  24. Chinese National Human Genome Center at Shanghai
  25. Columbia University in the City of New York
  26. Harvard University
  27. The University of Hong Kong
  28. Ontario Institute for Cancer Research
  29. University of Ibadan
  30. Howard University
  31. Ministry of Science and Technology of the People's Republic of China
  32. Wellcome Trust Sanger Institute
  33. Scripps Research Institute
  34. Riken
  35. null
  36. International Epidemiology Institute
  37. Chinese Academy of Sciences
  38. National Center for Biotechnology Information
  39. Fred Hutchinson Cancer Research Center
  40. Health Sciences University of Hokkaido
  41. Novartis Pharma
  42. Kyoto University
  43. Fudan University
  44. University of Chicago
  45. University of Cambridge
  46. Case Western Reserve University
  47. University of Utah
  48. Scientific and Cultural Organization (UNESCO Bangkok)
  49. Solexa Ltd.
  50. null
  51. Hong Kong University of Science and Technology
  52. Affymetrix
  53. University of Tokyo
  54. University of Oxford
  55. University of California, Santa Cruz
  56. University of Leicester
  57. Shinshu University Faculty of Medicine
  58. The Johns Hopkins School of Medicine
  59. Illumina, Inc.
  60. Vanderbilt University
  61. Université de Montréal
  62. Chinese University of Hong Kong
  63. National Institutes of Health, Bethesda
  64. University of Michigan
  65. McGill University