Article: A second generation human haplotype map of over 3.1 million SNPs

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TitleA second generation human haplotype map of over 3.1 million SNPs
AuthorsFrazer, KA30
Ballinger, DG19
Cox, DR19
Hinds, DA19
Stuve, LL19
Gibbs, RA6
Belmont, JW6
Boudreau, A49
Hardenbol, P8
Leal, SM6
Pasternak, S11
Wheeler, DA6
Willis, TD49
Yu, F3
Yang, H34
Zeng, C34
Gao, Y34
Hu, H34
Hu, W34
Li, C34
Lin, W34
Liu, S34
Pan, H34
Tang, X34
Wang, J34
Wang, W34
Yu, J34
Zhang, B34
Zhang, Q34
Zhao, H34
Zhao, H34
Zhou, J34
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, Y22
Yao, Z22
Huang, W22
Chu, X22
He, Y22
Jin, L40
Liu, Y22
Shen, Y22
Sun, W22
Wang, H22
Wang, Y22
Wang, Y22
Xiong, X22
Xu, L22
Waye, MMY59
Tsui, SKW59
Xue, H48
Wong, JTF48
Galver, LM56
Fan, JB56
Gunderson, K56
Murray, SS30
Oliphant, AR20
Chee, MS32
Montpetit, A62
Chagnon, F62
Ferretti, V62
Leboeuf, M62
Olivier, JF49
Phillips, MS62
Roumy, S56
Sallée, C58
Verner, A62
Hudson, TJ25
Kwok, PY2
Cai, D2
Koboldt, DC10
Miller, RD10
Pawlikowska, L2
TaillonMiller, P10
Xiao, M2
Tsui, LC24
Mak, W24
You, QS24
Tam, PKH24
Nakamura, Y31 50
Kawaguchi, T31
Kitamoto, T31
Morizono, T31
Nagashima, A31
Ohnishi, Y31
Sekine, A31
Tanaka, T31
Tsunoda, T31
Deloukas, P29
Bird, CP29
Delgado, M29
Dermitzakis, ET29
Gwilliam, R29
Hunt, S29
Morrison, J42
Powell, D29
Stranger, BE29
Whittaker, P29
Bentley, DR46
Daly, MJ1 3
De Bakker, PIW1 3
Barrett, J1 3
Chretien, YR3
Maller, J1 3
McCarroll, S1 3
Patterson, N3
Pe'Er, I23
Price, A3
Purcell, S1
Richter, DJ3
Sabeti, P3
Saxena, R1 3
Schaffner, SF3
Sham, PC24
Varilly, P3
Stein, LD11
Krishnan, L11
Smith, AV11
TelloRuiz, MK11
Thorisson, GA53
Chakravarti, A55
Chen, PE55
Cutler, DJ55
Kashuk, CS55
Lin, S55
Abecasis, GR61
Guan, W61
Li, Y61
Munro, HM33
Qin, ZS61
Thomas, DJ52
McVean, G51
Auton, A51
Bottolo, L51
Cardin, N51
Eyheramendy, S51
Freeman, C51
Marchini, J51
Myers, S51
Spencer, C3
Stephens, M41
Donnelly, P51
Cardon, LR36
Clarke, G51
Evans, DM51
Morris, AP51
Weir, BS5
Johnson, TA31
Mullikin, JC12
Sherry, ST35
Feolo, M35
Skol, A41
Zhang, H4
Matsuda, I37
Fukushima, Y54
MacEr, DR45
Suda, E14
Rotimi, CN27
Adebamowo, CA26
Ajayi, I26
Aniagwu, T26
Marshall, PA43
Nkwodimmah, C26
Royal, CDM27
Leppert, MF44
Dixon, M44
Peiffer, A44
Qiu, R7
Kent, A9
Kato, K39
Niikawa, N21
Adewole, IF26
Knoppers, BM58
Foster, MW16
Clayton, EW57
Watkin, J13
Muzny, D6
Nazareth, L6
Sodergren, E6
Weinstock, GM6
Yakub, I6
Birren, BW3
Wilson, RK10
Fulton, LL10
Rogers, J29
Burton, J29
Carter, NP29
Clee, CM29
Griffiths, M29
Jones, MC29
McLay, K29
Plumb, RW29
Ross, MT29
Sims, SK29
Willey, DL29
Chen, Z34
Han, H34
Kang, L34
Godbout, M47
Wallenburg, JC62
L'Archevêque, P
Bellemare, G
Saeki, K15
Wang, H28
An, D28
Fu, H28
Li, Q28
Wang, Z28
Wang, R18
Holden, AL56
Brooks, LD12
McEwen, JE12
Guyer, MS12
Wang, VO12 60
Peterson, JL12
Shi, M38
Spiegel, J60
Sung, LM17
Zacharia, LF12
Collins, FS12
Kennedy, K47
Jamieson, R13
Stewart, J13
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. 851-861 [How to Cite?]
DOI: http://dx.doi.org/10.1038/nature06258
AbstractWe describe the Phase II HapMap, which characterizes over 3.1 million human single nucleotide polymorphisms (SNPs) genotyped in 270 individuals from four geographically diverse populations and includes 25-35% of common SNP variation in the populations surveyed. The map is estimated to capture untyped common variation with an average maximum r 2 of between 0.9 and 0.96 depending on population. We demonstrate that the current generation of commercial genome-wide genotyping products captures common Phase II SNPs with an average maximum r 2 of up to 0.8 in African and up to 0.95 in non-African populations, and that potential gains in power in association studies can be obtained through imputation. These data also reveal novel aspects of the structure of linkage disequilibrium. We show that 10-30% of pairs of individuals within a population share at least one region of extended genetic identity arising from recent ancestry and that up to 1% of all common variants are untaggable, primarily because they lie within recombination hotspots. We show that recombination rates vary systematically around genes and between genes of different function. Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations. ©2007 Nature Publishing Group.
ISSN0028-0836
2011 Impact Factor: 36.28
2011 SCImago Journal Rankings: 7.767
DOIhttp://dx.doi.org/10.1038/nature06258
ISI Accession Number IDWOS:000250230600036
PubMed Central IDPMC2689609
ReferencesReferences in Scopus
DC Field
Value
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.authorSabeti, P
dc.contributor.authorSaxena, R
dc.contributor.authorSchaffner, SF
dc.contributor.authorSham, PC
dc.contributor.authorVarilly, P
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.accessioned2010-09-06T08:39:55Z
dc.date.available2010-09-06T08:39:55Z
dc.date.issued2007
dc.description.abstractWe describe the Phase II HapMap, which characterizes over 3.1 million human single nucleotide polymorphisms (SNPs) genotyped in 270 individuals from four geographically diverse populations and includes 25-35% of common SNP variation in the populations surveyed. The map is estimated to capture untyped common variation with an average maximum r 2 of between 0.9 and 0.96 depending on population. We demonstrate that the current generation of commercial genome-wide genotyping products captures common Phase II SNPs with an average maximum r 2 of up to 0.8 in African and up to 0.95 in non-African populations, and that potential gains in power in association studies can be obtained through imputation. These data also reveal novel aspects of the structure of linkage disequilibrium. We show that 10-30% of pairs of individuals within a population share at least one region of extended genetic identity arising from recent ancestry and that up to 1% of all common variants are untaggable, primarily because they lie within recombination hotspots. We show that recombination rates vary systematically around genes and between genes of different function. Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations. ©2007 Nature Publishing Group.
dc.description.naturelink_to_OA_fulltext
dc.identifier.citationNature, 2007, v. 449 n. 7164, p. 851-861 [How to Cite?]
DOI: http://dx.doi.org/10.1038/nature06258
dc.identifier.citeulike1780948
dc.identifier.doihttp://dx.doi.org/10.1038/nature06258
dc.identifier.epage861
dc.identifier.hkuros139461
dc.identifier.isiWOS:000250230600036
dc.identifier.issn0028-0836
2011 Impact Factor: 36.28
2011 SCImago Journal Rankings: 7.767
dc.identifier.issue7164
dc.identifier.openurl
dc.identifier.pmcidPMC2689609
dc.identifier.pmid17943122
dc.identifier.scopuseid_2-s2.0-35348983887
dc.identifier.spage851
dc.identifier.urihttp://hdl.handle.net/10722/83344
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.titleA second generation human haplotype map of over 3.1 million SNPs
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. Japan Ministry of Education, Culture, Sports, Science and Technology
  16. University of Oklahoma
  17. University of Maryland School of Law
  18. Human Genetic Resource Administration of China
  19. Perlegen Sciences, Inc.
  20. Complete Genomics Inc.
  21. Nagasaki University
  22. Chinese National Human Genome Center at Shanghai
  23. Columbia University in the City of New York
  24. The University of Hong Kong
  25. Ontario Institute for Cancer Research
  26. University of Ibadan
  27. Howard University
  28. Ministry of Science and Technology of the People's Republic of China
  29. Wellcome Trust Sanger Institute
  30. Scripps Research Institute
  31. Riken
  32. null
  33. International Epidemiology Institute
  34. Chinese Academy of Sciences
  35. National Center for Biotechnology Information
  36. Fred Hutchinson Cancer Research Center
  37. Health Sciences University of Hokkaido
  38. Novartis Pharma
  39. Kyoto University
  40. Fudan University
  41. University of Chicago
  42. University of Cambridge
  43. Case Western Reserve University
  44. University of Utah
  45. Scientific and Cultural Organization (UNESCO Bangkok)
  46. Solexa Ltd.
  47. null
  48. Hong Kong University of Science and Technology
  49. Affymetrix
  50. University of Tokyo
  51. University of Oxford
  52. University of California, Santa Cruz
  53. University of Leicester
  54. Shinshu University Faculty of Medicine
  55. The Johns Hopkins School of Medicine
  56. Illumina, Inc.
  57. Vanderbilt University
  58. Université de Montréal
  59. Chinese University of Hong Kong
  60. National Institutes of Health, Bethesda
  61. University of Michigan
  62. McGill University