A second generation human haplotype map of over 3.1 million SNPs

Frazer K.A., Ballinger D.G., Cox D.R., Hinds D.A., Stuve L.L., Gibbs R.A., Belmont J.W., Boudreau A., Hardenbol P., Leal S.M., Pasternak S., Wheeler D.A., Willis T.D., Yu F., Yang H., Zeng C., Gao Y., Hu H., Hu W., Li C., Lin W., Liu S., Pan H., Tang X., Wang J., Wang W., Yu J., Zhang B., Zhang Q., Zhao H., Zhao H., Zhou J., Gabriel S.B., Barry R., Blumenstiel B., Camargo A., Defelice M., Faggart M., Goyette M., Gupta S., Moore J., Nguyen H., Onofrio R.C., Parkin M., Roy J., Stahl E., Winchester E., Ziaugra L., Altshuler D., Shen Y., Yao Z., Huang W., Chu X., He Y., Jin L., Liu Y., Shen Y., Sun W., Wang H., Wang Y., Wang Y., Xiong X., Xu L., Waye M.M.Y., Tsui S.K.W., Xue H., Wong J.T.-F., Galver L.M., Fan J.-B., Gunderson K., Murray S.S., Oliphant A.R., Chee M.S., Montpetit A., Chagnon F., Ferretti V., Leboeuf M., Olivier J.-F., Phillips M.S., Roumy S., Sallee C., Verner A., Hudson T.J., Kwok P.-Y., Cai D., Koboldt D.C., Miller R.D., Pawlikowska L., Taillon-Miller P., Xiao M., Tsui L.-C., Mak W., You Q.S., Tam P.K.H., Nakamura Y., Kawaguchi T., Kitamoto T., Morizono T., Nagashima A., Ohnishi Y., Sekine A., Tanaka T., Tsunoda T., Deloukas P., Bird C.P., Delgado M., Dermitzakis E.T., Gwilliam R., Hunt S., Morrison J., Powell D., Stranger B.E., Whittaker P., Bentley D.R., Daly M.J., De Bakker P.I.W., Barrett J., Chretien Y.R., Maller J., McCarroll S., Patterson N., Pe'Er I., Price A., Purcell S., Richter D.J., Sabeti P., Saxena R., Schaffner S.F., Sham P.C., Varilly P., Stein L.D., Krishnan L., Smith A.V., Tello-Ruiz M.K., Thorisson G.A., Chakravarti A., Chen P.E., Cutler D.J., Kashuk C.S., Lin S., Abecasis G.R., Guan W., Li Y., Munro H.M., Qin Z.S., Thomas D.J., McVean G., Auton A., Bottolo L., Cardin N., Eyheramendy S., Freeman C., Marchini J., Myers S., Spencer C., Stephens M., Donnelly P., Cardon L.R., Clarke G., Evans D.M., Morris A.P., Weir B.S., Johnson T.A., Mullikin J.C., Sherry S.T., Feolo M., Skol A., Zhang H., Matsuda I., Fukushima Y., MacEr D.R., Suda E., Rotimi C.N., Adebamowo C.A., Ajayi I., Aniagwu T., Marshall P.A., Nkwodimmah C., Royal C.D.M., Leppert M.F., Dixon M., Peiffer A., Qiu R., Kent A., Kato K., Niikawa N., Adewole I.F., Knoppers B.M., Foster M.W., Clayton E.W., Watkin J., Muzny D., Nazareth L., Sodergren E., Weinstock G.M., Yakub I., Birren B.W., Wilson R.K., Fulton L.L., Rogers J., Burton J., Carter N.P., Clee C.M., Griffiths M., Jones M.C., McLay K., Plumb R.W., Ross M.T., Sims S.K., Willey D.L., Chen Z., Han H., Kang L., Godbout M., Wallenburg J.C., L'Archeveque P., Bellemare G., Saeki K., Wang H., An D., Fu H., Li Q., Wang Z., Wang R., Holden A.L., Brooks L.D., McEwen J.E., Guyer M.S., Wang V.O., Peterson J.L., Shi M., Spiegel J., Sung L.M., Zacharia L.F., Collins F.S., Kennedy K., Jamieson R. and Stewart J. (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature, 449 7164: 851-861. doi:10.1038/nature06258

Author Frazer K.A.
Ballinger D.G.
Cox D.R.
Hinds D.A.
Stuve L.L.
Gibbs R.A.
Belmont J.W.
Boudreau A.
Hardenbol P.
Leal S.M.
Pasternak S.
Wheeler D.A.
Willis T.D.
Yu F.
Yang H.
Zeng C.
Gao Y.
Hu H.
Hu W.
Li C.
Lin W.
Liu S.
Pan H.
Tang X.
Wang J.
Wang W.
Yu J.
Zhang B.
Zhang Q.
Zhao H.
Zhao H.
Zhou J.
Gabriel S.B.
Barry R.
Blumenstiel B.
Camargo A.
Defelice M.
Faggart M.
Goyette M.
Gupta S.
Moore J.
Nguyen H.
Onofrio R.C.
Parkin M.
Roy J.
Stahl E.
Winchester E.
Ziaugra L.
Altshuler D.
Shen Y.
Yao Z.
Huang W.
Chu X.
He Y.
Jin L.
Liu Y.
Shen Y.
Sun W.
Wang H.
Wang Y.
Wang Y.
Xiong X.
Xu L.
Waye M.M.Y.
Tsui S.K.W.
Xue H.
Wong J.T.-F.
Galver L.M.
Fan J.-B.
Gunderson K.
Murray S.S.
Oliphant A.R.
Chee M.S.
Montpetit A.
Chagnon F.
Ferretti V.
Leboeuf M.
Olivier J.-F.
Phillips M.S.
Roumy S.
Sallee C.
Verner A.
Hudson T.J.
Kwok P.-Y.
Cai D.
Koboldt D.C.
Miller R.D.
Pawlikowska L.
Taillon-Miller P.
Xiao M.
Tsui L.-C.
Mak W.
You Q.S.
Tam P.K.H.
Nakamura Y.
Kawaguchi T.
Kitamoto T.
Morizono T.
Nagashima A.
Ohnishi Y.
Sekine A.
Tanaka T.
Tsunoda T.
Deloukas P.
Bird C.P.
Delgado M.
Dermitzakis E.T.
Gwilliam R.
Hunt S.
Morrison J.
Powell D.
Stranger B.E.
Whittaker P.
Bentley D.R.
Daly M.J.
De Bakker P.I.W.
Barrett J.
Chretien Y.R.
Maller J.
McCarroll S.
Patterson N.
Pe'Er I.
Price A.
Purcell S.
Richter D.J.
Sabeti P.
Saxena R.
Schaffner S.F.
Sham P.C.
Varilly P.
Stein L.D.
Krishnan L.
Smith A.V.
Tello-Ruiz M.K.
Thorisson G.A.
Chakravarti A.
Chen P.E.
Cutler D.J.
Kashuk C.S.
Lin S.
Abecasis G.R.
Guan W.
Li Y.
Munro H.M.
Qin Z.S.
Thomas D.J.
McVean G.
Auton A.
Bottolo L.
Cardin N.
Eyheramendy S.
Freeman C.
Marchini J.
Myers S.
Spencer C.
Stephens M.
Donnelly P.
Cardon L.R.
Clarke G.
Evans D.M.
Morris A.P.
Weir B.S.
Johnson T.A.
Mullikin J.C.
Sherry S.T.
Feolo M.
Skol A.
Zhang H.
Matsuda I.
Fukushima Y.
MacEr D.R.
Suda E.
Rotimi C.N.
Adebamowo C.A.
Ajayi I.
Aniagwu T.
Marshall P.A.
Nkwodimmah C.
Royal C.D.M.
Leppert M.F.
Dixon M.
Peiffer A.
Qiu R.
Kent A.
Kato K.
Niikawa N.
Adewole I.F.
Knoppers B.M.
Foster M.W.
Clayton E.W.
Watkin J.
Muzny D.
Nazareth L.
Sodergren E.
Weinstock G.M.
Yakub I.
Birren B.W.
Wilson R.K.
Fulton L.L.
Rogers J.
Burton J.
Carter N.P.
Clee C.M.
Griffiths M.
Jones M.C.
McLay K.
Plumb R.W.
Ross M.T.
Sims S.K.
Willey D.L.
Chen Z.
Han H.
Kang L.
Godbout M.
Wallenburg J.C.
L'Archeveque P.
Bellemare G.
Saeki K.
Wang H.
An D.
Fu H.
Li Q.
Wang Z.
Wang R.
Holden A.L.
Brooks L.D.
McEwen J.E.
Guyer M.S.
Wang V.O.
Peterson J.L.
Shi M.
Spiegel J.
Sung L.M.
Zacharia L.F.
Collins F.S.
Kennedy K.
Jamieson R.
Stewart J.
Title A second generation human haplotype map of over 3.1 million SNPs
Journal name Nature   Check publisher's open access policy
ISSN 0028-0836
Publication date 2007-10-18
Year available 2007
Sub-type Article (original research)
DOI 10.1038/nature06258
Open Access Status Not yet assessed
Volume 449
Issue 7164
Start page 851
End page 861
Total pages 11
Place of publication LONDON
Language eng
Subject 1000 General
Abstract We 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 r2 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 r2 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.
Keyword Multidisciplinary Sciences
Science & Technology - Other Topics
Q-Index Code C1
Q-Index Status Provisional Code
Grant ID 081682
Institutional Status Unknown

Document type: Journal Article
Sub-type: Article (original research)
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