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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
A second generation human haplotype map of over 3.1 million SNPs
Nature, Volume 449, No. 7164, Year 2007
Notification
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Description
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. ©2007 Nature Publishing Group.
Authors & Co-Authors
Frazer, Kelly A.
United States, San Diego
Scripps Research Institute
Cox, David R.
Unknown Affiliation
Hinds, David A.
Unknown Affiliation
Gibbs, Richard A.L.
United States, Houston
Baylor College of Medicine
Belmont, John W.
United States, Houston
Baylor College of Medicine
Hardenbol, Paul
United States, Menlo Park
Pacific Biosciences
Leal, Suzanne M.
United States, Houston
Baylor College of Medicine
Wheeler, David A.
United States, Houston
Baylor College of Medicine
Willis, Thomas D.
United States, Waltham
Thermo Fisher Scientific Inc.
Yu, Fuli
United States, Cambridge
Broad Institute
Yang, Huanming
China, Beijing
Beijing Institute of Genomics Chinese Academy of Sciences China National Center for Bioinformation
Zeng, Changqing
China, Beijing
Beijing Institute of Genomics Chinese Academy of Sciences China National Center for Bioinformation
Liu, Siqi
China, Beijing
Beijing Institute of Genomics Chinese Academy of Sciences China National Center for Bioinformation
Wang, Jian
China, Beijing
Beijing Institute of Genomics Chinese Academy of Sciences China National Center for Bioinformation
Yu, Jun
China, Beijing
Beijing Institute of Genomics Chinese Academy of Sciences China National Center for Bioinformation
Zhang, Qingrun
China, Beijing
Beijing Institute of Genomics Chinese Academy of Sciences China National Center for Bioinformation
Zhao, Hui
China, Beijing
Beijing Institute of Genomics Chinese Academy of Sciences China National Center for Bioinformation
Gabriel, Stacey Bolk
United States, Cambridge
Broad Institute
Blumenstiel, Brendan S.
United States, Cambridge
Broad Institute
Nguyen, Huy
United States, Cambridge
Broad Institute
Onofrio, Robert C.
United States, Cambridge
Broad Institute
Parkin, Melissa A.
United States, Cambridge
Broad Institute
Ziaugra, Liuda
United States, Cambridge
Broad Institute
Altshuler, David M.
United States, Cambridge
Broad Institute
United States, Boston
Massachusetts General Hospital
Shen, Yan
China, Shanghai
Chinese National Human Genome Center at Shanghai
Huang, Wei
China, Shanghai
Chinese National Human Genome Center at Shanghai
Jin, Li
China, Shanghai
Shanghai Institute of Nutrition and Health
Waye, Mary Miu Yee
Hong Kong, Hong Kong
Chinese University of Hong Kong
Tsui, Stephen Kwok Wing
Hong Kong, Hong Kong
Chinese University of Hong Kong
Wong, Jeffrey Tze Fei
Hong Kong, Hong Kong
Hong Kong University of Science and Technology
Galver, Luana M.
United States, San Diego
Illumina, Inc.
Fan, Jianbing
United States, San Diego
Illumina, Inc.
Murray, Sarah Shaw
United States, San Diego
Scripps Research Institute
Oliphant, Arnold R.
United States, Mountain View
Complete Genomics Inc.
Chee, Mark S.
Unknown Affiliation
Montpetit, Alexandre
Canada, Montreal
Université Mcgill
Chagnon, Fanny
Canada, Montreal
Université Mcgill
Ferretti, Vincent
Canada, Montreal
Université Mcgill
Leboeuf, Martin
Canada, Montreal
Université Mcgill
Phillips, Michael S.
Canada, Montreal
Université Mcgill
Verner, Andrei E.
Canada, Montreal
Université Mcgill
Kwok, Puiyan Yan
United States, San Francisco
University of California, San Francisco
Koboldt, Daniel C.
United States, St. Louis
Washington University School of Medicine in St. Louis
Miller, Raymond D.
United States, St. Louis
Washington University School of Medicine in St. Louis
Pawlikowska, Ludmila
United States, San Francisco
University of California, San Francisco
Taillon-Miller, Patricia A.
United States, St. Louis
Washington University School of Medicine in St. Louis
Xiao, Ming
United States, San Francisco
University of California, San Francisco
Tsui, Lap-Chee
Hong Kong, Hong Kong
The University of Hong Kong
Tam, Paul Kwong Hang
Hong Kong, Hong Kong
The University of Hong Kong
Nakamura, Yusuke
Japan, Tokyo
The University of Tokyo
Japan, Wako
Riken
Kawaguchi, Takahisa
Japan, Wako
Riken
Sekine, Akihiro
Japan, Wako
Riken
Tanaka, Toshihiro
Japan, Wako
Riken
Tsunoda, Tatsuhiko
Japan, Wako
Riken
Deloukas, Panos
United Kingdom, Hinxton
Wellcome Sanger Institute
Dermitzakis, Emmanouil Theophilos
United Kingdom, Hinxton
Wellcome Sanger Institute
Gwilliam, Rhian G.
United Kingdom, Hinxton
Wellcome Sanger Institute
Hunt, Sarah E.
United Kingdom, Hinxton
Wellcome Sanger Institute
Powell, Don
United Kingdom, Hinxton
Wellcome Sanger Institute
Whittaker, Pamela
United Kingdom, Hinxton
Wellcome Sanger Institute
Bentley, David R.
Unknown Affiliation
Daly, Mark J.
United States, Cambridge
Broad Institute
United States, Boston
Massachusetts General Hospital
De Bakker, Paul IW W.
United States, Cambridge
Broad Institute
United States, Boston
Massachusetts General Hospital
Barrett, Jeffrey Carl
United States, Cambridge
Broad Institute
United States, Boston
Massachusetts General Hospital
McCarroll, Steven A.
United States, Cambridge
Broad Institute
United States, Boston
Massachusetts General Hospital
Patterson, Nick J.
United States, Cambridge
Broad Institute
Price, Alkes L.
United States, Cambridge
Broad Institute
Purcell, Shaun M.
United States, Boston
Massachusetts General Hospital
Sabeti., Pardis C.
United States, Cambridge
Broad Institute
Meitinger, Thomas
United States, Cambridge
Broad Institute
United States, Boston
Massachusetts General Hospital
Schaffner, Stephen F.
United States, Cambridge
Broad Institute
Sham, Pak Chung
Hong Kong, Hong Kong
The University of Hong Kong
Smith, Albert Vernon
United States, Cold Spring Harbor
Cold Spring Harbor Laboratory
Thorisson, Gudmundur A.
United Kingdom, Leicester
University of Leicester
Chakravarti, Aravinda
United States, Baltimore
Johns Hopkins Medicine
Chen, Peter E.
United States, Baltimore
Johns Hopkins Medicine
Cutler, David J.
United States, Baltimore
Johns Hopkins Medicine
Kashuk, Carl S.
United States, Baltimore
Johns Hopkins Medicine
Abecasis, Gonçalo R.
United States, Ann Arbor
University of Michigan, Ann Arbor
Guan, Weihua
United States, Ann Arbor
University of Michigan, Ann Arbor
Li, Yun
United States, Ann Arbor
University of Michigan, Ann Arbor
Munro, Heather M.
United States, Rockville
International Epidemiology Institute
Qin, Zhaohui Steve
United States, Ann Arbor
University of Michigan, Ann Arbor
McVean, Gil
United Kingdom, Oxford
University of Oxford
Auton, Adam
United Kingdom, Oxford
University of Oxford
Bottolo, Leonardo
United Kingdom, Oxford
University of Oxford
Eyheramendy, Susana
United Kingdom, Oxford
University of Oxford
Freeman, Colin
United Kingdom, Oxford
University of Oxford
Marchini, Jonathan L.
United Kingdom, Oxford
University of Oxford
Myers, Simon R.
United Kingdom, Oxford
University of Oxford
Spencer, Chris C.A.
United States, Cambridge
Broad Institute
Stephens, Matthew K.
United States, Chicago
The University of Chicago
Donnelly, Peter K.
United Kingdom, Oxford
University of Oxford
Cardon, Lon R.
United States, Seattle
Fred Hutchinson Cancer Center
Clarke, Geraldine M.
United Kingdom, Oxford
University of Oxford
Evans, David M.
United Kingdom, Oxford
University of Oxford
Morris, Andrew Paul
United Kingdom, Oxford
University of Oxford
Weir, Bruce S.
United States, Seattle
University of Washington
Mullikin, James C.
United States, Bethesda
National Institutes of Health Nih
Sherry, Stephen T.
United States, Bethesda
National Center for Biotechnology Information Ncbi
Feolo, Michael L.
United States, Bethesda
National Center for Biotechnology Information Ncbi
Zhang, Houcan
China, Beijing
Beijing Normal University
Matsuda, Ichirou
Japan, Ishikari District
Health Sciences University of Hokkaido
Fukushima, Yoshimitsu
Japan, Matsumoto
Shinshu University Faculty of Medicine
Macer, Darryl R.J.
Unknown Affiliation
Suda, Eiko
Japan, Tsukuba
University of Tsukuba
Rotimi, Charles N.
United States, Washington, D.c.
Howard University
Adebamowo, Clement
Nigeria, Ibadan
College of Medicine, University of Ibadan
Ajayi, I. O.
Nigeria, Ibadan
College of Medicine, University of Ibadan
Aniagwu, Toyin I.G.
Nigeria, Ibadan
College of Medicine, University of Ibadan
Marshall, Patricia A.
United States, Cleveland
Case School of Medicine
Nkwodimmah, Chibuzor
Nigeria, Ibadan
College of Medicine, University of Ibadan
Royal, Charmaine D.M.
United States, Washington, D.c.
Howard University
Leppert, Mark F.
United States, Salt Lake City
The University of Utah
Dixon, Missy
United States, Salt Lake City
The University of Utah
Peiffer, Andy P.
United States, Salt Lake City
The University of Utah
Qiu, Renzong
China, Beijing
Chinese Academy of Social Sciences
Kent, Alastair
Unknown Affiliation
Kato, Kazuto
Japan, Kyoto
Kyoto University
Niikawa ., Norio
Japan, Nagasaki
Graduate School of Biomedical Sciences
Adewole, Isaac Folorunso A.
Nigeria, Ibadan
College of Medicine, University of Ibadan
Knoppers, Bartha Maria
Canada, Montreal
University of Montreal
Foster, Morris W.
United States, Norman
The University of Oklahoma
Watkin, Jessica
United Kingdom, London
Wellcome Trust
Muzny, Donna Marie
United States, Houston
Baylor College of Medicine
Nazareth, Lynne V.
United States, Houston
Baylor College of Medicine
Sodergren, Erica J.
United States, Houston
Baylor College of Medicine
Weinstock, George M.
United States, Houston
Baylor College of Medicine
Birren, Bruce W.
United States, Cambridge
Broad Institute
Wilson, Richard K.
United States, St. Louis
Washington University School of Medicine in St. Louis
Rogers, Jane
United Kingdom, Hinxton
Wellcome Sanger Institute
Burton, John
United Kingdom, Hinxton
Wellcome Sanger Institute
Carter, Nigel P.
United Kingdom, Hinxton
Wellcome Sanger Institute
Griffiths, Mark N.D.
United Kingdom, Hinxton
Wellcome Sanger Institute
McLay, Kirsten E.
United Kingdom, Hinxton
Wellcome Sanger Institute
Ross, Mark T.
United Kingdom, Hinxton
Wellcome Sanger Institute
Sims, Sarah K.
United Kingdom, Hinxton
Wellcome Sanger Institute
Chen, Zhu
China, Beijing
Chinese Academy of Sciences
Han, Hua
China, Beijing
Chinese Academy of Sciences
Kang, Le
China, Beijing
Chinese Academy of Sciences
Godbout, Martin
Canada, Ottawa
Genome Canada
Wallenburg, John C.
Canada, Montreal
Université Mcgill
L'Archevêque, Paul
Canada, Montreal
Génome Québec
Bellemare, Guy
Canada, Montreal
Génome Québec
Wang, Hongguang
Unknown Affiliation
Holden, Arthur L.
United States, San Diego
Illumina, Inc.
Brooks, Lisa D.
United States, Bethesda
National Institutes of Health Nih
McEwen, Jean E.
United States, Bethesda
National Institutes of Health Nih
Guyer, Mark S.
United States, Bethesda
National Institutes of Health Nih
Wang, Vivian Ota
United States, Bethesda
National Institutes of Health Nih
Peterson, Jane L.
United States, Bethesda
National Institutes of Health Nih
Collins, Francis S.
United States, Bethesda
National Institutes of Health Nih
Statistics
Citations: 3,662
Authors: 152
Affiliations: 55
Identifiers
Doi:
10.1038/nature06258
ISSN:
14764679
Research Areas
Genetics And Genomics
Study Design
Cross Sectional Study