Abstract
Inherited genetic variation has a critical but as yet largely uncharacterized role in human disease. Here we report a public database of common variation in the human genome: more than one million single nucleotide polymorphisms (SNPs) for which accurate and complete genotypes have been obtained in 269 DNA samples from four populations, including ten 500-kilobase regions in which essentially all information about common DNA variation has been extracted. These data document the generality of recombination hotspots, a block-like structure of linkage disequilibrium and low haplotype diversity, leading to substantial correlations of SNPs with many of their neighbours. We show how the HapMap resource can guide the design and analysis of genetic association studies, shed light on structural variation and recombination, and identify loci that may have been subject to natural selection during human evolution.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 1299-1320 |
| Number of pages | 22 |
| Journal | Nature |
| Volume | 437 |
| Issue number | 7063 |
| DOIs | |
| State | Published - Oct 27 2005 |
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A haplotype map of the human genome. / Belmont, John W.; Boudreau, Andrew; Leal, Suzanne M.; Hardenbol, Paul; Pasternak, Shiran; Wheeler, David A.; Willis, Thomas D.; Yu, Fuli; Yang, Huanming; Gao, Yang; Hu, Haoran; Hu, Weitao; Li, Chaohua; Lin, Wei; Liu, Siqi; Pan, Hao; Tang, Xiaoli; Wang, Jian; Wang, Wei; Yu, Jun; Zhang, Bo; Zhang, Qingrun; Zhao, Hongbin; Zhou, Jun; Barry, Rachel; Blumenstiel, Brendan; Camargo, Amy; Defelice, Matthew; Faggart, Maura; Goyette, Mary; Gupta, Supriya; Moore, Jamie; Nguyen, Huy; Parkin, Melissa; Roy, Jessica; Stahl, Erich; Winchester, Ellen; Altshuler, David; Shen, Yan; Yao, Zhijian; Huang, Wei; Chu, Xun; He, Yungang; Jin, Li; Liu, Yangfan; Shen, Yayun; Sun, Weiwei; Wang, Haifeng; Wang, Yi; Wang, Ying; Xiong, Xiaoyan; Xu, Liang; Waye, Mary M.Y.; Tsui, Stephen K.W.; Xue, Hong; Wong, J. Tze Fei; Galver, Launa M.; Fan, Jian Bing; Murray, Sarah S.; Oliphant, Arnold R.; Chee, Mark S.; Montpetit, Alexandre; Chagnon, Fanny; Ferretti, Vincent; Leboeuf, Martin; Olivier, Jean François; Phillips, Michael S.; Roumy, Stéphanie; Sallée, Clémentine; Verner, Andrei; Hudson, Thomas J.; Frazer, Kelly A.; Ballinger, Dennis G.; Cox, David R.; Hinds, David A.; Stuve, Laura L.; Kwok, Pui Yan; Cai, Dongmei; Koboldt, Daniel C.; Miller, Raymond D.; Pawlikowska, Ludmila; Taillon-Miller, Patricia; Xiao, Ming; Tsui, Lap Chee; Mak, William; Sham, Pak C.; Song, You Qiang; Tam, Paul K.H.; Nakamura, Yusuke; Kawaguchi, Takahisa; Kitamoto, Takuya; Morizono, Takashi; Nagashima, Atsushi; Ohnishi, Yozo; Sekine, Akihiro; Tanaka, Toshihiro; Deloukas, Panos; Bird, Christine P.; Delgado, Marcos; Dermitzakis, Emmanouil T.; Gwilliam, Rhian; Hunt, Sarah; Morrison, Jonathan; Powell, Don; Stranger, Barbara Elaine; Whittaker, Pamela; Bentley, David R.; De Bakker, Paul I.W.; Barrett, Jeff; Fry, Ben; Maller, Julian; McCarroll, Steve; Patterson, Nick; Pe'er, Itsik; Purcell, Shaun; Richter, Daniel J.; Sabeti, Pardis; Saxena, Richa; Schaffner, Stephen F.; Varilly, Patrick; Stein, Lincoln D.; Krishnan, Lalitha; Smith, Albert Vernon; Thorisson, Gudmundur A.; Chakravarti, Aravinda; Chen, Peter E.; Cutler, David J.; Kashuk, Carl S.; Lin, Shin; Abecasis, Gonçalo R.; Guan, Weihua; Munro, Heather M.; Qin, Zhaohui Steve; Thomas, Daryl J.; McVean, Gilean; Bottolo, Leonardo; Eyheramendy, Susana; Freeman, Colin; Marchini, Jonathan; Myers, Simon; Spencer, Chris; Stephens, Matthew; Donnelly, Peter; Cardon, Lon R.; Clarke, Geraldine; Evans, David M.; Morris, Andrew P.; Weir, Bruce S.; Tsunoda, Tatsuhiko; Mullikin, James C.; Sherry, Stephen T.; Feolo, Michael; Zhang, Houcan; Zeng, Changqing; Zhao, Hui; Matsuda, Ichiro; Fukushima, Yoshimitsu; Macer, Darryl R.; Suda, Eiko; Rotimi, Charles N.; Adebamowo, Clement A.; Ajayi, Ike; Aniagwu, Toyin; Marshall, Patricia A.; Nkwodimmah, Chibuzor; Royal, Charmaine D.M.; Leppert, Mark F.; Dixon, Missy; Peiffer, Andy; Qiu, Renzong; Kent, Alastair; Kato, Kazuto; Niikawa, Norio; Adewole, Isaac F.; Knoppers, Bartha M.; Foster, Morris W.; Clayton, Ellen Wright; Watkin, Jessica; Gibbs, Richard A.; Muzny, Donna; Nazareth, Lynne; Sodergren, Erica; Weinstock, George M.; Yakub, Imtiaz; Gabriel, Stacey B.; Onofrio, Robert C.; Ziaugra, Liuda; Birren, Bruce W.; Daly, Mark J.; Wilson, Richard K.; Fulton, Lucinda L.; Rogers, Jane; Burton, John; Carter, Nigel P.; Clee, Christopher M.; Griffiths, Mark; Jones, Matthew C.; McLay, Kirsten; Plumb, Robert W.; Ross, Mark T.; Sims, Sarah K.; Willey, David L.; Chen, Zhu; Han, Hua; Kang, Le; Godbout, Martin; Wallenburg, John C.; L'Archevêque, Paul; Bellemare, Guy; Saeki, Koji; Wang, Hongguang; An, Daochang; Fu, Hongbo; Li, Qing; Wang, Zhen; Wang, Renwu; Holden, Arthur L.; Brooks, Lisa D.; McEwen, Jean E.; Bird, Christianne R.; Guyer, Mark S.; Nailer, Patrick J.; Wang, Vivian Ota; Peterson, Jane L.; Shi, Michael; Spiegel, Jack; Sung, Lawrence M.; Witonsky, Jonathan; Zacharia, Lynn F.; Collins, Francis S.; Kennedy, Karen; Jamieson, Ruth; Stewart, John.
In: Nature, Vol. 437, No. 7063, 27.10.2005, p. 1299-1320.Research output: Contribution to journal › Article › peer-review
TY - JOUR
T1 - A haplotype map of the human genome
AU - Belmont, John W.
AU - Boudreau, Andrew
AU - Leal, Suzanne M.
AU - Hardenbol, Paul
AU - Pasternak, Shiran
AU - Wheeler, David A.
AU - Willis, Thomas D.
AU - Yu, Fuli
AU - Yang, Huanming
AU - Gao, Yang
AU - Hu, Haoran
AU - Hu, Weitao
AU - Li, Chaohua
AU - Lin, Wei
AU - Liu, Siqi
AU - Pan, Hao
AU - Tang, Xiaoli
AU - Wang, Jian
AU - Wang, Wei
AU - Yu, Jun
AU - Zhang, Bo
AU - Zhang, Qingrun
AU - Zhao, Hongbin
AU - Zhou, Jun
AU - Barry, Rachel
AU - Blumenstiel, Brendan
AU - Camargo, Amy
AU - Defelice, Matthew
AU - Faggart, Maura
AU - Goyette, Mary
AU - Gupta, Supriya
AU - Moore, Jamie
AU - Nguyen, Huy
AU - Parkin, Melissa
AU - Roy, Jessica
AU - Stahl, Erich
AU - Winchester, Ellen
AU - Altshuler, David
AU - Shen, Yan
AU - Yao, Zhijian
AU - Huang, Wei
AU - Chu, Xun
AU - He, Yungang
AU - Jin, Li
AU - Liu, Yangfan
AU - Shen, Yayun
AU - Sun, Weiwei
AU - Wang, Haifeng
AU - Wang, Yi
AU - Wang, Ying
AU - Xiong, Xiaoyan
AU - Xu, Liang
AU - Waye, Mary M.Y.
AU - Tsui, Stephen K.W.
AU - Xue, Hong
AU - Wong, J. Tze Fei
AU - Galver, Launa M.
AU - Fan, Jian Bing
AU - Murray, Sarah S.
AU - Oliphant, Arnold R.
AU - Chee, Mark S.
AU - Montpetit, Alexandre
AU - Chagnon, Fanny
AU - Ferretti, Vincent
AU - Leboeuf, Martin
AU - Olivier, Jean François
AU - Phillips, Michael S.
AU - Roumy, Stéphanie
AU - Sallée, Clémentine
AU - Verner, Andrei
AU - Hudson, Thomas J.
AU - Frazer, Kelly A.
AU - Ballinger, Dennis G.
AU - Cox, David R.
AU - Hinds, David A.
AU - Stuve, Laura L.
AU - Kwok, Pui Yan
AU - Cai, Dongmei
AU - Koboldt, Daniel C.
AU - Miller, Raymond D.
AU - Pawlikowska, Ludmila
AU - Taillon-Miller, Patricia
AU - Xiao, Ming
AU - Tsui, Lap Chee
AU - Mak, William
AU - Sham, Pak C.
AU - Song, You Qiang
AU - Tam, Paul K.H.
AU - Nakamura, Yusuke
AU - Kawaguchi, Takahisa
AU - Kitamoto, Takuya
AU - Morizono, Takashi
AU - Nagashima, Atsushi
AU - Ohnishi, Yozo
AU - Sekine, Akihiro
AU - Tanaka, Toshihiro
AU - Deloukas, Panos
AU - Bird, Christine P.
AU - Delgado, Marcos
AU - Dermitzakis, Emmanouil T.
AU - Gwilliam, Rhian
AU - Hunt, Sarah
AU - Morrison, Jonathan
AU - Powell, Don
AU - Stranger, Barbara Elaine
AU - Whittaker, Pamela
AU - Bentley, David R.
AU - De Bakker, Paul I.W.
AU - Barrett, Jeff
AU - Fry, Ben
AU - Maller, Julian
AU - McCarroll, Steve
AU - Patterson, Nick
AU - Pe'er, Itsik
AU - Purcell, Shaun
AU - Richter, Daniel J.
AU - Sabeti, Pardis
AU - Saxena, Richa
AU - Schaffner, Stephen F.
AU - Varilly, Patrick
AU - Stein, Lincoln D.
AU - Krishnan, Lalitha
AU - Smith, Albert Vernon
AU - Thorisson, Gudmundur A.
AU - Chakravarti, Aravinda
AU - Chen, Peter E.
AU - Cutler, David J.
AU - Kashuk, Carl S.
AU - Lin, Shin
AU - Abecasis, Gonçalo R.
AU - Guan, Weihua
AU - Munro, Heather M.
AU - Qin, Zhaohui Steve
AU - Thomas, Daryl J.
AU - McVean, Gilean
AU - Bottolo, Leonardo
AU - Eyheramendy, Susana
AU - Freeman, Colin
AU - Marchini, Jonathan
AU - Myers, Simon
AU - Spencer, Chris
AU - Stephens, Matthew
AU - Donnelly, Peter
AU - Cardon, Lon R.
AU - Clarke, Geraldine
AU - Evans, David M.
AU - Morris, Andrew P.
AU - Weir, Bruce S.
AU - Tsunoda, Tatsuhiko
AU - Mullikin, James C.
AU - Sherry, Stephen T.
AU - Feolo, Michael
AU - Zhang, Houcan
AU - Zeng, Changqing
AU - Zhao, Hui
AU - Matsuda, Ichiro
AU - Fukushima, Yoshimitsu
AU - Macer, Darryl R.
AU - Suda, Eiko
AU - Rotimi, Charles N.
AU - Adebamowo, Clement A.
AU - Ajayi, Ike
AU - Aniagwu, Toyin
AU - Marshall, Patricia A.
AU - Nkwodimmah, Chibuzor
AU - Royal, Charmaine D.M.
AU - Leppert, Mark F.
AU - Dixon, Missy
AU - Peiffer, Andy
AU - Qiu, Renzong
AU - Kent, Alastair
AU - Kato, Kazuto
AU - Niikawa, Norio
AU - Adewole, Isaac F.
AU - Knoppers, Bartha M.
AU - Foster, Morris W.
AU - Clayton, Ellen Wright
AU - Watkin, Jessica
AU - Gibbs, Richard A.
AU - Muzny, Donna
AU - Nazareth, Lynne
AU - Sodergren, Erica
AU - Weinstock, George M.
AU - Yakub, Imtiaz
AU - Gabriel, Stacey B.
AU - Onofrio, Robert C.
AU - Ziaugra, Liuda
AU - Birren, Bruce W.
AU - Daly, Mark J.
AU - Wilson, Richard K.
AU - Fulton, Lucinda L.
AU - Rogers, Jane
AU - Burton, John
AU - Carter, Nigel P.
AU - Clee, Christopher M.
AU - Griffiths, Mark
AU - Jones, Matthew C.
AU - McLay, Kirsten
AU - Plumb, Robert W.
AU - Ross, Mark T.
AU - Sims, Sarah K.
AU - Willey, David L.
AU - Chen, Zhu
AU - Han, Hua
AU - Kang, Le
AU - Godbout, Martin
AU - Wallenburg, John C.
AU - L'Archevêque, Paul
AU - Bellemare, Guy
AU - Saeki, Koji
AU - Wang, Hongguang
AU - An, Daochang
AU - Fu, Hongbo
AU - Li, Qing
AU - Wang, Zhen
AU - Wang, Renwu
AU - Holden, Arthur L.
AU - Brooks, Lisa D.
AU - McEwen, Jean E.
AU - Bird, Christianne R.
AU - Guyer, Mark S.
AU - Nailer, Patrick J.
AU - Wang, Vivian Ota
AU - Peterson, Jane L.
AU - Shi, Michael
AU - Spiegel, Jack
AU - Sung, Lawrence M.
AU - Witonsky, Jonathan
AU - Zacharia, Lynn F.
AU - Collins, Francis S.
AU - Kennedy, Karen
AU - Jamieson, Ruth
AU - Stewart, John
N1 - Funding Information: Acknowledgements We thank many people who contributed to this project: J. Beck, C. Beiswanger, D. Coppock, A. Leach, J. Mintzer and L. Toji (Coriell Institute for Medical Research) for transforming the Yoruba, Japanese and Han Chinese samples, distributing the DNA and cell lines, storing the samples for use in future research, and producing the community newsletters and reports; J. Greenberg and R. Anderson (NIH National Institute of General Medical Sciences) for providing funding and support for cell line transformation and storage in the NIGMS Human Genetic Cell Repository at the Coriell Institute; T. Dibling, T. Ishikura, S. Kanazawa, S. Mizusawa and S. Saito (SNP Research Center, RIKEN) for help with genotyping; C. Hind and A. Moghadam for technical support in genotyping and all members of the subcloning and sequencing teams at the Wellcome Trust Sanger Institute; X. Ke (Wellcome Trust Centre for Human Genetics at the University of Oxford) for help with data analysis; Oxford E-Science Centre for provision of high-performance computing resources; H. Chen, W. Chen, L. Deng, Y. Dong, C. Fu, L. Gao, H. Geng, J. Geng, M. He, H. Li, H. Li, S. Li, X. Li, B. Liu, Z. Liu, F. Lu, F. Lu, G. Lu, C. Luo, X. Wang, Z. Wang, C. Ye and X. Yu (Beijing Genomics Institute) for help with genotyping and sample collection; X. Feng, Y. Li, J. Ren and X. Zhou (Beijing Normal University) for help with sample collection; J. Fan, W. Gu, W. Guan, S. Hu, H. Jiang, R. Lei, Y. Lin, Z. Niu, B. Wang, L. Yang, W. Yang, Y. Wang, Z. Wang, S. Xu, W. Yan, H. Yang, W. Yuan, C. Zhang, J. Zhang, K. Zhang and G. Zhao (Chinese National Human Genome Center at Shanghai) for help with genotyping; P. Fong, C. Lai, C. Lau, T. Leung, L. Luk and W. Tong (University of Hong Kong, Genome Research Centre) for help with genotyping; C. Pang (Chinese University of Hong Kong) for help with genotyping; K. Ding, B. Qiang, J. Zhang, X. Zhang and K. Zhou (Chinese National Human Genome Center at Beijing) for help with genotyping; Q. Fu, S. Ghose, X. Lu, D. Nelson, A. Perez, S. Poole, R. Vega and H. Yonath (Baylor College of Medicine); C. Bruckner, T. Brundage, S. Chow, O. Iartchouk, M. Jain, M. Moorhead and K. Tran (ParAllele Bioscience Inc.); N. Addleman, J. Atilano, T. Chan, C. Chu, C. Ha, T. Nguyen, M. Minton and A. Phong (UCSF) for help with genotyping, and D. Lind (UCSF) for help with quality control and experimental design; R. Donaldson and S. Duan (Washington University) for help with genotyping, and J. Rice and N. Saccone (Washington University) for help with experimental design; J. Wigginton (University of Michigan) for help with implementing and testing QA/QC software; A. Clark, B. Keats, R. Myers, D. Nickerson and A. Williamson for providing advice to NIH; J. Melone, M. Weiss and E. DeHaut-Combs (NHGRI) for help with project management; M. Gray for organizing phone calls and meetings; D. Leja for help with figures; the Yoruba people of Ibadan, Nigeria, the people of Tokyo, Japan, and the community at Beijing Normal University, who participated in public consultations and community engagements; the people in these communities who were generous in donating their blood samples; and the people in the Utah CEPH community who allowed the samples they donated earlier to be used for the Project. We also thank A. Clark, E. Lander, C. Langley and R. Lifton for comments on earlier drafts of the manuscript. This work was supported by the Japanese Ministry of Education, Culture, Sports, Science, and Technology, the Wellcome Trust, Nuffield Trust, Wolfson Foundation, UK EPSRC, Genome Canada, Génome Québec, the Chinese Academy of Sciences, the Ministry of Science and Technology of the People’s Republic of China, the National Natural Science Foundation of China, the Hong Kong Innovation and Technology Commission, the University Grants Committee of Hong Kong, the SNP Consortium, the US National Institutes of Health (FIC, NCI, NCRR, NEI, NHGRI, NIA, NIAAA, NIAID, NIAMS, NIBIB, NIDA, NIDCD, NIDCR, NIDDK, NIEHS, NIGMS, NIMH, NINDS, NLM, OD), the W.M. Keck Foundation, and the Delores Dore Eccles Foundation.
PY - 2005/10/27
Y1 - 2005/10/27
N2 - Inherited genetic variation has a critical but as yet largely uncharacterized role in human disease. Here we report a public database of common variation in the human genome: more than one million single nucleotide polymorphisms (SNPs) for which accurate and complete genotypes have been obtained in 269 DNA samples from four populations, including ten 500-kilobase regions in which essentially all information about common DNA variation has been extracted. These data document the generality of recombination hotspots, a block-like structure of linkage disequilibrium and low haplotype diversity, leading to substantial correlations of SNPs with many of their neighbours. We show how the HapMap resource can guide the design and analysis of genetic association studies, shed light on structural variation and recombination, and identify loci that may have been subject to natural selection during human evolution.
AB - Inherited genetic variation has a critical but as yet largely uncharacterized role in human disease. Here we report a public database of common variation in the human genome: more than one million single nucleotide polymorphisms (SNPs) for which accurate and complete genotypes have been obtained in 269 DNA samples from four populations, including ten 500-kilobase regions in which essentially all information about common DNA variation has been extracted. These data document the generality of recombination hotspots, a block-like structure of linkage disequilibrium and low haplotype diversity, leading to substantial correlations of SNPs with many of their neighbours. We show how the HapMap resource can guide the design and analysis of genetic association studies, shed light on structural variation and recombination, and identify loci that may have been subject to natural selection during human evolution.
UR - http://www.scopus.com/inward/record.url?scp=79959524146&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=79959524146&partnerID=8YFLogxK
U2 - 10.1038/nature04226
DO - 10.1038/nature04226
M3 - Article
C2 - 16255080
AN - SCOPUS:79959524146
VL - 437
SP - 1299
EP - 1320
JO - Nature
JF - Nature
SN - 0028-0836
IS - 7063
ER -