A haplotype map of the human genome

John W. Belmont; Andrew Boudreau; Suzanne M. Leal; Paul Hardenbol; Shiran Pasternak; David A. Wheeler; Thomas D. Willis; Fuli Yu; Huanming Yang; Yang Gao; Haoran Hu; Weitao Hu; Chaohua Li; Wei Lin; Siqi Liu; Hao Pan; Xiaoli Tang; Jian Wang; Wei Wang; Jun Yu; Bo Zhang; Qingrun Zhang; Hongbin Zhao; Jun Zhou; Rachel Barry; Brendan Blumenstiel; Amy Camargo; Matthew Defelice; Maura Faggart; Mary Goyette; Supriya Gupta; Jamie Moore; Huy Nguyen; Melissa Parkin; Jessica Roy; Erich Stahl; Ellen Winchester; David Altshuler; Yan Shen; Zhijian Yao; Wei Huang; Xun Chu; Yungang He; Li Jin; Yangfan Liu; Yayun Shen; Weiwei Sun; Haifeng Wang; Yi Wang; Ying Wang; Xiaoyan Xiong; Liang Xu; Mary M.Y. Waye; Stephen K.W. Tsui; Hong Xue; J. Tze Fei Wong; Launa M. Galver; Jian Bing Fan; Sarah S. Murray; Arnold R. Oliphant; Mark S. Chee; Alexandre Montpetit; Fanny Chagnon; Vincent Ferretti; Martin Leboeuf; Jean François Olivier; Michael S. Phillips; Stéphanie Roumy; Clémentine Sallée; Andrei Verner; Thomas J. Hudson; Kelly A. Frazer; Dennis G. Ballinger; David R. Cox; David A. Hinds; Laura L. Stuve; Pui Yan Kwok; Dongmei Cai; Daniel C. Koboldt; Raymond D. Miller; Ludmila Pawlikowska; Patricia Taillon-Miller; Ming Xiao; Lap Chee Tsui; William Mak; Pak C. Sham; You Qiang Song; Paul K.H. Tam; Yusuke Nakamura; Takahisa Kawaguchi; Takuya Kitamoto; Takashi Morizono; Atsushi Nagashima; Yozo Ohnishi; Akihiro Sekine; Toshihiro Tanaka; Panos Deloukas; Christine P. Bird; Marcos Delgado; Emmanouil T. Dermitzakis; Rhian Gwilliam; Sarah Hunt; Jonathan Morrison; Don Powell; Barbara E. Stranger; Pamela Whittaker; David R. Bentley; Paul I.W. De Bakker; Jeff Barrett; Ben Fry; Julian Maller; Steve McCarroll; Nick Patterson; Itsik Pe'er; Shaun Purcell; Daniel J. Richter; Pardis Sabeti; Richa Saxena; Stephen F. Schaffner; Patrick Varilly; Lincoln D. Stein; Lalitha Krishnan; Albert Vernon Smith; Gudmundur A. Thorisson; Aravinda Chakravarti; Peter E. Chen; David J. Cutler; Carl S. Kashuk; Shin Lin; Gonçalo R. Abecasis; Weihua Guan; Heather M. Munro; Zhaohui Steve Qin; Daryl J. Thomas; Gilean McVean; Leonardo Bottolo; Susana Eyheramendy; Colin Freeman; Jonathan Marchini; Simon Myers; Chris Spencer; Matthew Stephens; Peter Donnelly; Lon R. Cardon; Geraldine Clarke; David M. Evans; Andrew P. Morris; Bruce S. Weir; Tatsuhiko Tsunoda; James C. Mullikin; Stephen T. Sherry; Michael Feolo; Houcan Zhang; Changqing Zeng; Hui Zhao; Ichiro Matsuda; Yoshimitsu Fukushima; Darryl R. Macer; Eiko Suda; Charles N. Rotimi; Clement A. Adebamowo; Ike Ajayi; Toyin Aniagwu; Patricia A. Marshall; Chibuzor Nkwodimmah; Charmaine D.M. Royal; Mark F. Leppert; Missy Dixon; Andy Peiffer; Renzong Qiu; Alastair Kent; Kazuto Kato; Norio Niikawa; Isaac F. Adewole; Bartha M. Knoppers; Morris W. Foster; Ellen Wright Clayton; Jessica Watkin; Richard A. Gibbs; Donna Muzny; Lynne Nazareth; Erica Sodergren; George M. Weinstock; Imtiaz Yakub; Stacey B. Gabriel; Robert C. Onofrio; Liuda Ziaugra; Bruce W. Birren; Mark J. Daly; Richard K. Wilson; Lucinda L. Fulton; Jane Rogers; John Burton; Nigel P. Carter; Christopher M. Clee; Mark Griffiths; Matthew C. Jones; Kirsten McLay; Robert W. Plumb; Mark T. Ross; Sarah K. Sims; David L. Willey; Zhu Chen; Hua Han; Le Kang; Martin Godbout; John C. Wallenburg; Paul L'Archevêque; Guy Bellemare; Koji Saeki; Hongguang Wang; Daochang An; Hongbo Fu; Qing Li; Zhen Wang; Renwu Wang; Arthur L. Holden; Lisa D. Brooks; Jean E. McEwen; Christianne R. Bird; Mark S. Guyer; Patrick J. Nailer; Vivian Ota Wang; Jane L. Peterson; Michael Shi; Jack Spiegel; Lawrence M. Sung; Jonathan Witonsky; Lynn F. Zacharia; Francis S. Collins; Karen Kennedy; Ruth Jamieson; John Stewart

doi:10.1038/nature04226

A haplotype map of the human genome

John W. Belmont, Andrew Boudreau, Suzanne M. Leal, Paul Hardenbol, Shiran Pasternak, David A. Wheeler, Thomas D. Willis, Fuli Yu, Huanming Yang, Yang Gao, Haoran Hu, Weitao Hu, Chaohua Li, Wei Lin, Siqi Liu, Hao Pan, Xiaoli Tang, Jian Wang, Wei Wang, Jun YuBo Zhang, Qingrun Zhang, Hongbin Zhao, Jun Zhou, Rachel Barry, Brendan Blumenstiel, Amy Camargo, Matthew Defelice, Maura Faggart, Mary Goyette, Supriya Gupta, Jamie Moore, Huy Nguyen, Melissa Parkin, Jessica Roy, Erich Stahl, Ellen Winchester, David Altshuler, Yan Shen, Zhijian Yao, Wei Huang, Xun Chu, Yungang He, Li Jin, Yangfan Liu, Yayun Shen, Weiwei Sun, Haifeng Wang, Yi Wang, Ying Wang, Xiaoyan Xiong, Liang Xu, Mary M.Y. Waye, Stephen K.W. Tsui, Hong Xue, J. Tze Fei Wong, Launa M. Galver, Jian Bing Fan, Sarah S. Murray, Arnold R. Oliphant, Mark S. Chee, Alexandre Montpetit, Fanny Chagnon, Vincent Ferretti, Martin Leboeuf, Jean François Olivier, Michael S. Phillips, Stéphanie Roumy, Clémentine Sallée, Andrei Verner, Thomas J. Hudson, Kelly A. Frazer, Dennis G. Ballinger, David R. Cox, David A. Hinds, Laura L. Stuve, Pui Yan Kwok, Dongmei Cai, Daniel C. Koboldt, Raymond D. Miller, Ludmila Pawlikowska, Patricia Taillon-Miller, Ming Xiao, Lap Chee Tsui, William Mak, Pak C. Sham, You Qiang Song, Paul K.H. Tam, Yusuke Nakamura, Takahisa Kawaguchi, Takuya Kitamoto, Takashi Morizono, Atsushi Nagashima, Yozo Ohnishi, Akihiro Sekine, Toshihiro Tanaka, Panos Deloukas, Christine P. Bird, Marcos Delgado, Emmanouil T. Dermitzakis, Rhian Gwilliam, Sarah Hunt, Jonathan Morrison, Don Powell, Barbara E. Stranger, Pamela Whittaker, David R. Bentley, Paul I.W. De Bakker, Jeff Barrett, Ben Fry, Julian Maller, Steve McCarroll, Nick Patterson, Itsik Pe'er, Shaun Purcell, Daniel J. Richter, Pardis Sabeti, Richa Saxena, Stephen F. Schaffner, Patrick Varilly, Lincoln D. Stein, Lalitha Krishnan, Albert Vernon Smith, Gudmundur A. Thorisson, Aravinda Chakravarti, Peter E. Chen, David J. Cutler, Carl S. Kashuk, Shin Lin, Gonçalo R. Abecasis, Weihua Guan, Heather M. Munro, Zhaohui Steve Qin, Daryl J. Thomas, Gilean McVean, Leonardo Bottolo, Susana Eyheramendy, Colin Freeman, Jonathan Marchini, Simon Myers, Chris Spencer, Matthew Stephens, Peter Donnelly, Lon R. Cardon, Geraldine Clarke, David M. Evans, Andrew P. Morris, Bruce S. Weir, Tatsuhiko Tsunoda, James C. Mullikin, Stephen T. Sherry, Michael Feolo, Houcan Zhang, Changqing Zeng, Hui Zhao, Ichiro Matsuda, Yoshimitsu Fukushima, Darryl R. Macer, Eiko Suda, Charles N. Rotimi, Clement A. Adebamowo, Ike Ajayi, Toyin Aniagwu, Patricia A. Marshall, Chibuzor Nkwodimmah, Charmaine D.M. Royal, Mark F. Leppert, Missy Dixon, Andy Peiffer, Renzong Qiu, Alastair Kent, Kazuto Kato, Norio Niikawa, Isaac F. Adewole, Bartha M. Knoppers, Morris W. Foster, Ellen Wright Clayton, Jessica Watkin, Richard A. Gibbs, Donna Muzny, Lynne Nazareth, Erica Sodergren, George M. Weinstock, Imtiaz Yakub, Stacey B. Gabriel, Robert C. Onofrio, Liuda Ziaugra, Bruce W. Birren, Mark J. Daly, Richard K. Wilson, Lucinda L. Fulton, Jane Rogers, John Burton, Nigel P. Carter, Christopher M. Clee, Mark Griffiths, Matthew C. Jones, Kirsten McLay, Robert W. Plumb, Mark T. Ross, Sarah K. Sims, David L. Willey, Zhu Chen, Hua Han, Le Kang, Martin Godbout, John C. Wallenburg, Paul L'Archevêque, Guy Bellemare, Koji Saeki, Hongguang Wang, Daochang An, Hongbo Fu, Qing Li, Zhen Wang, Renwu Wang, Arthur L. Holden, Lisa D. Brooks, Jean E. McEwen, Christianne R. Bird, Mark S. Guyer, Patrick J. Nailer, Vivian Ota Wang, Jane L. Peterson, Michael Shi, Jack Spiegel, Lawrence M. Sung, Jonathan Witonsky, Lynn F. Zacharia, Francis S. Collins, Karen Kennedy, Ruth Jamieson, John Stewart

McDonnell Genome Institute (MGI)

Research output: Contribution to journal › Article › peer-review

4890 Scopus citations

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
Pages (from-to)	1299-1320
Number of pages	22
Journal	Nature
Volume	437
Issue number	7063
DOIs	https://doi.org/10.1038/nature04226
State	Published - Oct 27 2005

Access to Document

10.1038/nature04226

Cite this

@article{918bedab7efb4829af5d460d4f18dd24,

title = "A haplotype map of the human genome",

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.",

author = "Belmont, {John W.} and Andrew Boudreau and Leal, {Suzanne M.} and Paul Hardenbol and Shiran Pasternak and Wheeler, {David A.} and Willis, {Thomas D.} and Fuli Yu and Huanming Yang and Yang Gao and Haoran Hu and Weitao Hu and Chaohua Li and Wei Lin and Siqi Liu and Hao Pan and Xiaoli Tang and Jian Wang and Wei Wang and Jun Yu and Bo Zhang and Qingrun Zhang and Hongbin Zhao and Jun Zhou and Rachel Barry and Brendan Blumenstiel and Amy Camargo and Matthew Defelice and Maura Faggart and Mary Goyette and Supriya Gupta and Jamie Moore and Huy Nguyen and Melissa Parkin and Jessica Roy and Erich Stahl and Ellen Winchester and David Altshuler and Yan Shen and Zhijian Yao and Wei Huang and Xun Chu and Yungang He and Li Jin and Yangfan Liu and Yayun Shen and Weiwei Sun and Haifeng Wang and Yi Wang and Ying Wang and Xiaoyan Xiong and Liang Xu and Waye, {Mary M.Y.} and Tsui, {Stephen K.W.} and Hong Xue and Wong, {J. Tze Fei} and Galver, {Launa M.} and Fan, {Jian Bing} and Murray, {Sarah S.} and Oliphant, {Arnold R.} and Chee, {Mark S.} and Alexandre Montpetit and Fanny Chagnon and Vincent Ferretti and Martin Leboeuf and Olivier, {Jean Fran{\c c}ois} and Phillips, {Michael S.} and St{\'e}phanie Roumy and Cl{\'e}mentine Sall{\'e}e and Andrei Verner and Hudson, {Thomas J.} and Frazer, {Kelly A.} and Ballinger, {Dennis G.} and Cox, {David R.} and Hinds, {David A.} and Stuve, {Laura L.} and Kwok, {Pui Yan} and Dongmei Cai and Koboldt, {Daniel C.} and Miller, {Raymond D.} and Ludmila Pawlikowska and Patricia Taillon-Miller and Ming Xiao and Tsui, {Lap Chee} and William Mak and Sham, {Pak C.} and Song, {You Qiang} and Tam, {Paul K.H.} and Yusuke Nakamura and Takahisa Kawaguchi and Takuya Kitamoto and Takashi Morizono and Atsushi Nagashima and Yozo Ohnishi and Akihiro Sekine and Toshihiro Tanaka and Panos Deloukas and Bird, {Christine P.} and Marcos Delgado and Dermitzakis, {Emmanouil T.} and Rhian Gwilliam and Sarah Hunt and Jonathan Morrison and Don Powell and Stranger, {Barbara E.} and Pamela Whittaker and Bentley, {David R.} and {De Bakker}, {Paul I.W.} and Jeff Barrett and Ben Fry and Julian Maller and Steve McCarroll and Nick Patterson and Itsik Pe'er and Shaun Purcell and Richter, {Daniel J.} and Pardis Sabeti and Richa Saxena and Schaffner, {Stephen F.} and Patrick Varilly and Stein, {Lincoln D.} and Lalitha Krishnan and Smith, {Albert Vernon} and Thorisson, {Gudmundur A.} and Aravinda Chakravarti and Chen, {Peter E.} and Cutler, {David J.} and Kashuk, {Carl S.} and Shin Lin and Abecasis, {Gon{\c c}alo R.} and Weihua Guan and Munro, {Heather M.} and Qin, {Zhaohui Steve} and Thomas, {Daryl J.} and Gilean McVean and Leonardo Bottolo and Susana Eyheramendy and Colin Freeman and Jonathan Marchini and Simon Myers and Chris Spencer and Matthew Stephens and Peter Donnelly and Cardon, {Lon R.} and Geraldine Clarke and Evans, {David M.} and Morris, {Andrew P.} and Weir, {Bruce S.} and Tatsuhiko Tsunoda and Mullikin, {James C.} and Sherry, {Stephen T.} and Michael Feolo and Houcan Zhang and Changqing Zeng and Hui Zhao and Ichiro Matsuda and Yoshimitsu Fukushima and Macer, {Darryl R.} and Eiko Suda and Rotimi, {Charles N.} and Adebamowo, {Clement A.} and Ike Ajayi and Toyin Aniagwu and Marshall, {Patricia A.} and Chibuzor Nkwodimmah and Royal, {Charmaine D.M.} and Leppert, {Mark F.} and Missy Dixon and Andy Peiffer and Renzong Qiu and Alastair Kent and Kazuto Kato and Norio Niikawa and Adewole, {Isaac F.} and Knoppers, {Bartha M.} and Foster, {Morris W.} and Clayton, {Ellen Wright} and Jessica Watkin and Gibbs, {Richard A.} and Donna Muzny and Lynne Nazareth and Erica Sodergren and Weinstock, {George M.} and Imtiaz Yakub and Gabriel, {Stacey B.} and Onofrio, {Robert C.} and Liuda Ziaugra and Birren, {Bruce W.} and Daly, {Mark J.} and Wilson, {Richard K.} and Fulton, {Lucinda L.} and Jane Rogers and John Burton and Carter, {Nigel P.} and Clee, {Christopher M.} and Mark Griffiths and Jones, {Matthew C.} and Kirsten McLay and Plumb, {Robert W.} and Ross, {Mark T.} and Sims, {Sarah K.} and Willey, {David L.} and Zhu Chen and Hua Han and Le Kang and Martin Godbout and Wallenburg, {John C.} and Paul L'Archev{\^e}que and Guy Bellemare and Koji Saeki and Hongguang Wang and Daochang An and Hongbo Fu and Qing Li and Zhen Wang and Renwu Wang and Holden, {Arthur L.} and Brooks, {Lisa D.} and McEwen, {Jean E.} and Bird, {Christianne R.} and Guyer, {Mark S.} and Nailer, {Patrick J.} and Wang, {Vivian Ota} and Peterson, {Jane L.} and Michael Shi and Jack Spiegel and Sung, {Lawrence M.} and Jonathan Witonsky and Zacharia, {Lynn F.} and Collins, {Francis S.} and Karen Kennedy and Ruth Jamieson and John Stewart",

note = "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, G{\'e}nome Qu{\'e}bec, the Chinese Academy of Sciences, the Ministry of Science and Technology of the People{\textquoteright}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.",

year = "2005",

month = oct,

day = "27",

doi = "10.1038/nature04226",

language = "English",

volume = "437",

pages = "1299--1320",

journal = "Nature",

issn = "0028-0836",

number = "7063",

}

Belmont, JW, Boudreau, A, Leal, SM, Hardenbol, P, Pasternak, S, Wheeler, DA, Willis, TD, Yu, F, Yang, H, 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, Zhou, J, Barry, R, Blumenstiel, B, Camargo, A, Defelice, M, Faggart, M, Goyette, M, Gupta, S, Moore, J, Nguyen, H, Parkin, M, Roy, J, Stahl, E, Winchester, E, 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, MMY, Tsui, SKW, Xue, H, Wong, JTF, Galver, LM, Fan, JB, Murray, SS, Oliphant, AR, Chee, MS, Montpetit, A, Chagnon, F, Ferretti, V, Leboeuf, M, Olivier, JF, Phillips, MS, Roumy, S, Sallée, C, Verner, A, Hudson, TJ, Frazer, KA, Ballinger, DG, Cox, DR, Hinds, DA, Stuve, LL, Kwok, PY, Cai, D, Koboldt, DC, Miller, RD, Pawlikowska, L, Taillon-Miller, P, Xiao, M, Tsui, LC, Mak, W, Sham, PC, Song, YQ, Tam, PKH, Nakamura, Y, Kawaguchi, T, Kitamoto, T, Morizono, T, Nagashima, A, Ohnishi, Y, Sekine, A, Tanaka, T, Deloukas, P, Bird, CP, Delgado, M, Dermitzakis, ET, Gwilliam, R, Hunt, S, Morrison, J, Powell, D, Stranger, BE, Whittaker, P, Bentley, DR, De Bakker, PIW, Barrett, J, Fry, B, Maller, J, McCarroll, S, Patterson, N, Pe'er, I, Purcell, S, Richter, DJ, Sabeti, P, Saxena, R, Schaffner, SF, Varilly, P, Stein, LD, Krishnan, L, Smith, AV, Thorisson, GA, Chakravarti, A, Chen, PE, Cutler, DJ, Kashuk, CS, Lin, S, Abecasis, GR, Guan, W, Munro, HM, Qin, ZS, Thomas, DJ, McVean, G, Bottolo, L, Eyheramendy, S, Freeman, C, Marchini, J, Myers, S, Spencer, C, Stephens, M, Donnelly, P, Cardon, LR, Clarke, G, Evans, DM, Morris, AP, Weir, BS, Tsunoda, T, Mullikin, JC, Sherry, ST, Feolo, M, Zhang, H, Zeng, C, Zhao, H, Matsuda, I, Fukushima, Y, Macer, DR, Suda, E, Rotimi, CN, Adebamowo, CA, Ajayi, I, Aniagwu, T, Marshall, PA, Nkwodimmah, C, Royal, CDM, Leppert, MF, Dixon, M, Peiffer, A, Qiu, R, Kent, A, Kato, K, Niikawa, N, Adewole, IF, Knoppers, BM, Foster, MW, Clayton, EW, Watkin, J, Gibbs, RA, Muzny, D, Nazareth, L, Sodergren, E, Weinstock, GM, Yakub, I, Gabriel, SB, Onofrio, RC, Ziaugra, L, Birren, BW, Daly, MJ, Wilson, RK, Fulton, LL, Rogers, J, Burton, J, Carter, NP, Clee, CM, Griffiths, M, Jones, MC, McLay, K, Plumb, RW, Ross, MT, Sims, SK, Willey, DL, Chen, Z, Han, H, Kang, L, Godbout, M, Wallenburg, JC, L'Archevêque, P, Bellemare, G, Saeki, K, Wang, H, An, D, Fu, H, Li, Q, Wang, Z, Wang, R, Holden, AL, Brooks, LD, McEwen, JE, Bird, CR, Guyer, MS, Nailer, PJ, Wang, VO, Peterson, JL, Shi, M, Spiegel, J, Sung, LM, Witonsky, J, Zacharia, LF, Collins, FS, Kennedy, K, Jamieson, R & Stewart, J 2005, 'A haplotype map of the human genome', Nature, vol. 437, no. 7063, pp. 1299-1320. https://doi.org/10.1038/nature04226

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 E.

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.

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AU - Wang, Vivian Ota

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AU - Shi, Michael

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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

U2 - 10.1038/nature04226

DO - 10.1038/nature04226

M3 - Article

C2 - 16255080

AN - SCOPUS:79959524146

SN - 0028-0836

VL - 437

SP - 1299

EP - 1320

JO - Nature

JF - Nature

IS - 7063

ER -

A haplotype map of the human genome

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