A second generation human haplotype map of over 3.1 million SNPs. Export

@article{citeulike:1780948, 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.}, author = {{International HapMap Consortium} and Frazer, Kelly A. and Ballinger, Dennis G. and Cox, David R. and Hinds, David A. and Stuve, Laura L. and Gibbs, Richard A. and Belmont, John W. and Boudreau, Andrew and Hardenbol, Paul and Leal, Suzanne M. and Pasternak, Shiran and Wheeler, David A. and Willis, Thomas D. and Yu, Fuli and Yang, Huanming and Zeng, Changqing and Gao, Yang and Hu, Haoran and Hu, Weitao and Li, Chaohua and Lin, Wei and Liu, Siqi and Pan, Hao and Tang, Xiaoli and Wang, Jian and Wang, Wei and Yu, Jun and Zhang, Bo and Zhang, Qingrun and Zhao, Hongbin and Zhao, Hui and Zhou, Jun and Gabriel, Stacey B. and Barry, Rachel and Blumenstiel, Brendan and Camargo, Amy and Defelice, Matthew and Faggart, Maura and Goyette, Mary and Gupta, Supriya and Moore, Jamie and Nguyen, Huy and Onofrio, Robert C. and Parkin, Melissa and Roy, Jessica and Stahl, Erich and Winchester, Ellen and Ziaugra, Liuda and Altshuler, David and Shen, Yan and Yao, Zhijian and Huang, Wei and Chu, Xun and He, Yungang and Jin, Li and Liu, Yangfan and Shen, Yayun and Sun, Weiwei and Wang, Haifeng and Wang, Yi and Wang, Ying and Xiong, Xiaoyan and Xu, Liang and Waye, Mary M. and Tsui, Stephen K. and Xue, Hong and Wong, J. Tze-Fei and Galver, Luana M. and Fan, Jian-Bing B. and Gunderson, Kevin and Murray, Sarah S. and Oliphant, Arnold R. and Chee, Mark S. and Montpetit, Alexandre and Chagnon, Fanny and Ferretti, Vincent and Leboeuf, Martin and Olivier, Jean-Fran\c{c}ois F. and Phillips, Michael S. and Roumy, St\'{e}phanie and Sall\'{e}e, Cl\'{e}mentine and Verner, Andrei and Hudson, Thomas J. and Kwok, Pui-Yan Y. and Cai, Dongmei and Koboldt, Daniel C. and Miller, Raymond D. and Pawlikowska, Ludmila and Taillon-Miller, Patricia and Xiao, Ming and Tsui, Lap-Chee C. and Mak, William and Song, You Qiang Q. and Tam, Paul K. and Nakamura, Yusuke and Kawaguchi, Takahisa and Kitamoto, Takuya and Morizono, Takashi and Nagashima, Atsushi and Ohnishi, Yozo and Sekine, Akihiro and Tanaka, Toshihiro and Tsunoda, Tatsuhiko and Deloukas, Panos and Bird, Christine P. and Delgado, Marcos and Dermitzakis, Emmanouil T. and Gwilliam, Rhian and Hunt, Sarah and Morrison, Jonathan and Powell, Don and Stranger, Barbara E. and Whittaker, Pamela and Bentley, David R. and Daly, Mark J. and de Bakker, Paul I. and Barrett, Jeff and Chretien, Yves R. and Maller, Julian and McCarroll, Steve and Patterson, Nick and Pe'er, Itsik and Price, Alkes and Purcell, Shaun and Richter, Daniel J. and Sabeti, Pardis and Saxena, Richa and Schaffner, Stephen F. and Sham, Pak C. and Varilly, Patrick and Altshuler, David and Stein, Lincoln D. and Krishnan, Lalitha and Smith, Albert Vernon V. and Tello-Ruiz, Marcela K. and Thorisson, Gudmundur A. and Chakravarti, Aravinda and Chen, Peter E. and Cutler, David J. and Kashuk, Carl S. and Lin, Shin and Abecasis, Gon\c{c}alo R. and Guan, Weihua and Li, Yun and Munro, Heather M. and Qin, Zhaohui Steve S. and Thomas, Daryl J. and McVean, Gilean and Auton, Adam and Bottolo, Leonardo and Cardin, Niall and Eyheramendy, Susana and Freeman, Colin and Marchini, Jonathan and Myers, Simon and Spencer, Chris and Stephens, Matthew and Donnelly, Peter and Cardon, Lon R. and Clarke, Geraldine and Evans, David M. and Morris, Andrew P. and Weir, Bruce S. and Tsunoda, Tatsuhiko and Mullikin, James C. and Sherry, Stephen T. and Feolo, Michael and Skol, Andrew and Zhang, Houcan and Zeng, Changqing and Zhao, Hui and Matsuda, Ichiro and Fukushima, Yoshimitsu and Macer, Darryl R. and Suda, Eiko and Rotimi, Charles N. and Adebamowo, Clement A. and Ajayi, Ike and Aniagwu, Toyin and Marshall, Patricia A. and Nkwodimmah, Chibuzor and Royal, Charmaine D. and Leppert, Mark F. and Dixon, Missy and Peiffer, Andy and Qiu, Renzong and Kent, Alastair and Kato, Kazuto and Niikawa, Norio and Adewole, Isaac F. and Knoppers, Bartha M. and Foster, Morris W. and Clayton, Ellen Wright W. and Watkin, Jessica and Gibbs, Richard A. and Belmont, John W. and Muzny, Donna and Nazareth, Lynne and Sodergren, Erica and Weinstock, George M. and Wheeler, David A. and Yakub, Imtaz and Gabriel, Stacey B. and Onofrio, Robert C. and Richter, Daniel J. and Ziaugra, Liuda and Birren, Bruce W. and Daly, Mark J. and Altshuler, David and Wilson, Richard K. and Fulton, Lucinda L. and Rogers, Jane and Burton, John and Carter, Nigel P. and Clee, Christopher M. and Griffiths, Mark and Jones, Matthew C. and McLay, Kirsten and Plumb, Robert W. and Ross, Mark T. and Sims, Sarah K. and Willey, David L. and Chen, Zhu and Han, Hua and Kang, Le and Godbout, Martin and Wallenburg, John C. and L'Archev\^{e}que, Paul and Bellemare, Guy and Saeki, Koji and Wang, Hongguang and An, Daochang and Fu, Hongbo and Li, Qing and Wang, Zhen and Wang, Renwu and Holden, Arthur L. and Brooks, Lisa D. and McEwen, Jean E. and Guyer, Mark S. and Wang, Vivian Ota O. and Peterson, Jane L. and Shi, Michael and Spiegel, Jack and Sung, Lawrence M. and Zacharia, Lynn F. and Collins, Francis S. and Kennedy, Karen and Jamieson, Ruth and Stewart, John}, citeulike-article-id = {1780948}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/nature06258}, citeulike-linkout-1 = {http://dx.doi.org/10.1038/nature06258}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/17943122}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=17943122}, day = {18}, doi = {10.1038/nature06258}, issn = {1476-4687}, journal = {Nature}, keywords = {humgen, lab, silico, snp}, month = {October}, number = {7164}, pages = {851--861}, posted-at = {2008-12-01 20:33:02}, priority = {2}, publisher = {Nature Publishing Group}, title = {A second generation human haplotype map of over 3.1 million SNPs.}, url = {http://dx.doi.org/10.1038/nature06258}, volume = {449}, year = {2007} }

TY - JOUR ID - citeulike:1780948 L3 - citeulike-article-id:1780948 N2 - 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. IS - 7164 JF - Nature SN - 1476-4687 EP - 861 TI - A second generation human haplotype map of over 3.1 million SNPs. PB - Nature Publishing Group VL - 449 SP - 851 KW - humgen KW - lab KW - silico KW - snp AU - Frazer, Kelly AU - Ballinger, Dennis AU - Cox, David AU - Hinds, David AU - Stuve, Laura AU - Gibbs, Richard AU - Belmont, John AU - Boudreau, Andrew AU - Hardenbol, Paul AU - Leal, Suzanne AU - Pasternak, Shiran AU - Wheeler, David AU - Willis, Thomas AU - Yu, Fuli AU - Yang, Huanming AU - Zeng, Changqing 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 - Zhao, Hui AU - Zhou, Jun AU - Gabriel, Stacey 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 - Onofrio, Robert AU - Parkin, Melissa AU - Roy, Jessica AU - Stahl, Erich AU - Winchester, Ellen AU - Ziaugra, Liuda 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 AU - Tsui, Stephen AU - Xue, Hong AU - Wong, Tze-Fei AU - Galver, Luana AU - Fan, Jian-Bing AU - Gunderson, Kevin AU - Murray, Sarah AU - Oliphant, Arnold AU - Chee, Mark AU - Montpetit, Alexandre AU - Chagnon, Fanny AU - Ferretti, Vincent AU - Leboeuf, Martin AU - Olivier, Jean-François AU - Phillips, Michael AU - Roumy, Stéphanie AU - Sallée, Clémentine AU - Verner, Andrei AU - Hudson, Thomas AU - Kwok, Pui-Yan AU - Cai, Dongmei AU - Koboldt, Daniel AU - Miller, Raymond AU - Pawlikowska, Ludmila AU - Taillon-Miller, Patricia AU - Xiao, Ming AU - Tsui, Lap-Chee AU - Mak, William AU - Song, You Qiang AU - Tam, Paul 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 - Tsunoda, Tatsuhiko AU - Deloukas, Panos AU - Bird, Christine AU - Delgado, Marcos AU - Dermitzakis, Emmanouil AU - Gwilliam, Rhian AU - Hunt, Sarah AU - Morrison, Jonathan AU - Powell, Don AU - Stranger, Barbara AU - Whittaker, Pamela AU - Bentley, David AU - Daly, Mark AU - de Bakker, Paul AU - Barrett, Jeff AU - Chretien, Yves AU - Maller, Julian AU - McCarroll, Steve AU - Patterson, Nick AU - Pe'er, Itsik AU - Price, Alkes AU - Purcell, Shaun AU - Richter, Daniel AU - Sabeti, Pardis AU - Saxena, Richa AU - Schaffner, Stephen AU - Sham, Pak AU - Varilly, Patrick AU - Altshuler, David AU - Stein, Lincoln AU - Krishnan, Lalitha AU - Smith, Albert Vernon AU - Tello-Ruiz, Marcela AU - Thorisson, Gudmundur AU - Chakravarti, Aravinda AU - Chen, Peter AU - Cutler, David AU - Kashuk, Carl AU - Lin, Shin AU - Abecasis, Gonçalo AU - Guan, Weihua AU - Li, Yun AU - Munro, Heather AU - Qin, Zhaohui Steve AU - Thomas, Daryl AU - McVean, Gilean AU - Auton, Adam AU - Bottolo, Leonardo AU - Cardin, Niall AU - Eyheramendy, Susana AU - Freeman, Colin AU - Marchini, Jonathan AU - Myers, Simon AU - Spencer, Chris AU - Stephens, Matthew AU - Donnelly, Peter AU - Cardon, Lon AU - Clarke, Geraldine AU - Evans, David AU - Morris, Andrew AU - Weir, Bruce AU - Tsunoda, Tatsuhiko AU - Mullikin, James AU - Sherry, Stephen AU - Feolo, Michael AU - Skol, Andrew AU - Zhang, Houcan AU - Zeng, Changqing AU - Zhao, Hui AU - Matsuda, Ichiro AU - Fukushima, Yoshimitsu AU - Macer, Darryl AU - Suda, Eiko AU - Rotimi, Charles AU - Adebamowo, Clement AU - Ajayi, Ike AU - Aniagwu, Toyin AU - Marshall, Patricia AU - Nkwodimmah, Chibuzor AU - Royal, Charmaine AU - Leppert, Mark AU - Dixon, Missy AU - Peiffer, Andy AU - Qiu, Renzong AU - Kent, Alastair AU - Kato, Kazuto AU - Niikawa, Norio AU - Adewole, Isaac AU - Knoppers, Bartha AU - Foster, Morris AU - Clayton, Ellen Wright AU - Watkin, Jessica AU - Gibbs, Richard AU - Belmont, John AU - Muzny, Donna AU - Nazareth, Lynne AU - Sodergren, Erica AU - Weinstock, George AU - Wheeler, David AU - Yakub, Imtaz AU - Gabriel, Stacey AU - Onofrio, Robert AU - Richter, Daniel AU - Ziaugra, Liuda AU - Birren, Bruce AU - Daly, Mark AU - Altshuler, David AU - Wilson, Richard AU - Fulton, Lucinda AU - Rogers, Jane AU - Burton, John AU - Carter, Nigel AU - Clee, Christopher AU - Griffiths, Mark AU - Jones, Matthew AU - McLay, Kirsten AU - Plumb, Robert AU - Ross, Mark AU - Sims, Sarah AU - Willey, David AU - Chen, Zhu AU - Han, Hua AU - Kang, Le AU - Godbout, Martin AU - Wallenburg, John 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 AU - Brooks, Lisa AU - McEwen, Jean AU - Guyer, Mark AU - Wang, Vivian Ota AU - Peterson, Jane AU - Shi, Michael AU - Spiegel, Jack AU - Sung, Lawrence AU - Zacharia, Lynn AU - Collins, Francis AU - Kennedy, Karen AU - Jamieson, Ruth AU - Stewart, John PY - 2007/10/18/ UR - http://dx.doi.org/10.1038/nature06258 ER -