Genome-wide detection and characterization of positive selection in human populations

Pardis C. Sabeti, Patrick Varilly, Ben Fry, Jason Lohmueller, Elizabeth Hostetter, Chris Cotsapas, Xiaohui Xie, Elizabeth H. Byrne, Steven A. McCarroll, Rachelle Gaudet, Stephen F. Schaffner, Eric S. Lander, Kelly A. Frazer, Dennis G. Ballinger, David R. Cox, David A. Hinds, Laura L. Stuve, Richard A. Gibbs, John W. Belmont, Andrew BoudreauPaul Hardenbol, Suzanne M. Leal, Shiran Pasternak, David A. Wheeler, Thomas D. Willis, Fuli Yu, Huanming Yang, Changqing Zeng, 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, Hui Zhao, Jun Zhou, Stacey B. Gabriel, Rachel Barry, Brendan Blumenstiel, Amy Camargo, Matthew Defelice, Maura Faggart, Mary Goyette, Supriya Gupta, Jamie Moore, Huy Nguyen, Robert C. Onofrio, Melissa Parkin, Jessica Roy, Erich Stahl, Ellen Winchester, Liuda Ziaugra, 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, Luana M. Galver, Jian Bing Fan, Kevin Gunderson, 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, Pui Yan Kwok, Dongmei Cai, Daniel C. Koboldt, Raymond D. Miller, Ludmila Pawlikowska, Patricia Taillon-Miller, Ming Xiao, Lap Chee Tsui, William Mak, Qiang Song You, Paul K.H. Tam, Yusuke Nakamura, Takahisa Kawaguchi, Takuya Kitamoto, Takashi Morizono, Atsushi Nagashima, Yozo Ohnishi, Akihiro Sekine, Toshihiro Tanaka, Tatsuhiko Tsunoda, 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, Mark J. Daly, Paul I.W. De Bakker, Jeff Barrett, Yves R. Chretien, Julian Maller, Steve McCarroll, Nick Patterson, Itsik Pe'Er, Alkes Price, Shaun Purcell, Daniel J. Richter, Richa Saxena, Pak C. Sham, Lincoln D. Stein, Lalitha Krishnan, Albert Vernon Smith, Marcela K. Tello-Ruiz, Gudmundur A. Thorisson, Aravinda Chakravarti, Peter E. Chen, David J. Cutler, Carl S. Kashuk, Shin Lin, Gonçalo R. Abecasis, Weihua Guan, Yun Li, Heather M. Munro, Zhaohui Steve Qin, Daryl J. Thomas, Gilean McVean, Adam Auton, Leonardo Bottolo, Niall Cardin, 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, Todd A. Johnson, James C. Mullikin, Stephen T. Sherry, Michael Feolo, Andrew Skol, Houcan Zhang, 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, Donna Muzny, Lynne Nazareth, Erica Sodergren, George M. Weinstock, Imtaz Yakub, Bruce W. Birren, 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, Mark S. Guyer, Vivian Ota Wang, Jane L. Peterson, Michael Shi, Jack Spiegel, Lawrence M. Sung, Lynn F. Zacharia, Francis S. Collins, Karen Kennedy, Ruth Jamieson, John Stewart

Research output: Contribution to journalArticle

Abstract

With the advent of dense maps of human genetic variation, it is now possible to detect positive natural selection across the human genome. Here we report an analysis of over 3 million polymorphisms from the International HapMap Project Phase 2 (HapMap2). We used 'long-range haplotype' methods, which were developed to identify alleles segregating in a population that have undergone recent selection, and we also developed new methods that are based on cross-population comparisons to discover alleles that have swept to near-fixation within a population. The analysis reveals more than 300 strong candidate regions. Focusing on the strongest 22 regions, we develop a heuristic for scrutinizing these regions to identify candidate targets of selection. In a complementary analysis, we identify 26 non-synonymous, coding, single nucleotide polymorphisms showing regional evidence of positive selection. Examination of these candidates highlights three cases in which two genes in a common biological process have apparently undergone positive selection in the same population:LARGE and DMD, both related to infection by the Lassa virus, in West Africa;SLC24A5 and SLC45A2, both involved in skin pigmentation, in Europe; and EDAR and EDA2R, both involved in development of hair follicles, in Asia.

Original languageEnglish (US)
Pages (from-to)913-918
Number of pages6
JournalNature
Volume449
Issue number7164
DOIs
StatePublished - Oct 18 2007
Externally publishedYes

ASJC Scopus subject areas

  • General

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    Sabeti, P. C., Varilly, P., Fry, B., Lohmueller, J., Hostetter, E., Cotsapas, C., Xie, X., Byrne, E. H., McCarroll, S. A., Gaudet, R., Schaffner, S. F., Lander, E. S., Frazer, K. A., Ballinger, D. G., Cox, D. R., Hinds, D. A., Stuve, L. L., Gibbs, R. A., Belmont, J. W., ... Stewart, J. (2007). Genome-wide detection and characterization of positive selection in human populations. Nature, 449(7164), 913-918. https://doi.org/10.1038/nature06250