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

Sabeti, Pc; de Bakker, Pi; Varilly, Patrick; Stuve, Laura Ll; Yu, Fuli; Yang, Huanming; Zeng, C.; Willis, T. D.; Sm, Leal; Td, Willis; Yu, Jun; Sa, McCarroll; Xie, Xiaohui; Zhang, Bo; Zhang, Qingrun; Zhao, H.; Zhao, Hongbin; Zhou, Jun; Sf, Schaffner; Tang, Xiaoli; Wang, W.; Wang, Jian; Wang, Wei; Sb, Gabriel; Ziaugra, L.; Yao, Zhijian; Rc, Onofrio; Yq, Song; Roy, Jessica; Stahl, Erich; Winchester, Ellen; Xiong, Xiaoyan; Wang, Y.; Xu, Liang; Shen, Yan; Xue, Hong; You, Q. S.; Wang, Yi; Wang, Ying; Yr, Chretien; Shen, Yayun; Sk, Tsui; Sun, Weiwei; Wang, Haifeng; Sabeti, Pardis C.; Wheeler, David A.; Tze Fei Wong, J.; Ra, Gibbs; Waye, M. M. Y.; Tsui, S. K. W.; Zs, Qin; Ss, Murray; Wong, J. T.-F.; Zeng, Changqing; Schaffner, Stephen F.; Zhao, Hui; Roumy, Stéphanie; Tj, Hudson; Sallée, Clémentine; Py, Kwok; Verner, Andrei; Rd, Miller; Taillon-Miller, Patricia; Xiao, Ming; Pk, Tam; Ziaugra, Liuda; Tsui, L.-C.; Qiang Song, You; Tam, P. K. H.; Sekine, Akihiro; Tanaka, Toshihiro; Tsunoda, T.; Powell, Don; Whittaker, Pamela; Stranger, B. E.; Price, Alkes; Varilly, P.; Purcell, Shaun; Zacharia, Lf F.; Saxena, Richa; Zhang, Houcan; Richter, Daniel J.; Tsunoda, Tatsuhiko; Sham, P. C.; Stein, L. D.; Smith, A.; Thorisson, G. A.; Tello-Ruiz, Mk K.; Vernon Smith, Albert; Yakub, Imtaz; Qin, Z. S.; Thomas, D. J.; Spencer, Chris; Stephens, Matthew; Ta, Johnson; Weir, B. S.; Skol, Andrew; St, Sherry; Sherry, S. T.; Suda, Eiko; Rotimi, C. N.; Qiu, Renzong; Royal, C. D. M.; Watkin, Jessica; Sodergren, Erica; Rk, Wilson; Weinstock, G. M.; Wilson, Rk K.; Rogers, Jane; Rw, Plumb; Plumb, Rw W.; Sk, Sims; Ross, Mt T.; Sims, Sk K.; Willey, Dl L.; Wallenburg, Jc C.; Wang, Z.; Saeki, Koji; Wang, Hongguang; Wang, Zhen; Wang, Renwu; Wang, Vo; Wang, Vivian Ota; Shi, Michael; Spiegel, Jack; Sung, L. M.; Stewart, John; Lohmueller, Jason; Ll, Stuve; Pasternak, Shiran; Lin, Wei; Liu, Siqi; Pan, Hao; Moore, Jamie; Nguyen, Huy; Parkin, Melissa; Liu, Yangfan; McCarroll, S. A.; Mm, Waye; Lm, Galver; Ms, Chee; Murray, Sarah Ss; Oliphant, A. R.; Montpetit, Alexandre; Ms, Phillips; Olivier, J.-F.; Onofrio, Robert C.; Pawlikowska, Ludmila; Miller, R. D.; Mak, William; Nakamura, Yusuke; Morizono, Takashi; Nagashima, Atsushi; Ohnishi, Yozo; McCarroll, Steven A.; Morrison, Jonathan; Mj, Daly; Maller, Julian; Patterson, Nick; Pe'er, Itsik; Pc, Sham; Pe’er, Itsik; Mk, Tello Ruiz; Pe, Chen; McVean, Gilean; Munro, H. M.; Marchini, Jonathan; Myers, Simon; Lr, Cardon; Phillips, Michael S.; Morris, A. P.; Mullikin, J. C.; Matsuda, Ichiro; MacEr, D. R.; Pa, Marshall; Nkwodimmah, Chibuzor; Mf, Leppert; Peiffer, Andy; Marshall, P. A.; Niikawa, Norio; Mw, Foster; Muzny, Donna; Nazareth, Lynne; Np, Carter; Ll, Fulton; Mc, Jones; McLay, Kirsten; Mt, Ross; McEwen, Je E.; Ms, Guyer; Ota Wang, Vivian; Peterson, J. L.; Lm, Sung; Others,; Fry, Ben; Frazer, K. A.; Ballinger, D. G.; Cox, D. R.; Hinds, D. A.; Dr, Cox; Leal, S. M.; Boudreau, Andrew; Belmont, John W.; Hostetter, Elizabeth; Hardenbol, Paul; Cotsapas, Chris; Eh, Byrne; Da, Wheeler; Gao, Yang; Hu, Haoran; Hu, Weitao; Li, Chaohua; Es, Lander; Barry, Rachel; Gaudet, Rachelle; Blumenstiel, Brendan; Camargo, Amy; Defelice, Matthew; Faggart, Maura; Goyette, Mary; Gupta, Supriya; Ka, Frazer; Dg, Ballinger; Byrne, Elizabeth H.; Huang, Wei; Chu, Xun; He, Yungang; Gibbs, Richard A.; Jin, Li; Da, Hinds; Altshuler, D.; Jt, Wong; Jb, Fan; Jw, Belmont; Ar, Oliphant; Galver, L. M.; Gunderson, Kevin; Fan, J.-B.; Chee, Mark S.; Jf, Olivier; Chagnon, Fanny; Lander, Eric S.; Ferretti, Vincent; Gabriel, Stacey B.; Leboeuf, Martin; Consortium, International HapMap; Altshuler, David; Dc, Koboldt; Cai, Dongmei; Hudson, T. J.; Kwok, P.-Y.; Lc, Tsui; Koboldt, D. C.; Kawaguchi, Takahisa; Kitamoto, Takuya; Cp, Bird; Deloukas, Panos; Delgado, Marcos; Et, Dermitzakis; Gwilliam, Rhian; Hunt, Sarah; Bird, C. P.; Be, Stranger; Dermitzakis, E. T.; Dr, Bentley; Barrett, Jeff; Bentley, D. R.; Daly, Mark J.; De Bakker, P. I. W.; Dj, Richter; Chretien, Y. R.; Ld, Stein; Krishnan, Lalitha; Av, Smith; Ga, Thorisson; Chakravarti, Aravinda; Dj, Cutler; Chen, P. E.; Cs, Kashuk; Dj, Thomas; Gr, Abecasis; Guan, Weihua; Cutler, D. J.; Li, Yun; Kashuk, C. S.; Hm, Munro; Abecasis, G. R.; Auton, Adam; Bottolo, Leonardo; Cardin, Niall; Eyheramendy, Susana; Freeman, Colin; Donnelly, Peter; Clarke, Geraldine; Dm, Evans; Ap, Morris; Cardon, L. R.; Bs, Weir; Evans, D. M.; Jc, Mullikin; Feolo, Michael; Johnson, T. A.; Fukushima, Yoshimitsu; Dr, Macer; Cn, Rotimi; Ajayi, Ike; Ca, Adebamowo; Aniagwu, Toyin; Adebamowo, C. A.; Cd, Royal; Dixon, Missy; Kent, Alastair; Kato, Kazuto; Leppert, Mark F.; If, Adewole; Bm, Knoppers; Lin, Shin; Ew, Clayton; Adewole, I. F.; Knoppers, B. M.; Foster, M. W.; Clayton, E. W.; Gm, Weinstock; Bw, Birren; Birren, Bw W.; Fulton, Lucinda Ll; Burton, John; Cm, Clee; Carter, Np P.; Clee, Cm M.; Griffiths, Mark; Jones, Mc C.; Dl, Willey; Chen, Z.; Chen, Zhu; Han, Hua; Kang, Le; Godbout, Martin; Jc, Wallenburg; L'Archevêque, Paul; Bellemare, Guy; An, Daochang; Fu, Hongbo; Li, Qing; Holden, Al L.; Brooks, Ld D.; Al, Holden; Ld, Brooks; Guyer, Mark S.; Je, McEwen; Jl, Peterson; Lf, Zacharia; Collins, Fs S.; Fs, Collins; Kennedy, Karen; Jamieson, Ruth

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Toshihiro Tanaka
Sabeti et al., 2007

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@article{Sabeti2007,
  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)1. We used ‘long-range haplotype’ methods, which were developed to identify alleles segregating in a population that have undergone recent selection2, 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 virus3, in West Africa; SLC24A5 and SLC45A2, both involved in skin pigmentation4,5, in Europe; and EDAR and EDA2R, both involved in development of hair follicles6, in Asia.},
  author = {Sabeti, Pc and de Bakker, Pi and Varilly, Patrick and Stuve, Laura Ll and Yu, Fuli and Yang, Huanming and Zeng, C. and Willis, T. D. and Sm, Leal and Td, Willis and Yu, Jun and Sa, McCarroll and Xie, Xiaohui and Zhang, Bo and Zhang, Qingrun and Zhao, H. and Zhao, Hongbin and Zhou, Jun and Sf, Schaffner and Tang, Xiaoli and Wang, W. and Wang, Jian and Wang, Wei and Sb, Gabriel and Ziaugra, L. and Yao, Zhijian and Rc, Onofrio and Yq, Song and Roy, Jessica and Stahl, Erich and Winchester, Ellen and Xiong, Xiaoyan and Wang, Y. and Xu, Liang and Shen, Yan and Xue, Hong and You, Q. S. and Wang, Yi and Wang, Ying and Yr, Chretien and Shen, Yayun and Sk, Tsui and Sun, Weiwei and Wang, Haifeng and Sabeti, Pardis C. and Wheeler, David A. and Tze Fei Wong, J. and Ra, Gibbs and Waye, M. M. Y. and Tsui, S. K. W. and Zs, Qin and Ss, Murray and Wong, J. T.-F. and Zeng, Changqing and Schaffner, Stephen F. and Zhao, Hui and Roumy, Stéphanie and Tj, Hudson and Sallée, Clémentine and Py, Kwok and Verner, Andrei and Rd, Miller and Taillon-Miller, Patricia and Xiao, Ming and Pk, Tam and Ziaugra, Liuda and Tsui, L.-C. and Qiang Song, You and Tam, P. K. H. and Sekine, Akihiro and Tanaka, Toshihiro and Tsunoda, T. and Powell, Don and Whittaker, Pamela and Stranger, B. E. and Price, Alkes and Varilly, P. and Purcell, Shaun and Zacharia, Lf F. and Saxena, Richa and Zhang, Houcan and Richter, Daniel J. and Tsunoda, Tatsuhiko and Sham, P. C. and Stein, L. D. and Smith, A. and Thorisson, G. A. and Tello-Ruiz, Mk K. and Vernon Smith, Albert and Yakub, Imtaz and Qin, Z. S. and Thomas, D. J. and Spencer, Chris and Stephens, Matthew and Ta, Johnson and Weir, B. S. and Skol, Andrew and St, Sherry and Sherry, S. T. and Suda, Eiko and Rotimi, C. N. and Qiu, Renzong and Royal, C. D. M. and Watkin, Jessica and Sodergren, Erica and Rk, Wilson and Weinstock, G. M. and Wilson, Rk K. and Rogers, Jane and Rw, Plumb and Plumb, Rw W. and Sk, Sims and Ross, Mt T. and Sims, Sk K. and Willey, Dl L. and Wallenburg, Jc C. and Wang, Z. and Saeki, Koji and Wang, Hongguang and Wang, Zhen and Wang, Renwu and Wang, Vo and Wang, Vivian Ota and Shi, Michael and Spiegel, Jack and Sung, L. M. and Stewart, John and Lohmueller, Jason and Ll, Stuve and Pasternak, Shiran and Lin, Wei and Liu, Siqi and Pan, Hao and Moore, Jamie and Nguyen, Huy and Parkin, Melissa and Liu, Yangfan and McCarroll, S. A. and Mm, Waye and Lm, Galver and Ms, Chee and Murray, Sarah Ss and Oliphant, A. R. and Montpetit, Alexandre and Ms, Phillips and Olivier, J.-F. and Onofrio, Robert C. and Pawlikowska, Ludmila and Miller, R. D. and Mak, William and Nakamura, Yusuke and Morizono, Takashi and Nagashima, Atsushi and Ohnishi, Yozo and McCarroll, Steven A. and Morrison, Jonathan and Mj, Daly and Maller, Julian and Patterson, Nick and Pe'er, Itsik and Pc, Sham and Pe’er, Itsik and Mk, Tello Ruiz and Pe, Chen and McVean, Gilean and Munro, H. M. and Marchini, Jonathan and Myers, Simon and Lr, Cardon and Phillips, Michael S. and Morris, A. P. and Mullikin, J. C. and Matsuda, Ichiro and MacEr, D. R. and Pa, Marshall and Nkwodimmah, Chibuzor and Mf, Leppert and Peiffer, Andy and Marshall, P. A. and Niikawa, Norio and Mw, Foster and Muzny, Donna and Nazareth, Lynne and Np, Carter and Ll, Fulton and Mc, Jones and McLay, Kirsten and Mt, Ross and McEwen, Je E. and Ms, Guyer and Ota Wang, Vivian and Peterson, J. L. and Lm, Sung and Others,  and Fry, Ben and Frazer, K. A. and Ballinger, D. G. and Cox, D. R. and Hinds, D. A. and Dr, Cox and Leal, S. M. and Boudreau, Andrew and Belmont, John W. and Hostetter, Elizabeth and Hardenbol, Paul and Cotsapas, Chris and Eh, Byrne and Da, Wheeler and Gao, Yang and Hu, Haoran and Hu, Weitao and Li, Chaohua and Es, Lander and Barry, Rachel and Gaudet, Rachelle and Blumenstiel, Brendan and Camargo, Amy and Defelice, Matthew and Faggart, Maura and Goyette, Mary and Gupta, Supriya and Ka, Frazer and Dg, Ballinger and Byrne, Elizabeth H. and Huang, Wei and Chu, Xun and He, Yungang and Gibbs, Richard A. and Jin, Li and Da, Hinds and Altshuler, D. and Jt, Wong and Jb, Fan and Jw, Belmont and Ar, Oliphant and Galver, L. M. and Gunderson, Kevin and Fan, J.-B. and Chee, Mark S. and Jf, Olivier and Chagnon, Fanny and Lander, Eric S. and Ferretti, Vincent and Gabriel, Stacey B. and Leboeuf, Martin and Consortium, International HapMap and Altshuler, David and Dc, Koboldt and Cai, Dongmei and Hudson, T. J. and Kwok, P.-Y. and Lc, Tsui and Koboldt, D. C. and Kawaguchi, Takahisa and Kitamoto, Takuya and Cp, Bird and Deloukas, Panos and Delgado, Marcos and Et, Dermitzakis and Gwilliam, Rhian and Hunt, Sarah and Bird, C. P. and Be, Stranger and Dermitzakis, E. T. and Dr, Bentley and Barrett, Jeff and Bentley, D. R. and Daly, Mark J. and De Bakker, P. I. W. and Dj, Richter and Chretien, Y. R. and Ld, Stein and Krishnan, Lalitha and Av, Smith and Ga, Thorisson and Chakravarti, Aravinda and Dj, Cutler and Chen, P. E. and Cs, Kashuk and Dj, Thomas and Gr, Abecasis and Guan, Weihua and Cutler, D. J. and Li, Yun and Kashuk, C. S. and Hm, Munro and Abecasis, G. R. and Auton, Adam and Bottolo, Leonardo and Cardin, Niall and Eyheramendy, Susana and Freeman, Colin and Donnelly, Peter and Clarke, Geraldine and Dm, Evans and Ap, Morris and Cardon, L. R. and Bs, Weir and Evans, D. M. and Jc, Mullikin and Feolo, Michael and Johnson, T. A. and Fukushima, Yoshimitsu and Dr, Macer and Cn, Rotimi and Ajayi, Ike and Ca, Adebamowo and Aniagwu, Toyin and Adebamowo, C. A. and Cd, Royal and Dixon, Missy and Kent, Alastair and Kato, Kazuto and Leppert, Mark F. and If, Adewole and Bm, Knoppers and Lin, Shin and Ew, Clayton and Adewole, I. F. and Knoppers, B. M. and Foster, M. W. and Clayton, E. W. and Gm, Weinstock and Bw, Birren and Birren, Bw W. and Fulton, Lucinda Ll and Burton, John and Cm, Clee and Carter, Np P. and Clee, Cm M. and Griffiths, Mark and Jones, Mc C. and Dl, Willey and Chen, Z. and Chen, Zhu and Han, Hua and Kang, Le and Godbout, Martin and Jc, Wallenburg and L'Archevêque, Paul and Bellemare, Guy and An, Daochang and Fu, Hongbo and Li, Qing and Holden, Al L. and Brooks, Ld D. and Al, Holden and Ld, Brooks and Guyer, Mark S. and Je, McEwen and Jl, Peterson and Lf, Zacharia and Collins, Fs S. and Fs, Collins and Kennedy, Karen and Jamieson, Ruth},
  doi = {10.1038/nature06250},
  month = {oct},
  title = {Genome-wide detection and characterization of positive selection in human populations},
  url = {http://www.nature.com/articles/nature06250.pdf},
  year = {2007}
}

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

Journal article published in 2007 by Pc Sabeti, Pi de Bakker, Patrick Varilly, Laura Ll Stuve, Fuli Yu, Huanming Yang, C. Zeng, T. D. Willis, Leal Sm, Willis Td, Jun Yu, McCarroll Sa, Xiaohui Xie, Bo Zhang, Qingrun Zhang and other authors. Pc Sabeti, Pi de Bakker, Patrick Varilly, Laura Ll Stuve, Fuli Yu, Huanming Yang, C. Zeng, T. D. Willis, Leal Sm, Willis Td, Jun Yu, McCarroll Sa, Xiaohui Xie, Bo Zhang, Qingrun Zhang, H. Zhao, Hongbin Zhao, Jun Zhou, Schaffner Sf, Xiaoli Tang, W. Wang, Jian Wang, Wei Wang, Gabriel Sb, L. Ziaugra, Zhijian Yao, Onofrio Rc, Song Yq, Jessica Roy, Erich Stahl, Ellen Winchester, Xiaoyan Xiong, Y. Wang, Liang Xu, Yan Shen, Hong Xue, Q. S. You, Yi Wang, Ying Wang, Chretien Yr, Yayun Shen, Tsui Sk, Weiwei Sun, Haifeng Wang, Pardis C. Sabeti, David A. Wheeler, J. Tze Fei Wong, Gibbs Ra, M. M. Y. Waye, S. K. W. Tsui, Qin Zs, Murray Ss, J. T.-F. Wong, Changqing Zeng, Stephen F. Schaffner, Hui Zhao, Stéphanie Roumy, Hudson Tj, Clémentine Sallée, Kwok Py, Andrei Verner, Miller Rd, Patricia Taillon-Miller, Ming Xiao, Tam Pk, Liuda Ziaugra, L.-C. Tsui, You Qiang Song, P. K. H. Tam, Akihiro Sekine, Toshihiro Tanaka

, T. Tsunoda, Don Powell, Pamela Whittaker, B. E. Stranger, Alkes Price, P. Varilly, Shaun Purcell, Lf F. Zacharia, Richa Saxena, Houcan Zhang, Daniel J. Richter, Tatsuhiko Tsunoda, P. C. Sham, L. D. Stein, A. Smith, G. A. Thorisson, Mk K. Tello-Ruiz, Albert Vernon Smith

, Imtaz Yakub, Z. S. Qin, D. J. Thomas, Chris Spencer, Matthew Stephens, Johnson Ta, B. S. Weir, Andrew Skol, Sherry St, S. T. Sherry, Eiko Suda, C. N. Rotimi, Renzong Qiu, C. D. M. Royal, Jessica Watkin, Erica Sodergren, Wilson Rk, G. M. Weinstock, Rk K. Wilson, Jane Rogers, Plumb Rw, Rw W. Plumb, Sims Sk, Mt T. Ross, Sk K. Sims, Dl L. Willey, Jc C. Wallenburg, Z. Wang, Koji Saeki, Hongguang Wang, Zhen Wang, Renwu Wang, Vo Wang, Vivian Ota Wang, Michael Shi, Jack Spiegel, L. M. Sung, John Stewart, Jason Lohmueller, Stuve Ll, Shiran Pasternak, Wei Lin, Siqi Liu, Hao Pan, Jamie Moore, Huy Nguyen, Melissa Parkin, Yangfan Liu, S. A. McCarroll, Waye Mm, Galver Lm, Chee Ms, Sarah Ss Murray, A. R. Oliphant, Alexandre Montpetit, Phillips Ms, J.-F. Olivier, Robert C. Onofrio, Ludmila Pawlikowska, R. D. Miller, William Mak, Yusuke Nakamura, Takashi Morizono, Atsushi Nagashima, Yozo Ohnishi, Steven A. McCarroll, Jonathan Morrison, Daly Mj, Julian Maller

, Nick Patterson, Itsik Pe'er, Sham Pc, Itsik Pe’er, Tello Ruiz Mk, Chen Pe, Gilean McVean, H. M. Munro, Jonathan Marchini, Simon Myers, Cardon Lr, Michael S. Phillips

, A. P. Morris, J. C. Mullikin, Ichiro Matsuda, D. R. MacEr, Marshall Pa, Chibuzor Nkwodimmah, Leppert Mf, Andy Peiffer, P. A. Marshall, Norio Niikawa, Foster Mw, Donna Muzny, Lynne Nazareth, Carter Np, Fulton Ll, Jones Mc, Kirsten McLay, Ross Mt, Je E. McEwen, Guyer Ms, Vivian Ota Wang, J. L. Peterson, Sung Lm, Others, Ben Fry, K. A. Frazer, D. G. Ballinger, D. R. Cox, D. A. Hinds, Cox Dr, S. M. Leal, Andrew Boudreau, John W. Belmont

, Elizabeth Hostetter, Paul Hardenbol, Chris Cotsapas

, Byrne Eh, Wheeler Da, Yang Gao, Haoran Hu, Weitao Hu, Chaohua Li, Lander Es, Rachel Barry, Rachelle Gaudet

, Brendan Blumenstiel, Amy Camargo, Matthew Defelice, Maura Faggart, Mary Goyette, Supriya Gupta, Frazer Ka, Ballinger Dg, Elizabeth H. Byrne, Wei Huang, Xun Chu, Yungang He, Richard A. Gibbs, Li Jin, Hinds Da, D. Altshuler, Wong Jt, Fan Jb, Belmont Jw, Oliphant Ar, L. M. Galver, Kevin Gunderson, J.-B. Fan, Mark S. Chee, Olivier Jf, Fanny Chagnon, Eric S. Lander, Vincent Ferretti, Stacey B. Gabriel, Martin Leboeuf, International HapMap Consortium, David Altshuler, Koboldt Dc, Dongmei Cai, T. J. Hudson, P.-Y. Kwok, Tsui Lc, D. C. Koboldt, Takahisa Kawaguchi, Takuya Kitamoto, Bird Cp, Panos Deloukas

, Marcos Delgado, Dermitzakis Et, Rhian Gwilliam, Sarah Hunt

, C. P. Bird, Stranger Be, E. T. Dermitzakis, Bentley Dr, Jeff Barrett, D. R. Bentley, Mark J. Daly, P. I. W. De Bakker, Richter Dj, Y. R. Chretien, Stein Ld, Lalitha Krishnan, Smith Av, Thorisson Ga, Aravinda Chakravarti, Cutler Dj, P. E. Chen, Kashuk Cs, Thomas Dj, Abecasis Gr, Weihua Guan, D. J. Cutler, Yun Li, C. S. Kashuk, Munro Hm, G. R. Abecasis, Adam Auton, Leonardo Bottolo, Niall Cardin, Susana Eyheramendy, Colin Freeman, Peter Donnelly, Geraldine Clarke, Evans Dm, Morris Ap, L. R. Cardon, Weir Bs, D. M. Evans, Mullikin Jc, Michael Feolo, T. A. Johnson, Yoshimitsu Fukushima, Macer Dr, Rotimi Cn, Ike Ajayi, Adebamowo Ca, Toyin Aniagwu, C. A. Adebamowo, Royal Cd, Missy Dixon, Alastair Kent, Kazuto Kato, Mark F. Leppert, Adewole If, Knoppers Bm, Shin Lin

, Clayton Ew, I. F. Adewole, B. M. Knoppers, M. W. Foster, E. W. Clayton, Weinstock Gm, Birren Bw, Bw W. Birren, Lucinda Ll Fulton, John Burton, Clee Cm, Np P. Carter, Cm M. Clee, Mark Griffiths, Mc C. Jones, Willey Dl, Z. Chen, Zhu Chen, Hua Han, Le Kang, Martin Godbout, Wallenburg Jc, Paul L'Archevêque, Guy Bellemare, Daochang An, Hongbo Fu, Qing Li, Al L. Holden, Ld D. Brooks, Holden Al, Brooks Ld, Mark S. Guyer, McEwen Je, Peterson Jl, Zacharia Lf, Fs S. Collins, Collins Fs, Karen Kennedy, Ruth Jamieson

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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)1. We used ‘long-range haplotype’ methods, which were developed to identify alleles segregating in a population that have undergone recent selection2, 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 virus3, in West Africa; SLC24A5 and SLC45A2, both involved in skin pigmentation4,5, in Europe; and EDAR and EDA2R, both involved in development of hair follicles6, in Asia.

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

Abstract