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6 results on '"Sabeti, P.C."'

1. Positive natural selection in the human lineage

Author

Sabeti, P.C., Schaffner, S.F., Fry, B., Lohmueller, J., Varily, P., Shamovsky, O., Palma, A., Mikkelsen, T.S., Altshuler, D., and Lander, E.S.

Subjects
Human beings -- Research, Human beings -- Natural history, Human beings -- Analysis, Man -- Research, Man -- Natural history, Man -- Analysis, Natural selection -- Research, Natural selection -- Analysis, Human ecology
Published
2006

2. Genome sequencing reveals Zika virus diversity and spread in the Americas

Author

Metsky, Hayden C, Matranga, Christian B, Wohl, Shirlee, Schaffner, Stephen F., Freije, Catherine A, Winnicki, Sarah, West, Kendra, Qu, J, Baniecki, Mary Lynn, Gladden-Young, Adrianne, Lin, Aaron E., Christopher, Tomkins-Tinch, Ye, S.H, Park, Daniel J, Luo, Cynthia, Barnes, Kayla G, Shah, R.R., Chak, Bridget, Barbosa-Lima, G., Delatorre, E., Vieira, Y.R., Paul, Lauren M, Tan, Amanda L, Barcellona, Carolyn M, Porcelli, Mario C, Vasquez, Chalmers, Cannons, Andrew C, Cone, Marshall R, Hogan, Kelly N, Kopp IV, Edgar W, Anzinger, J.J., Garcia, K.F., Parhap, L.A., Gelvez Ramirez, R.M., Montoya, Miranda, Rojas, D.P., Brown, C.M., Hennigan, S., Sabina, B., Scotland, S., Gangavarapu, K., Grubaugh, N.D., Oliveira, G., Robles-Sikisaka, R., Rambaut, Andrew, Gehrke, L., Smole, S., Halloran, M.E., Villar Centeno, L.A., Mattar, S., Lorenzana, I., Cerbino-Neto, J., Valim, C., Degrave, W., Bozza, P.T., Souza, T.M.L., Bosch, I., Yozwiak, N.L., MacInnis, B.L., and Sabeti, P.C.

Abstract

Despite great attention given to the recent Zika virus (ZIKV) epidemic in the Americas and its link to birth defects1,2, much remains unknown about ZIKV disease epidemiology and ZIKV evolution, in part due to a lack of genomic data. We applied multiple sequencing approaches to generate 110 ZIKV genomes from clinical and mosquito samples from 10 countries and territories, greatly expanding the observed viral genetic diversity from this outbreak. We analyzed the timing and patterns of introductions into distinct geographic regions; our phylogenetic evidence suggests rapid expansion of the outbreak in Brazil and multiple introductions of outbreak strains into Puerto Rico, Honduras, Colombia, other Caribbean islands, and the continental US. We find that ZIKV circulated undetected in multiple regions for many months before the first locally transmitted cases were confirmed, highlighting the importance of viral surveillance. We identify mutations with possible functional implications for ZIKV biology and pathogenesis, as well as those potentially relevant to the effectiveness of diagnostic tests.

Published
2017
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3. Virus genomes reveal factors that spread and sustained the Ebola epidemic

Author

Dudas, G. (Gytis), Carvalho, L.M. (Luiz Max), Bedford, T. (Trevor), Tatem, A.J. (Andrew J.), Baele, G. (Guy), Faria, R. (Rui), Park, D.J. (Daniel J.), Ladner, J.T. (Jason T.), Arias, A., Asogun, D. (Danny), Bielejec, F. (Filip), Caddy, S.L., Cotten, M. (Matthew), D'Ambrozio, J. (Jonathan), Dellicour, S. (Simon), Di Caro, A. (Antonino), Diclaro, J.W. (Joseph W.), Duraffour, S. (Sophie), Elmore, M.J. (Michael J.), Fakoli, L.S. (Lawrence S.), Faye, O. (Ousmane), Gilbert, M.L. (Merle L.), Gevao, S.M. (Sahr M.), Gire, S. (Stephen), Gladden-Young, A. (Adrianne), Gnirke, A. (Andreas), Goba, A. (Augustine), Grant, D.S. (Donald S.), Haagmans, B.L. (Bart), Hiscox, J.A. (Julian A.), Jah, U., Kugelman, J.R. (Jeffrey R.), Liu, D. (Di), Lu, J. (Jia), Malboeuf, C.M. (Christine M.), Mate, S. (Suzanne), Matthews, D.A. (David A.), Matranga, C.B. (Christian B.), Meredith, L.W. (Luke W.), Qu, J. (James), Quick, J. (Joshua), Pas, S.D. (Suzan), Phan, M.V.T. (My V. T.), Pollakis, G. (G.), Reusken, C.B.E.M. (Chantal), Sanchez-Lockhart, M. (Mariano), Schaffner, S.F. (Stephen F.), Schieffelin, J.S. (John S.), Sealfon, R.S. (Rachel S.), Simon-Loriere, E. (Etienne), Smits, S.L. (Saskia), Stoecker, K. (Kilian), Thorne, L. (Lucy), Tobin, E.A. (Ekaete Alice), Vandi, M.A. (Mohamed A.), Watson, S.J. (Simon J.), West, K. (Kendra), Whitmer, S. (Shannon), Wiley, M.R. (Michael R.), Winnicki, S.M. (Sarah M.), Wohl, S. (Shirlee), Wölfel, R. (Roman), Yozwiak, N.L. (Nathan L.), Andersen, K.G. (Kristian G.), Blyden, S.O. (Sylvia O.), Bolay, F. (Fatorma), Carroll, M.W. (Miles W.), Dahn, B. (Bernice), Diallo, B. (Boubacar), Formenty, P. (Pierre), Fraser, C. (Christophe), Gao, G.F. (George F.), Garry, R.F. (Robert F.), Goodfellow, I. (Ian), Günther, S. (Stephan), Happi, C.T. (Christian T.), Holmes, E.C. (Edward C.), Kargbo, B. (Brima), Keïta, S. (Sakoba), Kellam, P. (Paul), Koopmans D.V.M., M.P.G. (Marion), Kuhn, J.H. (Jens H.), Loman, N.J. (Nicholas J.), Magassouba, N. (N'Faly), Naidoo, D. (Dhamari), Nichol, S.T. (Stuart T.), Nyenswah, T. (Tolbert), Palacios, G. (Gustavo), Pybus, O. (Oliver), Sabeti, P.C. (Pardis C.), Sall, A. (Amadou), Ströher, U. (Ute), Wurie, I., Suchard, M.A. (Marc), Lemey, P. (Philippe), Rambaut, A. (Andrew), Dudas, G. (Gytis), Carvalho, L.M. (Luiz Max), Bedford, T. (Trevor), Tatem, A.J. (Andrew J.), Baele, G. (Guy), Faria, R. (Rui), Park, D.J. (Daniel J.), Ladner, J.T. (Jason T.), Arias, A., Asogun, D. (Danny), Bielejec, F. (Filip), Caddy, S.L., Cotten, M. (Matthew), D'Ambrozio, J. (Jonathan), Dellicour, S. (Simon), Di Caro, A. (Antonino), Diclaro, J.W. (Joseph W.), Duraffour, S. (Sophie), Elmore, M.J. (Michael J.), Fakoli, L.S. (Lawrence S.), Faye, O. (Ousmane), Gilbert, M.L. (Merle L.), Gevao, S.M. (Sahr M.), Gire, S. (Stephen), Gladden-Young, A. (Adrianne), Gnirke, A. (Andreas), Goba, A. (Augustine), Grant, D.S. (Donald S.), Haagmans, B.L. (Bart), Hiscox, J.A. (Julian A.), Jah, U., Kugelman, J.R. (Jeffrey R.), Liu, D. (Di), Lu, J. (Jia), Malboeuf, C.M. (Christine M.), Mate, S. (Suzanne), Matthews, D.A. (David A.), Matranga, C.B. (Christian B.), Meredith, L.W. (Luke W.), Qu, J. (James), Quick, J. (Joshua), Pas, S.D. (Suzan), Phan, M.V.T. (My V. T.), Pollakis, G. (G.), Reusken, C.B.E.M. (Chantal), Sanchez-Lockhart, M. (Mariano), Schaffner, S.F. (Stephen F.), Schieffelin, J.S. (John S.), Sealfon, R.S. (Rachel S.), Simon-Loriere, E. (Etienne), Smits, S.L. (Saskia), Stoecker, K. (Kilian), Thorne, L. (Lucy), Tobin, E.A. (Ekaete Alice), Vandi, M.A. (Mohamed A.), Watson, S.J. (Simon J.), West, K. (Kendra), Whitmer, S. (Shannon), Wiley, M.R. (Michael R.), Winnicki, S.M. (Sarah M.), Wohl, S. (Shirlee), Wölfel, R. (Roman), Yozwiak, N.L. (Nathan L.), Andersen, K.G. (Kristian G.), Blyden, S.O. (Sylvia O.), Bolay, F. (Fatorma), Carroll, M.W. (Miles W.), Dahn, B. (Bernice), Diallo, B. (Boubacar), Formenty, P. (Pierre), Fraser, C. (Christophe), Gao, G.F. (George F.), Garry, R.F. (Robert F.), Goodfellow, I. (Ian), Günther, S. (Stephan), Happi, C.T. (Christian T.), Holmes, E.C. (Edward C.), Kargbo, B. (Brima), Keïta, S. (Sakoba), Kellam, P. (Paul), Koopmans D.V.M., M.P.G. (Marion), Kuhn, J.H. (Jens H.), Loman, N.J. (Nicholas J.), Magassouba, N. (N'Faly), Naidoo, D. (Dhamari), Nichol, S.T. (Stuart T.), Nyenswah, T. (Tolbert), Palacios, G. (Gustavo), Pybus, O. (Oliver), Sabeti, P.C. (Pardis C.), Sall, A. (Amadou), Ströher, U. (Ute), Wurie, I., Suchard, M.A. (Marc), Lemey, P. (Philippe), and Rambaut, A. (Andrew)

Abstract

The 2013-2016 West African epidemic caused by the Ebola virus was of unprecedented magnitude, duration and impact. Here we reconstruct the dispersal, proliferation and decline of Ebola virus throughout the region by analysing 1,610 Ebola virus genomes, which represent over 5% of the known cases. We test the association of geography, climate and demography with viral movement among administrative regions, inferring a classic 'gravity' model, with intense dispersal between larger and closer populations. Despite attenuation of international dispersal after border closures, cross-border transmission had already sown the seeds for an international epidemic, rendering these measures ineffective at curbing the epidemic. We address why the epidemic did not spread into neighbouring countries, showing that these countries were susceptible to substantial outbreaks but at lower risk of introductions. Finally, we reveal that this large epidemic was a heterogeneous and spatially dissociated collection of transmission clusters of varying size, duration and connectivity. These insights will help to inform interventions in future epidemics.

Published
2017
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4. Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

Author

Delaneau O., Marchini J., McVeanh G.A., Donnelly P., Lunter G., Marchini J.L., Myers, S., Gupta-Hinch, A., Iqbal, Z., Mathieson I., Rimmer, A., Xifara, D.K., Kerasidou, A., Churchhouse, C., Altshuler, D.M., Gabriel, S.B., Lander, E.S., Gupta, N., Daly, M.J., DePristo, M.A., Banks, E., Bhatia G., Carneiro, M.O., Del Angel G., Genovese G., Handsaker, R.E., Hartl, C., McCarroll, S.A., Nemesh J.C., Poplin, R.E., Schaffner, S.F., Shakir, K., Sabeti P.C., Grossman, S.R., Tabrizi, S., Tariyal, R., Li H., Reich, D., Durbin, R.M., Hurles, M.E., Balasubramaniam, S., Burton J., Danecek P., Keane, T.M., Kolb-Kokocinski, A., McCarthy, S., Stalker J., Quail, M., Ayub Q., Chen, Y., Coffey, A.J., Colonna V., Huang, N., Jostins L., Scally, A., Walter, K., Xue, Y., Zhang, Y., Blackburne, B., Lindsay, S.J., Ning, Z., Frankish, A., Harrow J., Chris, T.-S., Abecasis G.R., Kang H.M., Anderson P., Blackwell, T., Busonero F., Fuchsberger, C., Jun G., Maschio, A., Porcu, E., Sidore, C., Tan, A., Trost, M.K., Bentley, D.R., Grocock, R., Humphray, S., James, T., Kingsbury, Z., Bauer, M., Cheetham, R.K., Cox, T., Eberle, M., Murray L., Shaw, R., Chakravarti, A., Clark, A.G., Keinan, A., Rodriguez-Flores J.L., De LaVega F.M., Degenhardt J., Eichler, E.E., Flicek P., Clarke L., Leinonen, R., Smith, R.E., Zheng-Bradley X., Beal, K., Cunningham F., Herrero J., McLaren W.M., Ritchie G.R.S., Barker J., Kelman G., Kulesha, E., Radhakrishnan, R., Roa, A., Smirnov, D., Streeter I., Toneva I., Gibbs, R.A., Dinh H., Kovar, C., Lee, S., Lewis L., Muzny, D., Reid J., Wang, M., Yu F., Bainbridge, M., Challis, D., Evani, U.S., Lu J., Nagaswamy, U., Sabo, A., Wang, Y., Yu J., Fowler G., Hale W., Kalra, D., Green, E.D., Knoppers, B.M., Korbel J.O., Rausch, T., Sttz, A.M., Lee, C., Griffin L., Hsieh, C.-H., Mills, R.E., Von Grotthuss, M., Zhang, C., Shi X., Lehrach H., Sudbrak, R., Amstislavskiy V.S., Lienhard, M., Mertes F., Sultan, M., Timmermann, B., Yaspo, M.L., Herwig, S.R., Mardis, E.R., Wilson, R.K., Fulton L., Fulton, R., Weinstock G.M., Chinwalla, A., Ding L., Dooling, D., Koboldt, D.C., McLellan, M.D., Wallis J.W., Wendl, M.C., Zhang Q., Marth G.T., Garrison, E.P., Kural, D., Lee W.-P., Leong W.F., Ward, A.N., Wu J., Zhang, M., Nickerson, D.A., Alkan, C., Hormozdiari F., Ko, A., Sudmant P.H., Schmidt J.P., Davies, C.J., Gollub J., Webster, T., Wong, B., Zhan, Y., Sherry, S.T., Xiao, C., Church, D., Ananiev V., Belaia, Z., Beloslyudtsev, D., Bouk, N., Chen, C., Cohen, R., Cook, C., Garner J., Hefferon, T., Kimelman, M., Liu, C., Lopez J., Meric P., Ostapchuk, Y., Phan L., Ponomarov, S., Schneider V., Shekhtman, E., Sirotkin, K., Slotta, D., Zhang H., Wang J., Fang X., Guo X., Jian, M., Jiang H., Jin X., Li G., Li J., Li, Y., Liu X., Lu, Y., Ma X., Tai, S., Tang, M., Wang, B., Wang G., Wu H., Wu, R., Yin, Y., Zhang W., Zhao J., Zhao, M., Zheng X., Lachlan H., Fang L., Li Q., Li, Z., Lin H., Liu, B., Luo, R., Shao H., Xie, Y., Ye, C., Yu, C., Zheng H., Zhu H., Cai H., Cao H., Su, Y., Tian, Z., Yang H., Yang L., Zhu J., Cai, Z., Albrecht, M.W., Borodina, T.A., Auton, A., Yoon, S.C., Lihm J., Makarov V., Jin H., Kim W., Kim, K.C., Gottipati, S., Jones, D., Cooper, D.N., Ball, E.V., Stenson P.D., Barnes, B., Kahn, S., Ye, K., Batzer, M.A., Konkel, M.K., Walker J.A., MacArthur, D.G., Lek, M., Shriver, M.D., Bustamante, C.D., Gravel, S., Kenny, E.E., Kidd J.M., Lacroute P., Maples, B.K., Moreno-Estrada, A., Zakharia F., Henn, B., Sandoval, K., Byrnes J.K., Halperin, E., Baran, Y., Craig, D.W., Christoforides, A., Izatt, T., Kurdoglu, A.A., Sinari, S.A., Homer, N., Squire, K., Sebat J., Bafna V., Burchard, E.G., Hernandez, R.D., Gignoux, C.R., Haussler, D., Katzman, S.J., Kent W.J., Howie, B., Ruiz-Linares, A., Dermitzakis, E.T., Lappalainen, T., Devine, S.E., Maroo, A., Tallon L.J., Rosenfeld J.A., Michelson L.P., Angius, A., Cucca F., Sanna, S., Bigham, A., Jones, C., Reinier F., Lyons, R., Schlessinger, D., Awadalla P., Hodgkinson, A., Oleksyk, T.K., Martinez-Cruzado J.C., Fu, Y., Xiong, M., Jorde L., Witherspoon, D., Xing J., Browning, B.L., Hajirasouliha I., Chen, K., Albers, C.A., Gerstein, M.B., Abyzov, A., Chen J., Habegger L., Harmanci, A.O., Mu X.J., Sisu, C., Balasubramanian, S., Jin, M., Khurana, E., Clarke, D., Michaelson J.J., OSullivan, C., Barnes, K.C., Gharani, N., Toji L.H., Gerry, N., Kaye J.S., Kent, A., Mathias, R., Ossorio P.N., Parker, M., Rotimi, C.N., Royal, C.D., Tishkoff, S., Via, M., Bodmer W., Bedoya G., Yang G., You, C.J., Garcia-Montero, A., Orfao, A., Dutil J., Brooks L.D., Felsenfeld, A.L., McEwen J.E., Clemm, N.C., Guyer, M.S., Peterson J.L., Duncanson, A., Dunn, M., Peltonen L., and 1000 Genomes Project Consortium

Subjects
haplotype, genetic association, genotype, General Physics and Astronomy, Genome-wide association study, genetic analysis, gene sequence, Biology, gene frequency, Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, Article, polymorphism, Gene Frequency, single nucleotide polymorphism, Humans, chromosome, human, 1000 Genomes Project, indel mutation, genome, Alleles, Genetic association, Genetics, Whole genome sequencing, Multidisciplinary, accuracy, Genome, Human, Haplotype, allele, article, reference database, General Chemistry, Microarray Analysis, chromosome 20, Haplotypes, Human genome, microarray analysis, Imputation (genetics), Algorithms, SNP array, Genome-Wide Association Study
Abstract

A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved.

Published
2014
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6. Genome-wide detection and characterization of positive selection in human populations

Author

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., Rotimi, C.N., Adebamowo, C.A., Ajayi, I., Aniagwu, T., Marshall, P.A., Nkwodimmah, C., Royal, C.D.M., Leppert, M.F., Dixon, M., Boudreau, A., Taillon-Miller, P., Peiffer, A., Qiu, R., Kent, A., Kato, K., Niikawa, N., Adewole, I.F., Knoppers, B.M., Foster, M.W., Clayton, E.W., Watkin, J., Xiao, M., Hardenbol, P., Muzny, D., Nazareth, L., Sodergren, E., Weinstock, G.M., Yakub, I., Birren, B.W., Wilson, R.K., Fulton, L.L., Rogers, J., Tsui, L.C., Burton, J., Leal, S.M., Carter, N.P., Clee, C.M., Griffiths, M., Jones, M.C., McLay, K., Plumb, R.W., Ross, M.T., Sims, S.K., Mak, W., Willey, D.L., Chen, Z., Pasternak, S., Han, H., Kang, L., Godbout, M., Wallenburg, J.C., L'Archevêque, P., Bellemare, G., Saeki, K., You, Q.S., Wang, H., An, D., Fu, H., Wheeler, D.A., Li, Q., Wang, Z., Wang, R., Holden, A.L., Brooks, L.D., McEwen, J.E., Tam, P.K.H., Guyer, M.S., Wang, V.O., Peterson, J.L., Shi, M., Willis, T.D., Spiegel, J., Sung, L.M., Zacharia, L.F., Collins, F.S., Kennedy, K., Nakamura, Y., Jamieson, R., Stewart, J., Yu, F., Yang, H., Zeng, C., Gao, Y., Hu, H., Hu, W., Li, C., Lin, W., Kawaguchi, T., Liu, S., Pan, H., Tang, X., Wang, J., Wang, W., Yu, J., Zhang, B., Zhang, Q., Zhao, H., Kitamoto, T., Zhou, J., Gabriel, S.B., Barry, R., Blumenstiel, B., Camargo, A., Defelice, M., Faggart, M., Goyette, M., Gupta, S., Moore, J., Morizono, T., Nguyen, H., Onofrio, R.C., Parkin, M., Roy, J., Stahl, E., Winchester, E., Ziaugra, L., Altshuler, D., Shen, Y., Yao, Z., Lander, E.S., Huang, W., Chu, X., He, Y., Jin, L., Liu, Y., Sun, W., Wang, Y., Nagashima, A., Xiong, X., Xu, L., Waye, M.M.Y., Tsui, S.K.W., Xue, H., Wong, J.T.F., Galver, L.M., Fan, J.B., Gunderson, K., Murray, S.S., Ohnishi, Y., Oliphant, A.R., Chee, M.S., Montpetit, A., Chagnon, F., Ferretti, V., Leboeuf, M., Olivier, J.F., Phillips, M.S., Roumy, S., Sallée, C., Sekine, A., Verner, A., Hudson, T.J., Kwok, P.Y., Cai, D., Koboldt, D.C., Miller, R.D., Pawlikowska, L., Tanaka, T., Tsunoda, T., Deloukas, P., Bird, C.P., Delgado, M., Dermitzakis, E.T., Gwilliam, R., Frazer, K.A., Hunt, S., Morrison, J., Powell, D., Stranger, B.E., Whittaker, P., Bentley, D.R., Daly, M.J., De Bakker, P.I.W., Barrett, J., Chretien, Y.R., Ballinger, D.G., Maller, J., McCarroll, S., Patterson, N., Pe'Er, I., Price, A., Purcell, S., Richter, D.J., Saxena, R., Sham, P.C., Stein, L.D., Cox, D.R., Krishnan, L., Smith, A.V., Tello-Ruiz, M.K., Thorisson, G.A., Chakravarti, A., Chen, P.E., Cutler, D.J., Kashuk, C.S., Lin, S., Abecasis, G.R., Hinds, D.A., Guan, W., Li, Y., Munro, H.M., Qin, Z.S., Thomas, D.J., McVean, G., Auton, A., Bottolo, L., Cardin, N., Eyheramendy, S., Stuve, L.L., Freeman, C., Marchini, J., Myers, S., Spencer, C., Stephens, M., Donnelly, P., Cardon, L.R., Clarke, G., Evans, D.M., Morris, A.P., Gibbs, R.A., Weir, B.S., Johnson, T.A., Mullikin, J.C., Sherry, S.T., Feolo, M., Skol, A., Zhang, H., Matsuda, I., Fukushima, Y., MacEr, D.R., Belmont, J.W., Suda, E., 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., Rotimi, C.N., Adebamowo, C.A., Ajayi, I., Aniagwu, T., Marshall, P.A., Nkwodimmah, C., Royal, C.D.M., Leppert, M.F., Dixon, M., Boudreau, A., Taillon-Miller, P., Peiffer, A., Qiu, R., Kent, A., Kato, K., Niikawa, N., Adewole, I.F., Knoppers, B.M., Foster, M.W., Clayton, E.W., Watkin, J., Xiao, M., Hardenbol, P., Muzny, D., Nazareth, L., Sodergren, E., Weinstock, G.M., Yakub, I., Birren, B.W., Wilson, R.K., Fulton, L.L., Rogers, J., Tsui, L.C., Burton, J., Leal, S.M., Carter, N.P., Clee, C.M., Griffiths, M., Jones, M.C., McLay, K., Plumb, R.W., Ross, M.T., Sims, S.K., Mak, W., Willey, D.L., Chen, Z., Pasternak, S., Han, H., Kang, L., Godbout, M., Wallenburg, J.C., L'Archevêque, P., Bellemare, G., Saeki, K., You, Q.S., Wang, H., An, D., Fu, H., Wheeler, D.A., Li, Q., Wang, Z., Wang, R., Holden, A.L., Brooks, L.D., McEwen, J.E., Tam, P.K.H., Guyer, M.S., Wang, V.O., Peterson, J.L., Shi, M., Willis, T.D., Spiegel, J., Sung, L.M., Zacharia, L.F., Collins, F.S., Kennedy, K., Nakamura, Y., Jamieson, R., Stewart, J., Yu, F., Yang, H., Zeng, C., Gao, Y., Hu, H., Hu, W., Li, C., Lin, W., Kawaguchi, T., Liu, S., Pan, H., Tang, X., Wang, J., Wang, W., Yu, J., Zhang, B., Zhang, Q., Zhao, H., Kitamoto, T., Zhou, J., Gabriel, S.B., Barry, R., Blumenstiel, B., Camargo, A., Defelice, M., Faggart, M., Goyette, M., Gupta, S., Moore, J., Morizono, T., Nguyen, H., Onofrio, R.C., Parkin, M., Roy, J., Stahl, E., Winchester, E., Ziaugra, L., Altshuler, D., Shen, Y., Yao, Z., Lander, E.S., Huang, W., Chu, X., He, Y., Jin, L., Liu, Y., Sun, W., Wang, Y., Nagashima, A., Xiong, X., Xu, L., Waye, M.M.Y., Tsui, S.K.W., Xue, H., Wong, J.T.F., Galver, L.M., Fan, J.B., Gunderson, K., Murray, S.S., Ohnishi, Y., Oliphant, A.R., Chee, M.S., Montpetit, A., 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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). 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. ©2007 Nature Publishing Group.

Published
2007

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