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Genome Biol. 2014 Jun 30;15(6):R88. doi: 10.1186/gb-2014-15-6-r88.

Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences.

Collaborators (688)

Altshuler DM, Durbin RM, Abecasis GR, Bentley DR, Chakravarti A, Clark AG, Donnelly P, Eichler EE, Flicek P, Gabriel SB, Gibbs RA, Green ED, Hurles ME, Knoppers BM, Korbel JO, Lander ES, Lee C, Lehrach H, Mardis ER, Marth GT, McVean GA, Nickerson DA, Schmidt JP, Sherry ST, Wang J, Wilson RK, Gibbs RA, Dinh H, Kovar C, Lee S, Lewis L, Muzny D, Reid J, Wang M, Wang J, Fang X, Guo X, Jian M, Jiang H, Jin X, Li G, Li J, Li Y, Li Z, Liu X, Lu Y, Ma X, Su Z, Tai S, Tang M, Wang B, Wang G, Wu H, Wu R, Yin Y, Zhang W, Zhao J, Zhao M, Zheng X, Zhou Y, Lander ES, Altshuler DM, Gabriel SB, Gupta N, Flicek P, Clarke L, Leinonen R, Smith RE, Zheng-Bradley X, Bentley DR, Grocock R, Humphray S, James T, Kingsbury Z, Lehrach H, Sudbrak R, Albrecht MW, Amstislavskiy VS, Borodina TA, Lienhard M, Mertes F, Sultan M, Timmermann B, Yaspo ML, Sherry ST, McVean GA, Mardis ER, Wilson RK, Fulton L, Fulton R, Weinstock GM, Durbin RM, Balasubramaniam S, Burton J, Danecek P, Keane TM, Kolb-Kokocinski A, McCarthy S, Stalker J, Quail M, Schmidt JP, Davies CJ, Gollub J, Webster T, Wong B, Zhan Y, Auton A, Gibbs RA, Yu F, Bainbridge M, Challis D, Evani US, Lu J, Muzny D, Nagaswamy U, Reid J, Sabo A, Wang Y, Yu J, Wang J, Coin LJ, Fang L, Guo X, Jin X, Li G, Li Q, Li Y, Li Z, Lin H, Liu B, Luo R, Qin N, Shao H, Wang B, Xie Y, Ye C, Yu C, Zhang F, Zheng H, Zhu H, Marth GT, Garrison EP, Kural D, Lee WP, Leong WF, Ward AN, Wu J, Zhang M, Lee C, Griffin L, Hsieh CH, Mills RE, Shi X, von Grotthuss M, Zhang C, Daly MJ, DePristo MA, Altshuler DM, Banks E, Bhatia G, Carneiro MO, del Angel G, Gabriel SB, Genovese G, Gupta N, Handsaker RE, Hartl C, Lander ES, McCarroll SA, Nemesh JC, Poplin RE, Schaffner SF, Shakir K, Yoon SC, Lihm J, Makarov V, Jin H, Kim W, Kim KC, Korbel JO, Rausch T, Flicek P, Beal K, Clarke L, Cunningham F, Herrero J, McLaren WM, Ritchie GR, Smith RE, Zheng-Bradley X, Clark AG, Gottipati S, Keinan A, Rodriguez-Flores JL, Sabeti PC, Grossman SR, Tabrizi S, Tariyal R, Cooper DN, Ball EV, Stenson PD, Bentley DR, Barnes B, Bauer M, Cheetham R, Cox T, Eberle M, Humphray S, Kahn S, Murray L, Peden J, Shaw R, Ye K, Batzer MA, Konkel MK, Walker JA, MacArthur DG, Lek M, Sudbrak R, Amstislavskiy VS, Herwig R, Shriver MD, Bustamante CD, Byrnes JK, De La Vega FM, Gravel S, Kenny EE, Kidd JM, Lacroute P, Maples BK, Moreno-Estrada A, Zakharia F, Halperin E, Baran Y, Craig DW, Christoforides A, Homer N, Izatt T, Kurdoglu AA, Sinari SA, Squire K, Sherry ST, Xiao C, Sebat J, Bafna V, Ye K, Burchard EG, Hernandez RD, Gignoux CR, Haussler D, Katzman SJ, Kent WJ, Howie B, Ruiz-Linares A, Dermitzakis ET, Lappalainen T, Devine SE, Liu X, Maroo A, Tallon LJ, Rosenfeld JA, Michelson LP, Anderson P, Angius A, Bigham A, Blackwell T, Busonero F, Cucca F, Fuchsberger C, Jones C, Li Y, Lyons R, Maschio A, Porcu E, Reinier F, Sanna S, Schlessinger D, Sidore C, Tan A, Trost MK, Awadalla P, Hodgkinson A, Lunter G, McVean GA, Marchini JL, Myers S, Churchhouse C, Delaneau O, Gupta-Hinch A, Iqbal Z, Mathieson I, Rimmer A, Xifara DK, Oleksyk TK, Fu Y, Liu X, Xiong M, Jorde L, Witherspoon D, Xing J, Browning BL, Alkan C, Hajirasouliha I, Hormozdiari F, Ko A, Sudmant PH, Mardis ER, Chen K, Chinwalla A, Ding L, Dooling D, Koboldt DC, McLellan MD, Wallis JW, Wendl MC, Zhang Q, Durbin RM, Hurles ME, Tyler-Smith C, Albers CA, Ayub Q, Balasubramaniam S, Chen Y, Coffey AJ, Colonna V, Danecek P, Huang N, Jostins L, Keane TM, Li H, McCarthy S, Scally A, Stalker J, Walter K, Xue Y, Zhang Y, Gerstein MB, Abyzov A, Balasubramanian S, Chen J, Clarke D, Fu Y, Habegger L, Harmanci AO, Jin M, Khurana E, Mu XJ, Sisu C, Li Y, Luo R, Zhu H, Lee C, Griffin L, Hsieh CH, Mills RE, Shi X, von Grotthuss M, Zhang C, Marth GT, Garrison EP, Kural D, Lee WP, Ward AN, Wu J, Zhang M, McCarroll SA, Altshuler DM, Banks E, del Angel G, Genovese G, Handsaker RE, Hartl C, Nemesh JC, Shakir K, Yoon SC, Lihm J, Makarov V, Degenhardt J, Flicek P, Clarke L, Smith RE, Zheng-Bradley X, Korbel JO, Rausch T, St├╝tz AM, Bentley DR, Barnes B, Cheetham R, Eberle M, Humphray S, Kahn S, Murray L, Shaw R, Ye K, Batzer MA, Konkel MK, Walker JA, Lacroute P, Craig DW, Homer N, Church D, Xiao C, Sebat J, Bafna V, Michaelson JJ, Ye K, Devine SE, Liu X, Maroo A, Tallon LJ, Lunter G, McVean GA, Iqbal Z, Witherspoon D, Xing J, Eichler EE, Alkan C, Hajirasouliha I, Hormozdiari F, Ko A, Sudmant PH, Chen K, Chinwalla A, Ding L, McLellan MD, Wallis JW, Hurles ME, Blackburne B, Li H, Lindsay SJ, Ning Z, Scally A, Walter K, Zhang Y, Gerstein MB, Abyzov A, Chen J, Clarke D, Khurana E, Mu XJ, Sisu C, Gibbs RA, Yu F, Bainbridge M, Challis D, Evani US, Kovar C, Lewis L, Lu J, Muzny D, Nagaswamy U, Reid J, Sabo A, Yu J, Guo X, Li Y, Wu R, Marth GT, Garrison EP, Leong WF, Ward AN, del Angel G, DePristo MA, Gabriel SB, Gupta N, Hartl C, Poplin RE, Clark AG, Rodriguez-Flores JL, Flicek P, Clarke L, Smith RE, Zheng-Bradley X, MacArthur DG, Bustamante CD, Gravel S, Craig DW, Christoforides A, Homer N, Izatt T, Sherry ST, Xiao C, Dermitzakis E, Abecasis GR, Kang HM, McVean GA, Mardis ER, Dooling D, Fulton L, Fulton R, Koboldt DC, Durbin RM, Balasubramaniam S, Keane TM, McCarthy S, Stalker J, Gerstein MB, Balasubramanian S, Habegger L, Garrison EP, Gibbs RA, Bainbridge M, Muzny D, Yu F, Yu J, del Angel G, Handsaker RE, Makarov V, Rodriguez-Flores JL, Jin H, Kim W, Kim KC, Flicek P, Beal K, Clarke L, Cunningham F, Herrero J, McLaren WM, Ritchie GR, Zheng-Bradley X, Tabrizi S, MacArthur DG, Lek M, Bustamante CD, De La Vega FM, Craig DW, Kurdoglu AA, Lappalainen T, Rosenfeld JA, Michelson LP, Awadalla P, Hodgkinson A, McVean GA, Chen K, Tyler-Smith C, Chen Y, Colonna V, Frankish A, Harrow J, Xue Y, Gerstein MB, Abyzov A, Balasubramanian S, Chen J, Clarke D, Fu Y, Harmanci AO, Jin M, Khurana E, Mu XJ, Sisu C, Gibbs RA, Kovar C, Kalra D, Hale W, Fowler G, Muzny D, Reid J, Wang J, Guo X, Li G, Li Y, Zheng X, Altshuler DM, Flicek P, Clarke L, Barker J, Kelman G, Kulesha E, Leinonen R, McLaren WM, Radhakrishnan R, Roa A, Smirnov D, Smith RE, Streeter I, Toneva I, Vaughan B, Zheng-Bradley X, Bentley DR, Cox T, Humphray S, Kahn S, Sudbrak R, Albrecht MW, Lienhard M, Craig DW, Izatt T, Kurdoglu AA, Sherry ST, Ananiev V, Belaia Z, Beloslyudtsev D, Bouk N, Chen C, Church D, Cohen R, Cook C, Garner J, Hefferon T, Kimelman M, Liu C, Lopez J, Meric P, O'Sullivan C, Ostapchuk Y, Ponomarov S, Schneider V, Shekhtman E, Sirotkin K, Slotta D, Xiao C, Zhang H, Haussler D, Abecasis GR, McVean GA, Alkan C, Ko A, Dooling D, Durbin RM, Balasubramaniam S, Keane TM, McCarthy S, Stalker J, Chakravarti A, Knoppers BM, Abecasis GR, Barnes KC, Beiswanger C, Burchard E, Bustamante CD, Cai H, Cao H, Durbin RM, Gharani N, Gibbs RA, Gignoux CR, Gravel S, Henn B, Jones D, Jorde L, Kaye JS, Keinan A, Kent A, Kerasidou A, Li Y, Mathias R, McVean G, Moreno-Estrada A, Ossorio PN, Parker M, Reich D, Rotimi CN, Royal CD, Sandoval K, Su Y, Sudbrak R, Tian Z, Timmermann B, Tishkoff S, Toji LH, Tyler-Smith C, Via M, Wang Y, Yang H, Yang L, Zhu J, Bodmer W, Bedoya G, Ruiz-Linares A, Ming CZ, Yang G, You CJ, Peltonen L, Garcia-Montero A, Orfao A, Dutil J, Martinez-Cruzado JC, Oleksyk TK, Brooks LD, Felsenfeld AL, McEwen JE, Clemm NC, Duncanson A, Dunn M, Green ED, Guyer MS, Peterson JL.

Abstract

BACKGROUND:

Population differentiation has proved to be effective for identifying loci under geographically localized positive selection, and has the potential to identify loci subject to balancing selection. We have previously investigated the pattern of genetic differentiation among human populations at 36.8 million genomic variants to identify sites in the genome showing high frequency differences. Here, we extend this dataset to include additional variants, survey sites with low levels of differentiation, and evaluate the extent to which highly differentiated sites are likely to result from selective or other processes.

RESULTS:

We demonstrate that while sites with low differentiation represent sampling effects rather than balancing selection, sites showing extremely high population differentiation are enriched for positive selection events and that one half may be the result of classic selective sweeps. Among these, we rediscover known examples, where we actually identify the established functional SNP, and discover novel examples including the genes ABCA12, CALD1 and ZNF804, which we speculate may be linked to adaptations in skin, calcium metabolism and defense, respectively.

CONCLUSIONS:

We identify known and many novel candidate regions for geographically restricted positive selection, and suggest several directions for further research.

PMID:
24980144
[PubMed - in process]
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