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Nature. 2012 Nov 1;491(7422):56-65. doi: 10.1038/nature11632.

An integrated map of genetic variation from 1,092 human genomes.

Collaborators (692)

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, Abecasis GR, Kang HM, Anderson P, Angius A, Bigham A, Blackwell T, Busonero F, Cucca F, Fuchsberger C, Jones C, Jun G, 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, Eichler EE, 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, Stütz 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, 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 ET, 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, Fowler G, Hale W, Kalra D, Kovar C, 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, Phan L, 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 EG, 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 GA, 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

By characterizing the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help to understand the genetic contribution to disease. Here we describe the genomes of 1,092 individuals from 14 populations, constructed using a combination of low-coverage whole-genome and exome sequencing. By developing methods to integrate information across several algorithms and diverse data sources, we provide a validated haplotype map of 38 million single nucleotide polymorphisms, 1.4 million short insertions and deletions, and more than 14,000 larger deletions. We show that individuals from different populations carry different profiles of rare and common variants, and that low-frequency variants show substantial geographic differentiation, which is further increased by the action of purifying selection. We show that evolutionary conservation and coding consequence are key determinants of the strength of purifying selection, that rare-variant load varies substantially across biological pathways, and that each individual contains hundreds of rare non-coding variants at conserved sites, such as motif-disrupting changes in transcription-factor-binding sites. This resource, which captures up to 98% of accessible single nucleotide polymorphisms at a frequency of 1% in related populations, enables analysis of common and low-frequency variants in individuals from diverse, including admixed, populations.

PMID:
23128226
[PubMed - indexed for MEDLINE]
PMCID:
PMC3498066
Free PMC Article

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