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Nature. 2010 Oct 28;467(7319):1061-73. doi: 10.1038/nature09534.

A map of human genome variation from population-scale sequencing.

Collaborators (544)

Altshuler D, Durbin RM, Abecasis GR, Bentley DR, Chakravarti A, Clark AG, Collins FS, De La Vega FM, Donnelly P, Egholm M, Flicek P, Gabriel SB, Gibbs RA, Knoppers BM, Lander ES, Lehrach H, Mardis ER, McVean GA, Nickerson DA, Peltonen L, Schafer AJ, Sherry ST, Wang J, Wilson R, Gibbs RA, Deiros D, Metzker M, Muzny D, Reid J, Wheeler D, Wang J, Li J, Jian M, Li G, Li R, Liang H, Tian G, Wang B, Wang J, Wang W, Yang H, Zhang X, Zheng H, Lander ES, Altshuler DL, Ambrogio L, Bloom T, Cibulskis K, Fennell TJ, Gabriel SB, Jaffe DB, Shefler E, Sougnez CL, Bentley DR, Gormley N, Humphray S, Kingsbury Z, Kokko-Gonzales P, Stone J, McKernan KJ, Costa GL, Ichikawa JK, Lee CC, Sudbrak R, Lehrach H, Borodina TA, Dahl A, Davydov AN, Marquardt P, Mertes F, Nietfeld W, Rosenstiel P, Schreiber S, Soldatov AV, Timmermann B, Tolzmann M, Egholm M, Affourtit J, Ashworth D, Attiya S, Bachorski M, Buglione E, Burke A, Caprio A, Celone C, Clark S, Conners D, Desany B, Gu L, Guccione L, Kao K, Kebbler J, Knowlton J, Labrecque M, McDade L, Mealmaker C, Minderman M, Nawrocki A, Niazi F, Pareja K, Ramenani R, Riches D, Song W, Turcotte C, Wang S, Mardis ER, Wilson RK, Dooling D, Fulton L, Fulton R, Weinstock G, Durbin RM, Burton J, Carter DM, Churcher C, Coffey A, Cox A, Palotie A, Quail M, Skelly T, Stalker J, Swerdlow HP, Turner D, De Witte A, Giles S, Gibbs RA, Wheeler D, Bainbridge M, Challis D, Sabo A, Yu F, Yu J, Wang J, Fang X, Guo X, Li R, Li Y, Luo R, Tai S, Wu H, Zheng H, Zheng X, Zhou Y, Li G, Wang J, Yang H, Marth GT, Garrison EP, Huang W, Indap A, Kural D, Lee WP, Leong WF, Quinlan AR, Stewart C, Stromberg MP, Ward AN, Wu J, Lee C, Mills RE, Shi X, Daly MJ, DePristo MA, Altshuler DL, Ball AD, Banks E, Bloom T, Browning BL, Cibulskis K, Fennell TJ, Garimella KV, Grossman SR, Handsaker RE, Hanna M, Hartl C, Jaffe DB, Kernytsky AM, Korn JM, Li H, Maguire JR, McCarroll SA, McKenna A, Nemesh JC, Philippakis AA, Poplin RE, Price A, Rivas MA, Sabeti PC, Schaffner SF, Shefler E, Shlyakhter IA, Cooper DN, Ball EV, Mort M, Phillips AD, Stenson PD, Sebat J, Makarov V, Ye K, Yoon SC, Bustamante CD, Clark AG, Boyko A, Degenhardt J, Gravel S, Gutenkunst RN, Kaganovich M, Keinan A, Lacroute P, Ma X, Reynolds A, Clarke L, Flicek P, Cunningham F, Herrero J, Keenen S, Kulesha E, Leinonen R, McLaren WM, Radhakrishnan R, Smith RE, Zalunin V, Zheng-Bradley X, Korbel JO, Stütz AM, Humphray S, Bauer M, Cheetham RK, Cox T, Eberle M, James T, Kahn S, Murray L, Chakravarti A, Ye K, De La Vega FM, Fu Y, Hyland FC, Manning JM, McLaughlin SF, Peckham HE, Sakarya O, Sun YA, Tsung EF, Batzer MA, Konkel MK, Walker JA, Sudbrak R, Albrecht MW, Amstislavskiy VS, Herwig R, Parkhomchuk DV, Sherry ST, Agarwala R, Khouri HM, Morgulis AO, Paschall JE, Phan LD, Rotmistrovsky KE, Sanders RD, Shumway MF, Xiao C, McVean GA, Auton A, Iqbal Z, Lunter G, Marchini JL, Moutsianas L, Myers S, Tumian A, Desany B, Knight J, Winer R, Craig DW, Beckstrom-Sternberg SM, Christoforides A, Kurdoglu AA, Pearson JV, Sinari SA, Tembe WD, Haussler D, Hinrichs AS, Katzman SJ, Kern A, Kuhn RM, Przeworski M, Hernandez RD, Howie B, Kelley JL, Melton SC, Abecasis GR, Li Y, Anderson P, Blackwell T, Chen W, Cookson WO, Ding J, Kang HM, Lathrop M, Liang L, Moffatt MF, Scheet P, Sidore C, Snyder M, Zhan X, Zöllner S, Awadalla P, Casals F, Idaghdour Y, Keebler J, Stone EA, Zilversmit M, Jorde L, Xing J, Eichler EE, Aksay G, Alkan C, Hajirasouliha I, Hormozdiari F, Kidd JM, Sahinalp SC, Sudmant PH, Mardis ER, Chen K, Chinwalla A, Ding L, Koboldt DC, McLellan MD, Dooling D, Weinstock G, Wallis JW, Wendl MC, Zhang Q, Durbin RM, Albers CA, Ayub Q, Balasubramaniam S, Barrett JC, Carter DM, Chen Y, Conrad DF, Danecek P, Dermitzakis ET, Hu M, Huang N, Hurles ME, Jin H, Jostins L, Keane TM, Le SQ, Lindsay S, Long Q, MacArthur DG, Montgomery SB, Parts L, Stalker J, Tyler-Smith C, Walter K, Zhang Y, Gerstein MB, Snyder M, Abyzov A, Balasubramanian S, Bjornson R, Du J, Grubert F, Habegger L, Haraksingh R, Jee J, Khurana E, Lam HY, Leng J, Mu XJ, Urban AE, Zhang Z, Li Y, Luo R, Marth GT, Garrison EP, Kural D, Quinlan AR, Stewart C, Stromberg MP, Ward AN, Wu J, Lee C, Mills RE, Shi X, McCarroll SA, Banks E, DePristo MA, Handsaker RE, Hartl C, Korn JM, Li H, Nemesh JC, Sebat J, Makarov V, Ye K, Yoon SC, Degenhardt J, Kaganovich M, Clarke L, Smith RE, Zheng-Bradley X, Korbel JO, Humphray S, Cheetham RK, Eberle M, Kahn S, Murray L, Ye K, De La Vega FM, Fu Y, Peckham HE, Sun YA, Batzer MA, Konkel MK, Walker JA, Xiao C, Iqbal Z, Desany B, Blackwell T, Snyder M, Xing J, Eichler EE, Aksay G, Alkan C, Hajirasouliha I, Hormozdiari F, Kidd JM, Chen K, Chinwalla A, Ding L, McLellan MD, Wallis JW, Hurles ME, Conrad DF, Walter K, Zhang Y, Gerstein MB, Snyder M, Abyzov A, Du J, Grubert F, Haraksingh R, Jee J, Khurana E, Lam HY, Leng J, Mu XJ, Urban AE, Zhang Z, Gibbs RA, Bainbridge M, Challis D, Coafra C, Dinh H, Kovar C, Lee S, Muzny D, Nazareth L, Reid J, Sabo A, Yu F, Yu J, Marth GT, Garrison EP, Indap A, Leong WF, Quinlan AR, Stewart C, Ward AN, Wu J, Cibulskis K, Fennell TJ, Gabriel SB, Garimella KV, Hartl C, Shefler E, Sougnez CL, Wilkinson J, Clark AG, Gravel S, Grubert F, Clarke L, Flicek P, Smith RE, Zheng-Bradley X, Sherry ST, Khouri HM, Paschall JE, Shumway MF, Xiao C, McVean GA, Katzman SJ, Abecasis GR, Mardis ER, Dooling D, Fulton L, Fulton R, Koboldt DC, Durbin RM, Balasubramaniam S, Coffey A, Keane TM, MacArthur DG, Palotie A, Scott C, Stalker J, Tyler-Smith C, Gerstein MB, Balasubramanian S, Chakravarti A, Knoppers BM, Abecasis GR, Bustamante CD, Gharani N, Gibbs RA, Jorde L, Kaye JS, Kent A, Li T, McGuire AL, McVean GA, Ossorio PN, Rotimi CN, Su Y, Toji LH, Tyler-Smith C, Brooks LD, Felsenfeld AL, McEwen JE, Abdallah A, Juenger CR, Clemm NC, Collins FS, Duncanson A, Green ED, Guyer MS, Peterson JL, Schafer AJ, Xue Y, Cartwright RA.

Erratum in

  • Nature. 2011 May 26;473(7348):544. Xue, Yali [added]; Cartwright, Reed A [added]; Altshuler, David L [corrected to Altshuler, David]; Kebbel, Andrew [corrected to Keebler, Jonathan]; Koko-Gonzales, Paula [corrected to Kokko-Gonzales, Paula]; Nickerson, Debbie A [corrected to Nickerson, Deborah A].

Abstract

The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype. Here we present results of the pilot phase of the project, designed to develop and compare different strategies for genome-wide sequencing with high-throughput platforms. We undertook three projects: low-coverage whole-genome sequencing of 179 individuals from four populations; high-coverage sequencing of two mother-father-child trios; and exon-targeted sequencing of 697 individuals from seven populations. We describe the location, allele frequency and local haplotype structure of approximately 15 million single nucleotide polymorphisms, 1 million short insertions and deletions, and 20,000 structural variants, most of which were previously undescribed. We show that, because we have catalogued the vast majority of common variation, over 95% of the currently accessible variants found in any individual are present in this data set. On average, each person is found to carry approximately 250 to 300 loss-of-function variants in annotated genes and 50 to 100 variants previously implicated in inherited disorders. We demonstrate how these results can be used to inform association and functional studies. From the two trios, we directly estimate the rate of de novo germline base substitution mutations to be approximately 10(-8) per base pair per generation. We explore the data with regard to signatures of natural selection, and identify a marked reduction of genetic variation in the neighbourhood of genes, due to selection at linked sites. These methods and public data will support the next phase of human genetic research.

Comment in

PMID:
20981092
[PubMed - indexed for MEDLINE]
PMCID:
PMC3042601
Free PMC Article

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