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Science. 2010 Oct 29;330(6004):641-6. doi: 10.1126/science.1197005.

Diversity of human copy number variation and multicopy genes.

Collaborators (552)

Altshuler DL, 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 RK, 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, Koko-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, Kebbel A, 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, Blackwell T, 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, Peltonen L, 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, Abecasis GR, Altshuler DL, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA.

Author information

  • 1Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.

Abstract

Copy number variants affect both disease and normal phenotypic variation, but those lying within heavily duplicated, highly identical sequence have been difficult to assay. By analyzing short-read mapping depth for 159 human genomes, we demonstrated accurate estimation of absolute copy number for duplications as small as 1.9 kilobase pairs, ranging from 0 to 48 copies. We identified 4.1 million "singly unique nucleotide" positions informative in distinguishing specific copies and used them to genotype the copy and content of specific paralogs within highly duplicated gene families. These data identify human-specific expansions in genes associated with brain development, reveal extensive population genetic diversity, and detect signatures consistent with gene conversion in the human species. Our approach makes ~1000 genes accessible to genetic studies of disease association.

Comment in

PMID:
21030649
[PubMed - indexed for MEDLINE]
PMCID:
PMC3020103
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