Integrating common and rare genetic variation in diverse human populations

被引：2119

作者：

Altshuler, David M. ^{[1
]}

Gibbs, Richard A. ^{[2
]}

Peltonen, Leena

Dermitzakis, Emmanouil ^{[3
]}

Schaffner, Stephen F. ^{[1
]}

Yu, Fuli ^{[2
]}

Bonnen, Penelope E. ^{[2
]}

de Bakker, Paul I. W. ^{[1
,4
]}

Deloukas, Panos ^{[5
]}

Gabriel, Stacey B. ^{[1
]}

Gwilliam, Rhian ^{[5
]}

Hunt, Sarah ^{[5
]}

Inouye, Michael ^{[5
]}

Jia, Xiaoming ^{[1
]}

Palotie, Aarno ^{[5
,6
,7
,8
]}

Parkin, Melissa ^{[1
]}

Whittaker, Pamela ^{[5
]}

Chang, Kyle ^{[2
]}

Hawes, Alicia ^{[2
]}

Lewis, Lora R. ^{[2
]}

Ren, Yanru ^{[2
]}

Wheeler, David ^{[2
]}

Muzny, Donna Marie ^{[2
]}

Barnes, Chris ^{[5
]}

Darvishi, Katayoon ^{[9
]}

Hurles, Matthew ^{[5
]}

Korn, Joshua M. ^{[1
]}

Kristiansson, Kati ^{[5
]}

Lee, Charles ^{[9
]}

McCarroll, Steven A. ^{[1
]}

Nemesh, James

Keinan, Alon ^{[10
]}

Montgomery, Stephen B. ^{[3
]}

Pollack, Samuela ^{[1
]}

Price, Alkes L. ^{[11
,12
]}

Soranzo, Nicole ^{[5
]}

Gonzaga-Jauregui, Claudia ^{[2
]}

Anttila, Verneri ^{[5
,6
,7
,8
]}

Brodeur, Wendy ^{[1
]}

Daly, Mark J. ^{[13
]}

Leslie, Stephen ^{[14
]}

McVean, Gil ^{[14
]}

Moutsianas, Loukas ^{[14
]}

Nguyen, Huy ^{[1
]}

Zhang, Qingrun ^{[5
]}

Ghori, Mohammed J. R. ^{[5
]}

McGinnis, Ralph ^{[5
]}

McLaren, William ^{[5
]}

Takeuchi, Fumihiko ^{[5
]}

Grossman, Sharon R. ^{[15
]}

机构：

[1] Broad Inst, Cambridge, MA 02138 USA

[2] Baylor Coll Med, Human Genome Sequencing Ctr, Dept Mol & Human Genet, Houston, TX 77030 USA

[3] Univ Geneva, Sch Med, Dept Genet Med & Dev, Fac Med, CH-1211 Geneva, Switzerland

[4] Harvard Univ, Sch Med, Brigham & Womens Hosp, Dept Med,Div Genet, Boston, MA 02115 USA

[5] Wellcome Trust Sanger Inst, Dept Human Genet, Cambridge CB10 1HH, England

[6] Univ Helsinki, Inst Mol Med Finland, FIN-00290 Helsinki, Finland

[7] Univ Helsinki, Dept Med Genet, FIN-00290 Helsinki, Finland

[8] Univ Cent Hosp, Helsinki 00290, Finland

[9] Harvard Univ, Sch Med, Brigham & Womens Hosp, Dept Pathol, Boston, MA 02115 USA

[10] Cornell Univ, Dept Biol Stat & Computat Biol, Ithaca, NY 14853 USA

[11] Harvard Univ, Sch Publ Hlth, Dept Epidemiol, Boston, MA 02115 USA

[12] Harvard Univ, Sch Publ Hlth, Dept Biostat, Boston, MA 02115 USA

[13] Massachusetts Gen Hosp, Ctr Human Genet Res, Simches Res Ctr, Boston, MA 02114 USA

[14] Univ Oxford, Dept Stat, Oxford OX1 3TG, England

[15] Harvard Univ, Dept Organism & Evolutionary Biol, Ctr Syst Biol, Cambridge, MA 02215 USA

[16] Univ Maryland, Sch Med, Dept Epidemiol & Preventat Med, Inst Human Virol N406, Baltimore, MD 21201 USA

[17] Univ Oklahoma, Dept Anthropol, Norman, OK 73019 USA

[18] Univ Calif San Francisco, Dept Anthropol Hist & Social Med, San Francisco, CA 94143 USA

[19] Australian Natl Univ, John Curtin Sch Med Res, Canberra, ACT 2603, Australia

[20] Inst Oncol Study & Prevent, I-50139 Florence, Italy

[21] Case Western Reserve Univ, Dept Bioeth, Sch Med TA200, Cleveland, OH 44106 USA

[22] Hlth Sci Univ Hokkaido, Tobetsu, Hokkaido 0610293, Japan

[23] Moi Univ, Dept Populat & Family Hlth, Eldoret 30100, Kenya

[24] NHGRI, NIH, Bethesda, MD 20892 USA

[25] Univ Houston Clear Lake City, Dept Anthropol, Houston, TX 77058 USA

[26] NHGRI, Ctr Res Genom & Global Hlth, Bethesda, MD 20892 USA

[27] Duke Univ, Inst Genome Sci & Policy, Durham, NC 27708 USA

[28] Cleveland Clin, Dept Bioeth, Cleveland, OH 44124 USA

[29] Chinese Acad Sci, Beijing Inst Genom, Beijing 101300, Peoples R China

来源：

NATURE | 2010年 / 467卷 / 7311期

基金：

美国国家卫生研究院; 英国医学研究理事会; 瑞士国家科学基金会; 英国惠康基金;

关键词：

GENOME-WIDE ASSOCIATION; COPY NUMBER VARIATION; POSITIVE SELECTION; HAPLOTYPE MAP; VARIANTS; DISEASES; SIGNALS; REGIONS; SNPS;

D O I：

10.1038/nature09298

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

070301 [无机化学]; 070403 [天体物理学]; 070507 [自然资源与国土空间规划学]; 090105 [作物生产系统与生态工程];

摘要：

Despite great progress in identifying genetic variants that influence human disease, most inherited risk remains unexplained. A more complete understanding requires genome-wide studies that fully examine less common alleles in populations with a wide range of ancestry. To inform the design and interpretation of such studies, we genotyped 1.6 million common single nucleotide polymorphisms (SNPs) in 1,184 reference individuals from 11 global populations, and sequenced ten 100-kilobase regions in 692 of these individuals. This integrated data set of common and rare alleles, called 'HapMap 3', includes both SNPs and copy number polymorphisms (CNPs). We characterized population-specific differences among low-frequency variants, measured the improvement in imputation accuracy afforded by the larger reference panel, especially in imputing SNPs with a minor allele frequency of <= 5%, and demonstrated the feasibility of imputing newly discovered CNPs and SNPs. This expanded public resource of genome variants in global populations supports deeper interrogation of genomic variation and its role in human disease, and serves as a step towards a high-resolution map of the landscape of human genetic variation.

引用

页码：52 / 58

页数：7

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