Integrating common and rare genetic variation in diverse human populations

David M. Altshuler, Richard A. Gibbs, Leena Peltonen, Stephen F. Schaffner, Fuli Yu, Emmanouil Dermitzakis, Penelope E. Bonnen, Paul I.W. De Bakker, Panos Deloukas, Stacey B. Gabriel, Rhian Gwilliam, Sarah Hunt, Michael Inouye, Xiaoming Jia, Palotie Aarno Palotie, Melissa Parkin, Pamela Whittaker, Kyle Chang, Alicia Hawes, Lora R. LewisYanru Ren, David Wheeler, Donna Marie Muzny, Chris Barnes, Katayoon Darvishi, Matthew Hurles, Joshua M. Korn, Kati Kristiansson, Charles Lee, Steven A. McCarroll, James Nemesh, Alon Keinan, Stephen B. Montgomery, Pollack Samuela Pollack, Alkes L. Price, Nicole Soranzo, Claudia Gonzaga-Jauregui, Verneri Anttila, Wendy Brodeur, Mark J. Daly, Stephen Leslie, Gil McVean, Loukas Moutsianas, Huy Nguyen, Qingrun Zhang, Mohammed J.R. Ghori, Ralph McGinnis, William McLaren, Samuela Pollack, Fumihiko Takeuchi, Sharon R. Grossman, Ilya Shlyakhter, Elizabeth B. Hostetter, Pardis C. Sabeti, Clement A. Adebamowo, Morris W. Foster, Deborah R. Gordon, Julio Licinio, Maria Cristina Manca, Patricia A. Marshall, Ichiro Matsuda, Duncan Ngare, Vivian Ota Wang, Deepa Reddy, Charles N. Rotimi, Charmaine D. Royal, Richard R. Sharp, Changqing Zeng, D. B. Brooks, Jean E. McEwen

Research output: Contribution to journalArticlepeer-review

1803 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)52-58
Number of pages7
Issue number7311
StatePublished - Sep 2 2010

ASJC Scopus subject areas

  • General


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