Integrating common and rare genetic variation in diverse human populations

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

    Research output: Contribution to journalArticle

    1704 Citations (Scopus)

    Abstract

    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
    Pages (from-to)52-58
    Number of pages7
    JournalNature
    Volume467
    Issue number7311
    DOIs
    Publication statusPublished - 2010

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  • Cite this

    Altshuler, D., Gibbs, R., Peltonen, L., Dermitzakis, E., Schaffner, S., Yu, F., Bonnen, P., de Bakker, P., Deloukas, P., Gabriel, S., Gwilliam, R., Hunt, S., Inouye, M., Jia, X., Palotie, A., Parkin, M., Whittaker, P., Chang, K., Hawes, A., ... McEwen, J. (2010). Integrating common and rare genetic variation in diverse human populations. Nature, 467(7311), 52-58. https://doi.org/10.1038/nature09298