Integrating common and rare genetic variation in diverse human populations

David M. Altshuler; Richard A. Gibbs; Leena Peltonen; Emmanouil Dermitzakis; Stephen F. Schaffner; Fuli Yu; Penelope E. Bonnen; Paul I. W. de Bakker; Panos Deloukas; Stacey B. Gabriel; Rhian Gwilliam; Sarah Hunt; Michael Inouye; Xiaoming Jia; Aarno Palotie; Melissa Parkin; Pamela Whittaker; Kyle Chang; Alicia Hawes; Lora R. Lewis; Yanru 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; 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; 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; Lisa D. Brooks; Jean E. McEwen; Int HapMap 3 Consortium

doi:10.1038/nature09298

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Integrating common and rare genetic variation in diverse human populations

Journal article

Peer reviewed

Integrating common and rare genetic variation in diverse human populations

David M. Altshuler, Richard A. Gibbs, Leena Peltonen, Emmanouil Dermitzakis, Stephen F. Schaffner, Fuli Yu, Penelope E. Bonnen, Paul I. W. de Bakker, Panos Deloukas, Stacey B. Gabriel, …

Nature (London), Vol.467(7311), pp.52-58

02/09/2010

DOI: https://doi.org/10.1038/nature09298

PMCID: PMC3173859

PMID: 20811451

Abstract

Multidisciplinary Sciences

Science & Technology

Science & Technology - Other Topics

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.

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Title: Integrating common and rare genetic variation in diverse human populations
Creators - without role: David M. Altshuler - Broad Institute
Richard A. Gibbs - College Station Medical Center
Leena Peltonen
Emmanouil Dermitzakis - University of Geneva
Stephen F. Schaffner - Broad Institute
Fuli Yu - College Station Medical Center
Penelope E. Bonnen - College Station Medical Center
Paul I. W. de Bakker - Broad Institute
Panos Deloukas - Wellcome Sanger Institute
Stacey B. Gabriel - Broad Institute
Rhian Gwilliam - Wellcome Sanger Institute
Sarah Hunt - Wellcome Sanger Institute
Michael Inouye - Wellcome Sanger Institute
Xiaoming Jia - Broad Institute
Aarno Palotie - Wellcome Sanger Institute
Melissa Parkin - Broad Institute
Pamela Whittaker - Wellcome Sanger Institute
Kyle Chang - College Station Medical Center
Alicia Hawes - College Station Medical Center
Lora R. Lewis - College Station Medical Center
Yanru Ren - College Station Medical Center
David Wheeler - College Station Medical Center
Donna Marie Muzny - College Station Medical Center
Chris Barnes - Wellcome Sanger Institute
Katayoon Darvishi - Harvard University
Matthew Hurles - Wellcome Sanger Institute
Joshua M. Korn - Broad Institute
Kati Kristiansson - Wellcome Sanger Institute
Charles Lee - Harvard University
Steven A. McCarroll - Broad Institute
James Nemesh
Alon Keinan - Cornell University
Stephen B. Montgomery - University of Geneva
Samuela Pollack - Broad Institute
Alkes L. Price - Harvard University
Nicole Soranzo - Wellcome Sanger Institute
Claudia Gonzaga-Jauregui - College Station Medical Center
Verneri Anttila - Wellcome Sanger Institute
Wendy Brodeur - Broad Institute
Mark J. Daly - Massachusetts Gen Hosp, Ctr Human Genet Res, Simches Res Ctr, Boston, MA 02114 USA
Stephen Leslie - University of Oxford
Gil McVean - University of Oxford
Loukas Moutsianas - University of Oxford
Huy Nguyen - Broad Institute
Qingrun Zhang - Wellcome Sanger Institute
Mohammed J. R. Ghori - Wellcome Sanger Institute
Ralph McGinnis - Wellcome Sanger Institute
William McLaren - Wellcome Sanger Institute
Fumihiko Takeuchi - Wellcome Sanger Institute
Sharon R. Grossman - Harvard University
Ilya Shlyakhter - Broad Institute
Elizabeth B. Hostetter - Harvard University
Pardis C. Sabeti - Harvard University
Clement A. Adebamowo - Supreme Council Of Health
Morris W. Foster - University of Oklahoma
Deborah R. Gordon - College Station Medical Center
Julio Licinio - Supreme Council Of Health
Maria Cristina Manca - Florence
Patricia A. Marshall - Case Western Reserve University
Ichiro Matsuda - Hlth Sci Univ Hokkaido, Tobetsu, Hokkaido 0610293, Japan
Duncan Ngare - Moi University
Vivian Ota Wang - NHGRI, NIH, Bethesda, MD 20892 USA
Deepa Reddy - University of Houston - Clear Lake
Charles N. Rotimi - NHGRI, Ctr Res Genom & Global Hlth, Bethesda, MD 20892 USA
Charmaine D. Royal - Duke University
Richard R. Sharp - Cleveland Clin, Dept Bioeth, Cleveland, OH 44124 USA
Changqing Zeng - Chinese Acad Sci, Beijing Inst Genom, Beijing 101300, Peoples R China
Lisa D. Brooks - NHGRI, NIH, Bethesda, MD 20892 USA
Jean E. McEwen - NHGRI, NIH, Bethesda, MD 20892 USA
Int HapMap 3 Consortium
Publication Details: Nature (London), Vol.467(7311), pp.52-58
Publisher: Springer Nature
Number of pages: 7
Grant note: P30DK043351 / NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of Diabetes & Digestive & Kidney Diseases (NIDDK) 068545/Z/02; 076113 / Wellcome Trust; European Commission G0000934 / UK Medical Research Council; UK Research & Innovation (UKRI); Medical Research Council UK (MRC) G0000934 / MRC; UK Research & Innovation (UKRI); Medical Research Council UK (MRC) G0000934 / Medical Research Council; UK Research & Innovation (UKRI); Medical Research Council UK (MRC); European Commission NCCR 'Frontiers in Genetics' (Swiss National Science Foundation); Swiss National Science Foundation (SNSF) Louis-Jeantet Foundation USA National Institutes of Health; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA U54HG003273 / NATIONAL HUMAN GENOME RESEARCH INSTITUTE; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Human Genome Research Institute (NHGRI) National Human Genome Research Institute; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Human Genome Research Institute (NHGRI) National Institute on Deafness and Other Communication Disorders; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute on Deafness & Other Communication Disorders (NIDCD)
Identifiers: 9938850608331
Academic Unit: King Abdulaziz University
Language: English
Resource Type: Journal article