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Integrating common and rare genetic variation in diverse human populations.


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

SUBMITTER: International HapMap 3 Consortium 

PROVIDER: S-EPMC3173859 | biostudies-literature | 2010 Sep

REPOSITORIES: biostudies-literature

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Integrating common and rare genetic variation in diverse human populations.

Altshuler David M DM   Gibbs Richard A RA   Peltonen Leena L   Altshuler David M DM   Gibbs Richard A RA   Peltonen Leena L   Dermitzakis Emmanouil E   Schaffner Stephen F SF   Yu Fuli F   Peltonen Leena L   Dermitzakis Emmanouil E   Bonnen Penelope E PE   Altshuler David M DM   Gibbs Richard A RA   de Bakker Paul I W PI   Deloukas Panos P   Gabriel Stacey B SB   Gwilliam Rhian R   Hunt Sarah S   Inouye Michael M   Jia Xiaoming X   Palotie Aarno A   Parkin Melissa M   Whittaker Pamela P   Yu Fuli F   Chang Kyle K   Hawes Alicia A   Lewis Lora R LR   Ren Yanru Y   Wheeler David D   Gibbs Richard A RA   Muzny Donna Marie DM   Barnes Chris C   Darvishi Katayoon K   Hurles Matthew M   Korn Joshua M JM   Kristiansson Kati K   Lee Charles C   McCarrol Steven A SA   Nemesh James J   Dermitzakis Emmanouil E   Keinan Alon A   Montgomery Stephen B SB   Pollack Samuela S   Price Alkes L AL   Soranzo Nicole N   Bonnen Penelope E PE   Gibbs Richard A RA   Gonzaga-Jauregui Claudia C   Keinan Alon A   Price Alkes L AL   Yu Fuli F   Anttila Verneri V   Brodeur Wendy W   Daly Mark J MJ   Leslie Stephen S   McVean Gil G   Moutsianas Loukas L   Nguyen Huy H   Schaffner Stephen F SF   Zhang Qingrun Q   Ghori Mohammed J R MJ   McGinnis Ralph R   McLaren William W   Pollack Samuela S   Price Alkes L AL   Schaffner Stephen F SF   Takeuchi Fumihiko F   Grossman Sharon R SR   Shlyakhter Ilya I   Hostetter Elizabeth B EB   Sabeti Pardis C PC   Adebamowo Clement A CA   Foster Morris W MW   Gordon Deborah R DR   Licinio Julio J   Manca Maria Cristina MC   Marshall Patricia A PA   Matsuda Ichiro I   Ngare Duncan D   Wang Vivian Ota VO   Reddy Deepa D   Rotimi Charles N CN   Royal Charmaine D CD   Sharp Richard R RR   Zeng Changqing C   Brooks Lisa D LD   McEwen Jean E JE  

Nature 20100901 7311


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 6  ...[more]

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