A global reference for human genetic variation
Corresponding authorsDepartment of Genetics, Albert Einstein College of Medicine, Bronx, 10461, New York, USAAdam AutonDepartment of Genetics, Albert Einstein College of Medicine, Bronx, 10461, New York, USAGonçalo R. AbecasisCenter for Statistical Genetics, Biostatistics, University of Michigan, Ann Arbor, 48109, Michigan, USADavid M. AltshulerVertex Pharmaceuticals, Boston, 02210, Massachusetts, USARichard DurbinWellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UKGonçalo R. AbecasisCenter for Statistical Genetics, Biostatistics, University of Michigan, Ann Arbor, 48109, Michigan, USADavid R. BentleyIllumina United Kingdom, Chesterford Research Park, Little Chesterford, Nr Saffron Walden, CB10 1XL, Essex, UKAravinda ChakravartiMcKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, 21205, Maryland, USAAndrew G. ClarkCenter for Comparative and Population Genomics, Cornell University, Ithaca, 14850, New York, USAPeter DonnellyDepartment of Statistics, University of Oxford, Oxford, OX1 3TG, UKEvan E. EichlerDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, 98195, Washington, USAPaul FlicekEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UKStacey B. GabrielThe Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, 02142, Massachusetts, USARichard A. GibbsBaylor College of Medicine, Human Genome Sequencing Center, Houston, 77030, Texas, USAEric D. GreenUS National Institutes of Health, National Human Genome Research Institute, 31 Center Drive, Bethesda, 20892, Maryland, USAMatthew E. HurlesWellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UKBartha M. KnoppersCentre of Genomics and Policy, McGill University, Montreal, H3A 1A4, Quebec, CanadaJan O. KorbelEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UKEric S. LanderThe Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, 02142, Massachusetts, USACharles LeeDepartment of Life Sciences, Ewha Womans University, Ewhayeodae-gil, Seodaemun-gu, Seoul, South Korea, 120-750Hans LehrachDahlem Centre for Genome Research and Medical Systems Biology, D-14195 Berlin-Dahlem, GermanyElaine R. MardisMcDonnell Genome Institute at Washington University, Washington University School of Medicine, St Louis, 63108, Missouri, USAGábor MarthUSTAR Center for Genetic Discovery & Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, 84112, Utah, USAGil A. McVeanDepartment of Statistics, University of Oxford, Oxford, OX1 3TG, UKDeborah A. NickersonDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, 98195, Washington, USAJeanette P. SchmidtAffymetrix, Santa Clara, California, 95051, USAStephen T. SherryUS National Institutes of Health, National Center for Biotechnology Information, 45 Center Drive, Bethesda, 20892, Maryland, USAJun WangBGI-Shenzhen, Shenzhen 518083, ChinaRichard K. WilsonMcDonnell Genome Institute at Washington University, Washington University School of Medicine, St Louis, 63108, Missouri, USAProduction groupBaylor College of Medicine, Human Genome Sequencing Center, Houston, 77030, Texas, USARichard A. GibbsBaylor College of Medicine, Human Genome Sequencing Center, Houston, 77030, Texas, USAEric BoerwinkleBaylor College of Medicine, Human Genome Sequencing Center, Houston, 77030, Texas, USAHarshaVardhan DoddapaneniBaylor College of Medicine, Human Genome Sequencing Center, Houston, 77030, Texas, USAYi HanBaylor College of Medicine, Human Genome Sequencing Center, Houston, 77030, Texas, USAViktoriya KorchinaBaylor College of Medicine, Human Genome Sequencing Center, Houston, 77030, Texas, USAChristie KovarBaylor College of Medicine, Human Genome Sequencing Center, Houston, 77030, Texas, USASandra LeeBaylor College of Medicine, Human Genome Sequencing Center, Houston, 77030, Texas, USADonna M. MuznyBaylor College of Medicine, Human Genome Sequencing Center, Houston, 77030, Texas, USAJeffrey G. ReidUniversity of Hong KongYiming ZhuBaylor College of Medicine, Human Genome Sequencing Center, Houston, 77030, Texas, USABGI-ShenzhenDepartment of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, 2200, DenmarkJun WangBGI-Shenzhen, Shenzhen 518083, ChinaYuqi ChangBGI-Shenzhen, Shenzhen 518083, ChinaQiang FengBGI-Shenzhen, Shenzhen 518083, ChinaXiaodong FangBGI-Shenzhen, Shenzhen 518083, ChinaXiaosen GuoBGI-Shenzhen, Shenzhen 518083, ChinaMin JianBGI-Shenzhen, Shenzhen 518083, ChinaHui JiangBGI-Shenzhen, Shenzhen 518083, ChinaXin JinBGI-Shenzhen, Shenzhen 518083, ChinaTianming LanBGI-Shenzhen, Shenzhen 518083, ChinaGuoqing LiBGI-Shenzhen, Shenzhen 518083, ChinaJingxiang LiBGI-Shenzhen, Shenzhen 518083, ChinaYingrui LiBGI-Shenzhen, Shenzhen 518083, ChinaShengmao LiuBGI-Shenzhen, Shenzhen 518083, ChinaXiao LiuBGI-Shenzhen, Shenzhen 518083, ChinaYao LuBGI-Shenzhen, Shenzhen 518083, ChinaXuedi MaBGI-Shenzhen, Shenzhen 518083, ChinaMeifang TangBGI-Shenzhen, Shenzhen 518083, ChinaBo WangBGI-Shenzhen, Shenzhen 518083, ChinaGuangbiao WangBGI-Shenzhen, Shenzhen 518083, ChinaHonglong WuBGI-Shenzhen, Shenzhen 518083, ChinaRenhua WuBGI-Shenzhen, Shenzhen 518083, ChinaXun XuBGI-Shenzhen, Shenzhen 518083, ChinaYe YinBGI-Shenzhen, Shenzhen 518083, ChinaDandan ZhangBGI-Shenzhen, Shenzhen 518083, ChinaWenwei ZhangBGI-Shenzhen, Shenzhen 518083, ChinaJiao ZhaoBGI-Shenzhen, Shenzhen 518083, ChinaMeiru ZhaoBGI-Shenzhen, Shenzhen 518083, ChinaXiaole ZhengBGI-Shenzhen, Shenzhen 518083, ChinaDavid M. AltshulerVertex Pharmaceuticals, Boston, 02210, Massachusetts, USAStacey GabrielThe Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, 02142, Massachusetts, USANamrata GuptaThe Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, 02142, Massachusetts, USANeda GharaniCoriell Institute for Medical Research, Camden, 08103, New Jersey, USALorraine H. TojiCoriell Institute for Medical Research, Camden, 08103, New Jersey, USANorman P. GerryCoriell Institute for Medical Research, Camden, 08103, New Jersey, USAAlissa ReschCoriell Institute for Medical Research, Camden, 08103, New Jersey, USAPaul FlicekEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UKJonathan BarkerEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UKLaura ClarkeEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UKLaurent GilEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UKSarah HuntEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UKGavin KelmanEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UKEugene KuleshaEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UKRasko LeinonenEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UKWilliam McLarenEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UKRajesh RadhakrishnanEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UKAsier RoaEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UKDmitriy SmirnovEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UKRichard E. SmithEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UKIan StreeterEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UKAnja ThormannEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UKIliana TonevaEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UKBrendan VaughanEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UKXiangqun Zheng-BradleyEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UKIlluminaIllumina United Kingdom, Chesterford Research Park, Little Chesterford, Nr Saffron Walden, CB10 1XL, Essex, UKDavid R. BentleyIllumina United Kingdom, Chesterford Research Park, Little Chesterford, Nr Saffron Walden, CB10 1XL, Essex, UKRussell GrocockIllumina United Kingdom, Chesterford Research Park, Little Chesterford, Nr Saffron Walden, CB10 1XL, Essex, UKSean HumphrayIllumina United Kingdom, Chesterford Research Park, Little Chesterford, Nr Saffron Walden, CB10 1XL, Essex, UKTerena JamesIllumina United Kingdom, Chesterford Research Park, Little Chesterford, Nr Saffron Walden, CB10 1XL, Essex, UK
2015en
ABI
Annotatsiya
The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies. Results for the final phase of the 1000 Genomes Project are presented including whole-genome sequencing, targeted exome sequencing, and genotyping on high-density SNP arrays for 2,504 individuals across 26 populations, providing a global reference data set to support biomedical genetics. The 1000 Genomes Project has sought to comprehensively catalogue human genetic variation across populations, providing a valuable public genomic resource. The data obtained so far have found applications ranging from association studies and fine mapping studies to the filtering of likely neutral variants in rare-disease cohorts. The authors now report on the final phase of the project, phase 3, which covers previously uncharacterized areas of human genetic diversity in terms of the populations sampled and categories of characterized variation. The sample now includes more than 2,500 individuals from 26 global populations, with low coverage whole-genome and deep exome sequencing, as well as dense microarray genotyping. They find that while most common variants are shared across populations, rarer variants are often restricted to closely related populations. The authors also demonstrate the use of the phase 3 dataset as a reference panel for imputation to improve the resolution in genetic association studies.
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