A global reference for human genetic variation
Corresponding authorsDepartment of Genetics, Albert Einstein College of Medicine, Bronx, 10461, New York, USAAdam AutonCenter for Statistical Genetics, Biostatistics, University of Michigan, Ann Arbor, 48109, Michigan, USAGonçalo R. AbecasisCenter for Statistical Genetics, Biostatistics, University of Michigan, Ann Arbor, 48109, Michigan, USADavid M. AltshulerWellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UKRichard 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)Aravinda 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 DonnellyHoward Hughes Medical Institute, University of Washington, Seattle, 98195, Washington, USAEvan 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. GabrielBaylor GeneticsRichard A. GibbsBaylor GeneticsEric D. GreenNational Human Genome Research InstituteMatthew E. HurlesWellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UKBartha M. KnoppersEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UKJan O. KorbelEuropean Molecular Biology Laboratory, Genome Biology Research Unit, Meyerhofstr. 1, Heidelberg, GermanyEric S. LanderThe Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, 02142, Massachusetts, USACharles LeeMax Planck Institute for Molecular Genetics, D-14195 Berlin-Dahlem, GermanyHans LehrachDahlem Centre for Genome Research and Medical Systems Biology, D-14195 Berlin-Dahlem, GermanyElaine R. MardisUSTAR Center for Genetic Discovery & Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, 84112, Utah, USAGábor MarthStar CenterGil A. McVeanWellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UKDeborah A. NickersonDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, 98195, Washington, USAJeanette P. SchmidtAffymetrix, Santa Clara, California, 95051, USAStephen T. SherryBGI-Shenzhen, Shenzhen 518083, ChinaJun WangMacau University of Science and Technology, Avenida Wai long, Taipa, 999078, Macau, 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 GeneticsEric BoerwinkleBaylor GeneticsHarshaVardhan DoddapaneniBaylor GeneticsYi HanBaylor GeneticsViktoriya KorchinaBaylor GeneticsChristie KovarBaylor GeneticsSandra 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. ReidMacau University of Science and Technology, Avenida Wai long, Taipa, 999078, Macau, ChinaYiming ZhuBaylor GeneticsBGI-ShenzhenDepartment of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, 2200, DenmarkJun WangMacau University of Science and Technology, Avenida Wai long, Taipa, 999078, Macau, ChinaYuqi ChangBGI-Shenzhen, Shenzhen 518083, ChinaQiang FengDepartment of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, 2200, DenmarkXiaodong FangDepartment of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, 2200, DenmarkXiaosen GuoBGI-Shenzhen, Shenzhen 518083, ChinaMin JianBGI-Shenzhen, Shenzhen 518083, ChinaHui JiangDepartment of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, 2200, DenmarkXin JinBGI-Shenzhen, Shenzhen 518083, ChinaTianming LanBGI-Shenzhen, Shenzhen 518083, ChinaGuoqing LiBGI-Shenzhen, Shenzhen 518083, ChinaJingxiang LiDepartment of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, 2200, DenmarkYingrui LiDepartment of Genetics, Department of Biostatistics, Department of Computer Science, University of Chapel Hill, North Carolina, 27599, USAShengmao 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 ZhaoThe Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, 02142, Massachusetts, USAMeiru ZhaoBGI-Shenzhen, Shenzhen 518083, ChinaXiaole ZhengBGI-Shenzhen, Shenzhen 518083, ChinaDavid M. AltshulerCoriell Institute for Medical Research, Camden, 08103, New Jersey, USAStacey GabrielCoriell Institute for Medical Research, Camden, 08103, New Jersey, USANamrata GuptaCoriell Institute for Medical Research, Camden, 08103, New Jersey, 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 ReschEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UKPaul 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 TonevaIllumina United Kingdom, Chesterford Research Park, Little Chesterford, Nr Saffron Walden, CB10 1XL, Essex, UKBrendan VaughanIllumina United Kingdom, Chesterford Research Park, Little Chesterford, Nr Saffron Walden, CB10 1XL, Essex, 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)Terena JamesIllumina United Kingdom, Chesterford Research Park, Little Chesterford, Nr Saffron Walden, CB10 1XL, Essex, UK
2015en
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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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