A global reference for human genetic variation
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Abstract
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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The record
- Venue
- Nature
- Topic
- Genetic Associations and Epidemiology
- Field
- Biochemistry, Genetics and Molecular Biology
- Canadian institutions
- Université de MontréalOntario Institute for Cancer ResearchMcGill University and Génome Québec Innovation CentreMcGill University
- Funders
- National Institute of Diabetes and Digestive and Kidney DiseasesNational Institute of Allergy and Infectious DiseasesNational Cancer InstituteNational Human Genome Research InstituteNational Heart, Lung, and Blood InstituteOntario Ministry of Research and InnovationNational Key Research and Development Program of ChinaNational High-tech Research and Development ProgramInstituto de Salud Carlos IIIMedical Research CouncilFonds de Recherche du Québec - SantéCanadian Institutes of Health ResearchNational Institutes of HealthNational Institute of General Medical SciencesH. Lundbeck A/SMinistero dello Sviluppo EconomicoUniversité de GenèveUniversity of OxfordEwha Womans UniversitySchweizerischer Nationalfonds zur Förderung der Wissenschaftlichen ForschungDeutsche ForschungsgemeinschaftBritish Heart FoundationBilkent ÜniversitesiSimons Foundation Autism Research InitiativeEuropean Molecular Biology LaboratoryBiotechnology and Biological Sciences Research CouncilWellcome TrustBroad InstituteHoward Hughes Medical InstituteNational Natural Science Foundation of ChinaLouisiana State UniversityGovernment of Jiangxi ProvinceBundesministerium für Bildung und ForschungNational Institute for Health and Care ResearchNational Science FoundationMassachusetts General HospitalHarvard UniversityMax-Planck-GesellschaftLundbeckfondenSimons FoundationJapan Society for the Promotion of ScienceDirectorate for Biological SciencesBoston CollegeAlfred P. Sloan Foundation
- Keywords
- 1000 Genomes ProjectGenomeBiologyReference genomeGenetic variationExome sequencingSingle-nucleotide polymorphismGeneticsHaplotypeIndelStructural variationTag SNPGenotypingHuman genomeComputational biologyHuman genetic variationExomeSNP genotypingGenome-wide association studyGenotypeMutationGene
- Has abstract in OpenAlex
- yes