A global reference for human genetic variation
Глобальный эталон генетической вариабельности человека
2015-09-29
SCID: 54.1/y72rn58w
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1000 Genomes Projectglobal reference datasethuman genetic variationsingle nucleotide polymorphismswhole-genome sequencing
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Abstract (AI)
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.
Key Findings
1
All identified variants were phased into high-quality haplotypes, enabling characterization of genetic variation across populations.
2
The completed 1000 Genomes Project reconstructed genomes from 2,504 individuals representing 26 global populations using sequencing and dense genotyping.
3
The project catalogued over 88 million variants, including 84.7 million SNPs, 3.6 million short indels, and 60,000 structural variants.
4
The resource captures more than 99% of SNP variants with frequencies above 1% across diverse ancestries.
5
The resulting global reference dataset supports biomedical applications including association studies, fine mapping, and filtering likely neutral variants in rare-disease cohorts.
Research Object
Comprehensive catalogue/resource of human genetic variation (genomes and phased variants derived from 2,504 individuals across 26 populations)
Research Subject
the distribution and comprehensive catalogue of common genetic variants, including SNPs, indels, and structural variants, across populations and its relevance to common-disease studies
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2015-09-29
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