A global reference for human genetic variation

TLDR

The 1000 Genomes Project aimed to comprehensively describe common human genetic variation by sequencing a diverse global sample and to characterize its distribution and implications for common disease studies. The project applied whole‑genome sequencing to a diverse set of individuals from multiple populations to generate a comprehensive catalogue of common human genetic variation. The project completed sequencing of 2,504 genomes from 26 populations, identifying over 88 million variants—including 84.7 million SNPs, 3.6 million indels, and 60 000 structural variants—phased onto high‑quality haplotypes and covering more than 99 % of common SNPs across diverse ancestries.

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.