High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios

Human Genome Structural Variation Consortium

Research output: Contribution to journalArticlepeer-review

21 Scopus citations

Abstract

The 1000 Genomes Project (1kGP) is the largest fully open resource of whole-genome sequencing (WGS) data consented for public distribution without access or use restrictions. The final, phase 3 release of the 1kGP included 2,504 unrelated samples from 26 populations and was based primarily on low-coverage WGS. Here, we present a high-coverage 3,202-sample WGS 1kGP resource, which now includes 602 complete trios, sequenced to a depth of 30X using Illumina. We performed single-nucleotide variant (SNV) and short insertion and deletion (INDEL) discovery and generated a comprehensive set of structural variants (SVs) by integrating multiple analytic methods through a machine learning model. We show gains in sensitivity and precision of variant calls compared to phase 3, especially among rare SNVs as well as INDELs and SVs spanning frequency spectrum. We also generated an improved reference imputation panel, making variants discovered here accessible for association studies.

Original languageEnglish
Pages (from-to)3426-3440.e19
JournalCell
Volume185
Issue number18
DOIs
StatePublished - Sep 1 2022

Keywords

  • 1000 Genomes Project
  • INDEL
  • SNV
  • population genetics
  • reference imputation panel
  • structural variation
  • trio sequencing
  • whole-genome sequencing

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