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

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…

• WT
  Wellcome Trust

  Award: WT104947/Z/14/Z
• EM
  European Molecular Biology Laboratory
• NI
  National Institutes of Health

  Award: U24HG007497
• NI
  National Institute of Mental Health

  Award: MH115957
• NH
  National Human Genome Research Institute

  Awards: UM1HG008901, UM1HG008853
• UN
  U.S. National Library of Medicine
• EK
  Eunice Kennedy Shriver National Institute of Child Health and Human Development

  Awards: HD081256, UM1HG008895