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Cell DOI:10.1016/j.cell.2022.08.004

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

Publication TypeJournal Article
Year of Publication2022
AuthorsByrska-Bishop, M, Evani, US, Zhao, X, Basile, AO, Abel, HJ, Regier, AA, Corvelo, A, Clarke, WE, Musunuri, R, Nagulapalli, K, Fairley, S, Runnels, A, Winterkorn, L, Lowy, E, Germer, S, Brand, H, Hall, IM, Talkowski, ME, Narzisi, G, Zody, MC
Corporate AuthorsHuman Genome Structural Variation Consortium
JournalCell
Volume185
Issue18
Pages3426-3440.e19
Date Published2022 Sep 01
ISSN1097-4172
KeywordsGenome, Human, High-Throughput Nucleotide Sequencing, Humans, INDEL Mutation, Polymorphism, Single Nucleotide, Whole Genome Sequencing
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.

DOI10.1016/j.cell.2022.08.004
Pubmed

https://www.ncbi.nlm.nih.gov/pubmed/36055201?dopt=Abstract

Alternate JournalCell
PubMed ID36055201