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April 21, 2020  |  

Characterizing the major structural variant alleles of the human genome.

Authors: Audano, Peter A and Sulovari, Arvis and Graves-Lindsay, Tina A and Cantsilieris, Stuart and Sorensen, Melanie and Welch, AnneMarie E and Dougherty, Max L and Nelson, Bradley J and Shah, Ankeeta and Dutcher, Susan K and Warren, Wesley C and Magrini, Vincent and McGrath, Sean D and Li, Yang I and Wilson, Richard K and Eichler, Evan E

In order to provide a comprehensive resource for human structural variants (SVs), we generated long-read sequence data and analyzed SVs for fifteen human genomes. We sequence resolved 99,604 insertions, deletions, and inversions including 2,238 (1.6 Mbp) that are shared among all discovery genomes with an additional 13,053 (6.9 Mbp) present in the majority, indicating minor alleles or errors in the reference. Genotyping in 440 additional genomes confirms the most common SVs in unique euchromatin are now sequence resolved. We report a ninefold SV bias toward the last 5 Mbp of human chromosomes with nearly 55% of all VNTRs (variable number of tandem repeats) mapping to this portion of the genome. We identify SVs affecting coding and noncoding regulatory loci improving annotation and interpretation of functional variation. These data provide the framework to construct a canonical human reference and a resource for developing advanced representations capable of capturing allelic diversity. Copyright © 2018 Elsevier Inc. All rights reserved.

Journal: Cell
DOI: 10.1016/j.cell.2018.12.019
Year: 2019

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