Journal Article

A robust benchmark for detection of germline large deletions and insertions

Alkan Can, Hajirasouliha Iman, Ghaffari Noushin, Barrio, Alvaro Martinez, Alexander, Noah, Sedlazeck, Fritz J, Olson, Nathan D, Sahraeian Sayed Mohammad E, Chaisson Mark J P, English, Adam C, Catalano, Anthony P, Tearle Rick, Rodriguez, Oscar L, Koren Sergey, Mills, Ryan E, Boutros, Paul C, Carroll, Andrew, Marschall, Tobias, Rosenfeld, Jeffrey A, Sage, Jay M, Oliver, John S, Lee, Joyce, Chapman, Lesley, Xiao Chunlin, Zhou Weichen, Phillippy, Adam M, Salit Marc, Jackman, Shaun, Mason, Christopher E, Schatz, Michael C, Soylev Arda, Hansen, Nancy F, Mullikin, James C, Huang, Vincent, Farrell, John J, Wenger, Aaron M, Church, George, Wala Jeremiah, Ricketts Camir, Kaiser, Michael D, Spies, Noah, Garg Shilpa, Davis, Jennifer R, Sherry, Stephen, Zook, Justin M, Fiddes, Ian T, Bashir, Ali, Chen, Ken, Fan Xian, Rouette Alexandre

2020

Overview

New technologies and analysis methods are enabling genomic structural variants (SVs) to be detected with ever-increasing accuracy, resolution and comprehensiveness. To help translate these methods to routine research and clinical practice, we developed a sequence-resolved benchmark set for identification of both false-negative and false-positive germline large insertions and deletions. To create this benchmark for a broadly consented son in a Personal Genome Project trio with broadly available cells and DNA, the Genome in a Bottle Consortium integrated 19 sequence-resolved variant calling methods from diverse technologies. The final benchmark set contains 12,745 isolated, sequence-resolved insertion (7,281) and deletion (5,464) calls ≥50 base pairs (bp). The Tier 1 benchmark regions, for which any extra calls are putative false positives, cover 2.51 Gbp and 5,262 insertions and 4,095 deletions supported by ≥1 diploid assembly. We demonstrate that the benchmark set reliably identifies false negatives and false positives in high-quality SV callsets from short-, linked- and long-read sequencing and optical mapping.Detection of structural variants in the human genome is facilitated by a benchmark set of large deletions and insertions.

• Publisher: Nature Publishing Group
• Subject: Benchmarks / Consortia / Deoxyribonucleic acid / Diploids / DNA / Gene deletion / Gene mapping / Genomes / Insertion / New technology / Nucleotide sequence