A robust benchmark for detection of germline large deletions and insertions. Academic Article uri icon

Overview

abstract

  • 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.

authors

publication date

  • June 15, 2020

Research

keywords

  • Germ-Line Mutation
  • INDEL Mutation

Identity

PubMed Central ID

  • PMC8454654

Scopus Document Identifier

  • 85087696791

Digital Object Identifier (DOI)

  • 10.1101/735928

PubMed ID

  • 32541955

Additional Document Info

volume

  • 38

issue

  • 11