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GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing.

ABSTRACT: GRIDSS2 is the first structural variant caller to explicitly report single breakends-breakpoints in which only one side can be unambiguously determined. By treating single breakends as a fundamental genomic rearrangement signal on par with breakpoints, GRIDSS2 can explain 47% of somatic centromere copy number changes using single breakends to non-centromere sequence. On a cohort of 3782 deeply sequenced metastatic cancers, GRIDSS2 achieves an unprecedented 3.1% false negative rate and 3.3% false discovery rate and identifies a novel 32-100 bp duplication signature. GRIDSS2 simplifies complex rearrangement interpretation through phasing of structural variants with 16% of somatic calls phasable using paired-end sequencing.

SUBMITTER: Cameron DL

PROVIDER: S-EPMC8274009 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature

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GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing.

Cameron Daniel L DL Baber Jonathan J Shale Charles C Valle-Inclan Jose Espejo JE Besselink Nicolle N van Hoeck Arne A Janssen Roel R Cuppen Edwin E Priestley Peter P Papenfuss Anthony T AT

Genome biology 20210712 1

GRIDSS2 is the first structural variant caller to explicitly report single breakends-breakpoints in which only one side can be unambiguously determined. By treating single breakends as a fundamental genomic rearrangement signal on par with breakpoints, GRIDSS2 can explain 47% of somatic centromere copy number changes using single breakends to non-centromere sequence. On a cohort of 3782 deeply sequenced metastatic cancers, GRIDSS2 achieves an unprecedented 3.1% false negative rate and 3.3% false ...[more]

PMID: 34253237

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