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

GRIDSS2 is the first structural variant caller to explicitly report single breakendsbreakpoints 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.

Automated summary

GRIDSS2 is the first structural variant caller that explicitly reports single breakends breakpoints where only one side can be unambiguously determined. It can explain somatic centromere copy number changes using single breakends to non-centromere sequence.GRIDSS2 achieves a low false negative rate and false discovery rate in metastatic cancers, also identifying a novel duplication signature.