GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing
2021
Daniel L. Cameron | Jonathan Baber | Charles Shale | Jose Espejo Valle-Inclan | Nicolle Besselink | Arne van Hoeck | Roel Janssen | Edwin Cuppen | Peter Priestley | Anthony T. Papenfuss
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.
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