Journal article

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

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

GENOME BIOLOGY | BMC | Published : 2021

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 phasabl..

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University of Melbourne Researchers

Grants

Awarded by National Health and Medical Research Council (NHMRC)


Funding Acknowledgements

A.T.P. was supported by a National Health and Medical Research Council (NHMRC) Senior Research Fellowship [1116955] and the Lorenzo and Pamela Galli Charitable Trust. D.L.C. and A.T.P. were supported by an NHMRC Ideas Grant [1188098]. The research benefitted by support from the Victorian State Government Operational Infrastructure Support and Australian Government NHMRC Independent Research Institute Infrastructure Support.