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GRIDSS2: harnessing the power of phasing and single breakends in somatic structural variant detection

Daniel L Cameron; Jonathor Baber; Charles Shale; Jose Espejo Valle-Inclan; Nicolle Besselink; Edwin Cuppen; Peter Priestley; Anthony T Papenfuss

2020-07-10 bioinformatics
10.1101/2020.07.09.196527 bioRxiv
Show 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 centromeric copy number changes using single breakends to non-centromeric sequence, with chromosome 1 exhibiting a unique centromeric rearrangement signature. On a cohort of 3,782 deeply sequenced metastatic cancers, GRIDSS2 achieved an unprecedented 3.1% false negative rate and identified a novel 32-100bp duplication signature. Somatic structural variants are highly clustered with GRIDSS2 phasing 16% using just paired-end sequencing.

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.