GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing
- Author(s)
- Cameron, DL; Baber, J; Shale, C; Valle-Inclan, JE; Besselink, N; van Hoeck, A; Janssen, R; Cuppen, E; Priestley, P; Papenfuss, AT;
- Journal Title
- Genome Biology
- Publication Type
- Research article
- 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.
- Keywords
- *Chromosome Breakpoints; Contig Mapping; *DNA Copy Number Variations; Databases, Genetic; Datasets as Topic; Genome, Human; Genomics; Humans; Neoplasm Metastasis; Neoplasms/*genetics/pathology; *Software
- Department(s)
- Laboratory Research
- PubMed ID
- 34253237
- Publisher's Version
- https://doi.org/10.1186/s13059-021-02423-x
- Open Access at Publisher's Site
https://doi.org/10.1186/s13059-021-02423-x- Terms of Use/Rights Notice
- Refer to copyright notice on published article.
Creation Date: 2025-06-20 03:31:52
Last Modified: 2025-06-20 03:33:48