PT  - JOURNAL ARTICLE
AU  - Cameron, Daniel L.
AU  - Baber, Jonathan
AU  - Shale, Charles
AU  - Papenfuss, Anthony T.
AU  - Valle-Inclan, Jose Espejo
AU  - Besselink, Nicolle
AU  - Cuppen, Edwin
AU  - Priestley, Peter
TI  - GRIDSS, PURPLE, LINX: Unscrambling the tumor genome via integrated analysis of structural variation and copy number
AID  - 10.1101/781013
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 781013
4099  - http://biorxiv.org/content/early/2019/09/25/781013.short
4100  - http://biorxiv.org/content/early/2019/09/25/781013.full
AB  - We have developed a novel, integrated and comprehensive purity, ploidy, structural variant and copy number somatic analysis toolkit for whole genome sequencing data of paired tumor/normal samples. We show that the combination of using GRIDSS for somatic structural variant calling and PURPLE for somatic copy number alteration calling allows highly sensitive, precise and consistent copy number and structural variant determination, as well as providing novel insights for short structural variants and regions of complex local topology. LINX, an interpretation tool, leverages the integrated structural variant and copy number calling to cluster individual structural variants into higher order events and chains them together to predict local derivative chromosome structure. LINX classifies and extensively annotates genomic rearrangements including simple and reciprocal breaks, LINE, viral and pseudogene insertions, and complex events such as chromothripsis. LINX also comprehensively calls genic fusions including chained fusions. Finally, our toolkit provides novel visualisation methods providing insight into complex genomic rearrangements.