RT Journal Article
SR Electronic
T1 GRIDSS, PURPLE, LINX: Unscrambling the tumor genome via integrated analysis of structural variation and copy number
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 781013
DO 10.1101/781013
A1 Daniel L. Cameron
A1 Jonathan Baber
A1 Charles Shale
A1 Anthony T. Papenfuss
A1 Jose Espejo Valle-Inclan
A1 Nicolle Besselink
A1 Edwin Cuppen
A1 Peter Priestley
YR 2019
UL http://biorxiv.org/content/early/2019/09/25/781013.abstract
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.