RT Journal Article
SR Electronic
T1 GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 110387
DO 10.1101/110387
A1 Daniel L Cameron
A1 Jan Schroeder
A1 Jocelyn Sietsma Penington
A1 Hongdo Do
A1 Ramyar Molania
A1 Alexander Dobrovic
A1 Terence P Speed
A1 Anthony T Papenfuss
YR 2017
UL http://biorxiv.org/content/early/2017/02/21/110387.abstract
AB The identification of genomic rearrangements, particularly in cancers, with high sensitivity and specificity using massively parallel sequencing remains a major challenge. Here, we describe the Genome Rearrangement IDentification Software Suite (GRIDSS), a high-speed structural variant (SV) caller that performs efficient genome-wide break-end assembly prior to variant calling using a novel positional de Bruijn graph assembler. By combining assembly, split read and read pair evidence using a probabilistic scoring, GRIDSS achieves high sensitivity and specificity on simulated, cell line and patient tumour data, recently winning SV sub-challenge #5 of the ICGC-TCGA DREAM Somatic Mutation Calling Challenge. On human cell line data, GRIDSS halves the false discovery rate compared to other recent methods. GRIDSS identifies non-template sequence insertions, micro-homologies and large imperfect homologies, and supports multi-sample analysis. GRIDSS is freely available at https://github.com/PapenfussLab/gridss.