Complex Genomic Rearrangements (CGRs) are emerging as a new feature of cancer genomes. CGRs are characterized by multiple genomic breakpoints, and thus have the potential to simultaneously affect multiple genes, fusing some genes and interrupting other genes.
A team led by researchers at Simon Fraser University have developed an algorithmic method for identifying CGRs in whole genome shotgun sequencing data that underlie fusion transcripts predicted from matched high-throughput RNA-Seq data based on shortest alternating paths in breakpoint graphs.
The nFuse method is applied to the discovery of CGRs in publicly available data from the well-studied breast cancer cell line HCC1954 and primary prostate tumour sample 963.
The nFuse source code and manual can be downloaded at: http://n-fuse.sourceforge.net/
- McPherson AW, Wu C, Wyatt A, Shah SP, Collins C, Sahinalp SC. (2012) nFuse: Discovery of complex genomic rearrangements in cancer using high-throughput sequencing. Genome Res [Epub ahead of print]. [abstract]