PT  - JOURNAL ARTICLE
AU  - Nadia M. Davidson
AU  - Ian J. Majewski
AU  - Alicia Oshlack
TI  - JAFFA: High sensitivity transcriptome-focused fusion gene detection
AID  - 10.1101/013698
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 013698
4099  - http://biorxiv.org/content/early/2015/01/23/013698.short
4100  - http://biorxiv.org/content/early/2015/01/23/013698.full
AB  - Genomic instability is a hallmark of cancer and, as such, structural alterations and fusion genes are common events in the cancer landscape. RNA sequencing (RNA-Seq) is a powerful method for profiling cancers, but current methods for identifying fusion genes are optimized for short reads. JAFFA (https://code.google.com/p/jaffa-project/) is a sensitive fusion detection method that clearly out-performs other methods with reads of 100bp or greater. JAFFA compares a cancer transcriptome to the reference transcriptome, rather than the genome, where the cancer transcriptome is inferred using long reads directly or by de novo assembling short reads.