September 22, 2019  |  

JAFFA: High sensitivity transcriptome-focused fusion gene detection.

Authors: Davidson, Nadia M and Majewski, Ian J and Oshlack, Alicia

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 optimised for short reads. JAFFA ( is a sensitive fusion detection method that outperforms other methods with reads of 100 bp 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.

Journal: Genome medicine
DOI: 10.1186/s13073-015-0167-x
Year: 2015

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