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JAFFA: High sensitivity transcriptome-focused fusion gene detection.

ABSTRACT: 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 (https://github.com/Oshlack/JAFFA/wiki) 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.

SUBMITTER: Davidson NM

PROVIDER: S-EPMC4445815 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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JAFFA: High sensitivity transcriptome-focused fusion gene detection.

Davidson Nadia M NM Majewski Ian J IJ Oshlack Alicia A

Genome medicine 20150511 1

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 (https://github.com/Oshlack/JAFFA/wiki) 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 transc ...[more]

PMID: 26019724

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