Friday, June 29, 2012

Fwd: FusionFinder: A Software Tool to Identify Expressed Gene Fusion Candidates from RNA-Seq Data

Fwd: please follow footer link
FusionFinder: A Software Tool to Identify Expressed Gene Fusion Candidates from RNA-Seq Data:

by Richard W. Francis, Katherine Thompson-Wicking, Kim W. Carter, Denise Anderson, Ursula R. Kees, Alex H. Beesley


The hallmarks of many haematological malignancies and solid tumours are chromosomal translocations, which may lead to gene fusions. Recently, next-generation sequencing techniques at the transcriptome level (RNA-Seq) have been used to verify known and discover novel transcribed gene fusions. We present FusionFinder, a Perl-based software designed to automate the discovery of candidate gene fusion partners from single-end (SE) or paired-end (PE) RNA-Seq read data. FusionFinder was applied to data from a previously published analysis of the K562 chronic myeloid leukaemia (CML) cell line. Using FusionFinder we successfully replicated the findings of this study and detected additional previously unreported fusion genes in their dataset, which were confirmed experimentally. These included two isoforms of a fusion involving the genes BRK1 and VHL, whose co-deletion has previously been associated with the prevalence and severity of renal-cell carcinoma. FusionFinder is made freely available for non-commercial use and can be downloaded from the project website (http://bioinformatics.childhealthresearch.org.au/software/fusionfinder/).

(Original Post: PLoS ONE Alerts: Computational Biology.)