title: FusionFinder: a software tool to identify expressed gene fusion candidates from RNA-Seq data.
abstract: 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/).
authors: Division of Bioinformatics and Biostatistics, Telethon Institute for Child Health Research, Centre for Child Health Research, The University of Western Australia, Perth, Australia. rfrancis@ichr.uwa.edu.au
authors: Richard W
authors: RW
authors: Francis
authors: Katherine
authors: K
authors: Thompson-Wicking
authors: Kim W
authors: KW
authors: Carter
authors: Denise
authors: D
authors: Anderson
authors: Ursula R
authors: UR
authors: Kees
authors: Alex H
authors: AH
authors: Beesley
mesh_terms: D001331:Automation; D001483:Base Sequence; D050939:Gene Fusion; D006801:Humans; D020014:K562 Cells; D008969:Molecular Sequence Data; D012313:RNA / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D059467:Transcriptome
chemical_list: D012313:RNA