FusionFinder: a software tool to identify expressed gene fusion candidates from RNA-Seq data.

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 pres...

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Main Authors:	Richard W Francis, Katherine Thompson-Wicking, Kim W Carter, Denise Anderson, Ursula R Kees, Alex H Beesley
Format:	article
Language:	EN
Published:	Public Library of Science (PLoS) 2012
Subjects:	Medicine R Science Q
Online Access:	https://doaj.org/article/5a4ece483d374a75936bb06a1368bb61
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id	oai:doaj.org-article:5a4ece483d374a75936bb06a1368bb61
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spelling	oai:doaj.org-article:5a4ece483d374a75936bb06a1368bb612021-11-18T07:14:11ZFusionFinder: a software tool to identify expressed gene fusion candidates from RNA-Seq data.1932-620310.1371/journal.pone.0039987https://doaj.org/article/5a4ece483d374a75936bb06a1368bb612012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22761941/?tool=EBIhttps://doaj.org/toc/1932-6203The 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/).Richard W FrancisKatherine Thompson-WickingKim W CarterDenise AndersonUrsula R KeesAlex H BeesleyPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 6, p e39987 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Richard W Francis Katherine Thompson-Wicking Kim W Carter Denise Anderson Ursula R Kees Alex H Beesley FusionFinder: a software tool to identify expressed gene fusion candidates from RNA-Seq data.
description	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/).
format	article
author	Richard W Francis Katherine Thompson-Wicking Kim W Carter Denise Anderson Ursula R Kees Alex H Beesley
author_facet	Richard W Francis Katherine Thompson-Wicking Kim W Carter Denise Anderson Ursula R Kees Alex H Beesley
author_sort	Richard W Francis
title	FusionFinder: a software tool to identify expressed gene fusion candidates from RNA-Seq data.
title_short	FusionFinder: a software tool to identify expressed gene fusion candidates from RNA-Seq data.
title_full	FusionFinder: a software tool to identify expressed gene fusion candidates from RNA-Seq data.
title_fullStr	FusionFinder: a software tool to identify expressed gene fusion candidates from RNA-Seq data.
title_full_unstemmed	FusionFinder: a software tool to identify expressed gene fusion candidates from RNA-Seq data.
title_sort	fusionfinder: a software tool to identify expressed gene fusion candidates from rna-seq data.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/5a4ece483d374a75936bb06a1368bb61
work_keys_str_mv	AT richardwfrancis fusionfinderasoftwaretooltoidentifyexpressedgenefusioncandidatesfromrnaseqdata AT katherinethompsonwicking fusionfinderasoftwaretooltoidentifyexpressedgenefusioncandidatesfromrnaseqdata AT kimwcarter fusionfinderasoftwaretooltoidentifyexpressedgenefusioncandidatesfromrnaseqdata AT deniseanderson fusionfinderasoftwaretooltoidentifyexpressedgenefusioncandidatesfromrnaseqdata AT ursularkees fusionfinderasoftwaretooltoidentifyexpressedgenefusioncandidatesfromrnaseqdata AT alexhbeesley fusionfinderasoftwaretooltoidentifyexpressedgenefusioncandidatesfromrnaseqdata
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FusionFinder: a software tool to identify expressed gene fusion candidates from RNA-Seq data.

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