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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2012
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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) |
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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 |
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