FusionAnalyser: a new graphical, event-driven tool for fusion rearrangements discovery.

Nucleic Acids Research
Rocco PiazzaCarlo Gambacorti-Passerini

Abstract

Gene fusions are common driver events in leukaemias and solid tumours; here we present FusionAnalyser, a tool dedicated to the identification of driver fusion rearrangements in human cancer through the analysis of paired-end high-throughput transcriptome sequencing data. We initially tested FusionAnalyser by using a set of in silico randomly generated sequencing data from 20 known human translocations occurring in cancer and subsequently using transcriptome data from three chronic and three acute myeloid leukaemia samples. in all the cases our tool was invariably able to detect the presence of the correct driver fusion event(s) with high specificity. In one of the acute myeloid leukaemia samples, FusionAnalyser identified a novel, cryptic, in-frame ETS2-ERG fusion. A fully event-driven graphical interface and a flexible filtering system allow complex analyses to be run in the absence of any a priori programming or scripting knowledge. Therefore, we propose FusionAnalyser as an efficient and robust graphical tool for the identification of functional rearrangements in the context of high-throughput transcriptome sequencing data.

References

Aug 22, 2001·Seminars in Cancer Biology·P J Shteper, D Ben-Yehuda
Mar 16, 2007·Nature Reviews. Cancer·Felix MitelmanFredrik Mertens
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jul 14, 2009·Proceedings of the National Academy of Sciences of the United States of America·Christopher A MaherArul M Chinnaiyan
Dec 18, 2009·Nature·Erin D PleasancePeter J Campbell
Feb 11, 2011·Nature·Michael F BergerLevi A Garraway

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Citations

Dec 12, 2012·Nature Genetics·Rocco PiazzaCarlo Gambacorti-Passerini
Feb 15, 2013·Biological Procedures Online·Derek Shyr, Qi Liu
Oct 26, 2014·Blood·Carlo B Gambacorti-PasseriniRocco Piazza
Dec 18, 2013·Cancer Genetics·Fengqi Chang, Marilyn M Li
Jul 24, 2014·Nucleic Acids Research·Chun-Ying YuTrees-Juen Chuang
Oct 7, 2015·American Journal of Hematology·Rocco PiazzaCarlo Gambacorti-Passerini
Feb 6, 2014·Molecular Genetics & Genomic Medicine·Roberta SpinelliCarlo Gambacorti-Passerini
Oct 10, 2015·Database : the Journal of Biological Databases and Curation·Manonanthini Thangam, Ramesh Kumar Gopal
Jan 30, 2015·Biology of the Cell·Monika A Davare, Cristina E Tognon
Oct 6, 2012·Methods : a Companion to Methods in Enzymology·Jochen SupperMartin Seifert
Aug 4, 2016·Wiley Interdisciplinary Reviews. RNA·Shailesh KumarHui Li
Mar 30, 2020·Science China. Life Sciences·Cong LiuZhihua Zhang
Nov 17, 2020·HemaSphere·Diletta FontanaCarlo Gambacorti-Passerini

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Methods Mentioned

BETA
chromosomal aberrations
PCR
FusionSeq
while

Software Mentioned

SAM
JPA
Windows
FusionHunter
BWA
FusionAnalyser
FusionSeq
Bowtie
Galaxy
Linux

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