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

被引:34
作者
Francis, Richard W. [1 ]
Thompson-Wicking, Katherine [2 ]
Carter, Kim W. [1 ]
Anderson, Denise [1 ]
Kees, Ursula R. [2 ]
Beesley, Alex H. [2 ]
机构
[1] Univ Western Australia, Ctr Child Hlth Res, Telethon Inst Child Hlth Res, Div Bioinformat & Biostat, Perth, WA 6009, Australia
[2] Univ Western Australia, Ctr Child Hlth Res, Telethon Inst Child Hlth Res, Div Childrens Leukaemia & Canc Res, Perth, WA 6009, Australia
来源
PLOS ONE | 2012年 / 7卷 / 06期
关键词
CHRONIC MYELOGENOUS LEUKEMIA; BREAST-CANCER; TRANSCRIPT; IDENTIFICATION; TRANSLOCATION; DISCOVERY; PATIENT; ABL;
D O I
10.1371/journal.pone.0039987
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
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/).
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页数:12
相关论文
共 36 条
[1]   A novel BCR-ABL fusion gene (e2/1a) in a patient with Philadelphia-positive chronic myelogenous leukaemia and an aggressive clinical course [J].
Byrne, JL ;
Carter, GI ;
Davies, JM ;
Haynes, AP ;
Russell, NH ;
Cross, NCP .
BRITISH JOURNAL OF HAEMATOLOGY, 1998, 103 (03) :791-794
[2]   Identification of fusion genes in breast cancer by paired-end RNA-sequencing [J].
Edgren, Henrik ;
Murumagi, Astrid ;
Kangaspeska, Sara ;
Nicorici, Daniel ;
Hongisto, Vesa ;
Kleivi, Kristine ;
Rye, Inga H. ;
Nyberg, Sandra ;
Wolf, Maija ;
Borresen-Dale, Anne-Lise ;
Kallioniemi, Olli .
GENOME BIOLOGY, 2011, 12 (01)
[3]   Brick1 Is an Essential Regulator of Actin Cytoskeleton Required for Embryonic Development and Cell Transformation [J].
Escobar, Beatriz ;
de Carcer, Guillermo ;
Fernandez-Miranda, Gonzalo ;
Cascon, Alberto ;
Bravo-Cordero, Jose J. ;
Montoya, Maria C. ;
Robledo, Mercedes ;
Canamero, Marta ;
Malumbres, Marcos .
CANCER RESEARCH, 2010, 70 (22) :9349-9359
[4]   Ensembl 2011 [J].
Flicek, Paul ;
Amode, M. Ridwan ;
Barrell, Daniel ;
Beal, Kathryn ;
Brent, Simon ;
Chen, Yuan ;
Clapham, Peter ;
Coates, Guy ;
Fairley, Susan ;
Fitzgerald, Stephen ;
Gordon, Leo ;
Hendrix, Maurice ;
Hourlier, Thibaut ;
Johnson, Nathan ;
Kaehaeri, Andreas ;
Keefe, Damian ;
Keenan, Stephen ;
Kinsella, Rhoda ;
Kokocinski, Felix ;
Kulesha, Eugene ;
Larsson, Pontus ;
Longden, Ian ;
McLaren, William ;
Overduin, Bert ;
Pritchard, Bethan ;
Riat, Harpreet Singh ;
Rios, Daniel ;
Ritchie, Graham R. S. ;
Ruffier, Magali ;
Schuster, Michael ;
Sobral, Daniel ;
Spudich, Giulietta ;
Tang, Y. Amy ;
Trevanion, Stephen ;
Vandrovcova, Jana ;
Vilella, Albert J. ;
White, Simon ;
Wilder, Steven P. ;
Zadissa, Amonida ;
Zamora, Jorge ;
Aken, Bronwen L. ;
Birney, Ewan ;
Cunningham, Fiona ;
Dunham, Ian ;
Durbin, Richard ;
Fernandez-Suarez, Xose M. ;
Herrero, Javier ;
Hubbard, Tim J. P. ;
Parker, Anne ;
Proctor, Glenn .
NUCLEIC ACIDS RESEARCH, 2011, 39 :D800-D806
[5]  
Forbes S A, 2008, Curr Protoc Hum Genet, VChapter 10, DOI 10.1002/0471142905.hg1011s57
[6]  
Ge Huanying., 2011, Bioinformatics
[7]   Transcriptional consequences of genomic structural aberrations in breast cancer [J].
Inaki, Koichiro ;
Hillmer, Axel M. ;
Ukil, Leena ;
Yao, Fei ;
Woo, Xing Yi ;
Vardy, Leah A. ;
Zawack, Kelson Folkvard Braaten ;
Lee, Charlie Wah Heng ;
Ariyaratne, Pramila Nuwantha ;
Chan, Yang Sun ;
Desai, Kartiki Vasant ;
Bergh, Jonas ;
Hall, Per ;
Putti, Thomas Choudary ;
Ong, Wai Loon ;
Shahab, Atif ;
Cacheux-Rataboul, Valere ;
Karuturi, Radha Krishna Murthy ;
Sung, Wing-Kin ;
Ruan, Xiaoan ;
Bourque, Guillaume ;
Ruan, Yijun ;
Liu, Edison T. .
GENOME RESEARCH, 2011, 21 (05) :676-687
[8]   TopHat-Fusion: an algorithm for discovery of novel fusion transcripts [J].
Kim, Daehwan ;
Salzberg, Steven L. .
GENOME BIOLOGY, 2011, 12 (08)
[9]  
Langmead Ben, 2010, Curr Protoc Bioinformatics, VChapter 11, DOI 10.1002/0471250953.bi1107s32
[10]   Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts [J].
Levin, Joshua Z. ;
Berger, Michael F. ;
Adiconis, Xian ;
Rogov, Peter ;
Melnikov, Alexandre ;
Fennell, Timothy ;
Nusbaum, Chad ;
Garraway, Levi A. ;
Gnirke, Andreas .
GENOME BIOLOGY, 2009, 10 (10)