Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data

被引：37

作者：

Fernandez-Cuesta, Lynnette ^{[1
,2
]}

Sun, Ruping ^{[3
,4
]}

Menon, Roopika ^{[5
,7
,8
]}

George, Julie ^{[1
,6
]}

Lorenz, Susanne

Meza-Zepeda, Leonardo A.

Peifer, Martin ^{[1
,9
]}

Plenker, Dennis ^{[1
]}

Heuckmann, Johannes M.

Leenders, Frauke ^{[1
]}

Zander, Thomas ^{[1
,11
]}

Dahmen, Ilona ^{[1
]}

Koker, Mirjam ^{[1
]}

Schoettle, Jakob ^{[1
,12
]}

Ullrich, Roland T. ^{[9
,10
,12
]}

Altmueller, Janine ^{[13
,14
,15
]}

Becker, Christian

Nuernberg, Peter ^{[13
,14
]}

Seidel, Henrik ^{[16
]}

Boehm, Diana

Goeke, Friederike

Ansen, Sascha

Russell, Prudence A. ^{[17
]}

Wright, Gavin M. ^{[18
]}

Wainer, Zoe ^{[18
]}

Solomon, Benjamin ^{[19
]}

Petersen, Iver ^{[20
]}

Clement, Joachim H. ^{[21
]}

Saenger, Joerg ^{[22
]}

Brustugun, Odd-Terje ^{[23
]}

Helland, Aslaug ^{[23
,24
]}

Solberg, Steinar ^{[25
]}

Lund-Iversen, Marius ^{[26
]}

Buettner, Reinhard ^{[27
]}

Wolf, Juergen

Brambilla, Elisabeth ^{[28
]}

Vingron, Martin ^{[3
]}

Perner, Sven

Haas, Stefan A.

Thomas, Roman K. ^{[1
,27
]}

机构：

[1] Univ Cologne, Fac Med, Ctr Integrated Oncol Cologne Bonn, Dept Translat Gen, D-50924 Cologne, Germany

[2] WHO, IARC, Genet Canc Susceptibil Grp, Genet Sect, F-69008 Lyon, France

[3] Max Planck Inst Mol Genet, Computat Mol Biol Grp, D-14195 Berlin, Germany

[4] Columbia Univ, Dept Syst Biol, New York, NY 10032 USA

[5] Univ Hosp Bonn, Ctr Integrated Oncol Cologne Bonn, Inst Pathol, Dept Prostate Canc Res, Bonn, Germany

[6] Blackfield AG, D-51105 Cologne, Germany

[7] Oslo Univ Hosp, Norwegian Radium Hosp, Dept Tumor Biol, N-0310 Oslo, Norway

[8] Oslo Univ Hosp, Norwegian Radium Hosp, Genom Core Facil, N-0310 Oslo, Norway

[9] Univ Cologne, CMMC, D-50931 Cologne, Germany

[10] Univ Cologne, Ctr Integrated Oncol Cologne Bonn, Dept Internal Med, D-50924 Cologne, Germany

[11] Univ Hosp Cologne, Ctr Integrated Oncol Cologne Bonn, Network Genom Med, D-50924 Cologne, Germany

[12] Max Planck Inst Neurol Res, D-50931 Cologne, Germany

[13] Univ Cologne, CCG, D-50931 Cologne, Germany

[14] Univ Cologne, Cologne Excellence Cluster Cellular Stress Respon, Cologne, Germany

[15] Univ Cologne, Inst Human Genet, D-50931 Cologne, Germany

[16] Bayer Schering, Berlin, Germany

[17] St Vincents Hosp, Dept Pathol, Melbourne, Vic 3065, Australia

[18] Univ Melbourne, St Vincents Hosp, Dept Surg, Melbourne, Vic 3065, Australia

[19] Peter MacCallum Canc Ctr, Dept Haematol & Med Oncol, Melbourne, Vic 3002, Australia

[20] Univ Jena, Jena Univ Hosp, Inst Pathol, D-07743 Jena, Germany

[21] Univ Jena, Jena Univ Hosp, Dept Internal Med 2, D-07743 Jena, Germany

[22] Inst Pathol Bad Berka, D-99438 Bad Berka, Germany

[23] Univ Oslo, Fac Med, Inst Clin Med, N-0424 Oslo, Norway

[24] Oslo Univ Hosp, Norwegian Radium Hosp, Dept Oncol, N-0310 Oslo, Norway

[25] Oslo Univ Hosp, Rikshosp, Dept Thorac Surg, N-0027 Oslo, Norway

[26] Oslo Univ Hosp, Norwegian Radium Hosp, Dept Pathol, N-0310 Oslo, Norway

[27] Univ Cologne, Univ Hosp Med Ctr, Dept Pathol, D-50937 Cologne, Germany

[28] CHU Grenoble, INSERM, Inst Albert Bonniot, Dept Pathol,U823, F-38043 Grenoble, France

来源：

GENOME BIOLOGY | 2015年 / 16卷

关键词：

END RNA-SEQ; TUMOR; ALGORITHMS; MUTATIONS; DISCOVERY; RASSF8;

D O I：

10.1186/s13059-014-0558-0

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Genomic translocation events frequently underlie cancer development through generation of gene fusions with oncogenic properties. Identification of such fusion transcripts by transcriptome sequencing might help to discover new potential therapeutic targets. We developed TRUP (Tumor-specimen suited RNA-seq Unified Pipeline) (https://github.com/ruping/TRUP), a computational approach that combines split-read and read-pair analysis with de novo assembly for the identification of chimeric transcripts in cancer specimens. We apply TRUP to RNA-seq data of different tumor types, and find it to be more sensitive than alternative tools in detecting chimeric transcripts, such as secondary rearrangements in EML4-ALK-positive lung tumors, or recurrent inactivating rearrangements affecting RASSF8.

引用

页数：11

共 28 条

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