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

Fernandez-Cuesta, Lynnette; Sun, Ruping; Menon, Roopika; George, Julie; Lorenz, Susanne; Meza-Zepeda, Leonardo A.; Peifer, Martin; Plenker, Dennis; Heuckmann, Johannes M.; Leenders, Frauke; Zander, Thomas; Dahmen, Ilona; Koker, Mirjam; Schöttle, Jakob; Ullrich, Roland T.; Altmüller, Janine; Becker, Christian; Nürnberg, Peter; Seidel, Henrik; Böhm, Diana; Göke, Friederike; Ansen, Sascha; Russell, Prudence A.; Wright, Gavin M.; Wainer, Zoe; Solomon, Benjamin; Petersen, Iver; Clement, Joachim H.; Sänger, Jörg; Brustugun, Odd Terje; Helland, Aslaug; Solberg, Steinar; Lund-Iversen, Marius; Büttner, Reinhard; Wolf, Jürgen; Brambilla, Elisabeth; Vingron, Martin; Perner, Sven; Haas, Stefan A.; Thomas, Roman K.

doi:10.1186/s13059-014-0558-0

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

Fernandez-Cuesta, L., Sun, R., Menon, R., George, J., Lorenz, S., Meza-Zepeda, L. A., et al. (2015). Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data. Genome Biology: Biology for the Post-Genomic Era, 16: 16:7. doi:10.1186/s13059-014-0558-0.

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Fernandez-Cuesta, Lynnette¹, Author
Sun, Ruping¹, Author
Menon, Roopika¹, Author
George, Julie¹, Author
Lorenz, Susanne¹, Author
Meza-Zepeda, Leonardo A.¹, Author
Peifer, Martin², Author
Plenker, Dennis¹, Author
Heuckmann, Johannes M.², Author
Leenders, Frauke¹, Author
Zander, Thomas³, Author
Dahmen, Ilona¹, Author
Koker, Mirjam², Author
Schöttle, Jakob³, Author
Ullrich, Roland T.³, Author
Altmüller, Janine¹, Author
Becker, Christian¹, Author
Nürnberg, Peter¹, Author
Seidel, Henrik¹, Author
Böhm, Diana¹, Author
Göke, Friederike¹, AuthorAnsen, Sascha¹, AuthorRussell, Prudence A.¹, AuthorWright, Gavin M.¹, AuthorWainer, Zoe¹, AuthorSolomon, Benjamin¹, AuthorPetersen, Iver¹, AuthorClement, Joachim H.¹, AuthorSänger, Jörg¹, AuthorBrustugun, Odd Terje¹, AuthorHelland, Aslaug¹, AuthorSolberg, Steinar¹, AuthorLund-Iversen, Marius¹, AuthorBüttner, Reinhard¹, AuthorWolf, Jürgen¹, AuthorBrambilla, Elisabeth¹, AuthorVingron, Martin⁴, Author         Perner, Sven¹, AuthorHaas, Stefan A.⁵, Author         Thomas, Roman K.², Author          more..

Affiliations:
1[ 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 ] Univ Cologne, CCG, D-50931 Cologne, Germany [ 13 ] Univ Cologne, Cologne Excellence Cluster Cellular Stress Respon, Cologne, Germany [ 14 ] Univ Cologne, Inst Human Genet, D-50931 Cologne, Germany [ 15 ] Bayer Schering, Berlin, Germany [ 16 ] St Vincents Hosp, Dept Pathol, Melbourne, Vic 3065, Australia [ 17 ] Univ Melbourne, St Vincents Hosp, Dept Surg, Melbourne, Vic 3065, Australia [ 18 ] Peter MacCallum Canc Ctr, Dept Haematol & Med Oncol, Melbourne, Vic 3002, Australia [ 19 ] Univ Jena, Jena Univ Hosp, Inst Pathol, D-07743 Jena, Germany [ 20 ] Univ Jena, Jena Univ Hosp, Dept Internal Med 2, D-07743 Jena, Germany [ 21 ] Inst Pathol Bad Berka, D-99438 Bad Berka, Germany [ 22 ] Univ Oslo, Fac Med, Inst Clin Med, N-0424 Oslo, Norway [ 23 ] Oslo Univ Hosp, Norwegian Radium Hosp, Dept Oncol, N-0310 Oslo, Norway [ 24 ] Oslo Univ Hosp, Rikshosp, Dept Thorac Surg, N-0027 Oslo, Norway [ 25 ] Oslo Univ Hosp, Norwegian Radium Hosp, Dept Pathol, N-0310 Oslo, Norway [ 26 ] Univ Cologne, Univ Hosp Med Ctr, Dept Pathol, D-50937 Cologne, Germany [ 27 ] CHU Grenoble, INSERM, Inst Albert Bonniot, Dept Pathol,U823, F-38043 Grenoble, France, ou_persistent22
2Funktionelle Krebsgenomforschung, Junior Research Groups, Max-Planck-Institut für neurologische Forschung, Managing Director: D. Yves von Cramon, Max Planck Institute for Metabolism Research, Managing Director: Jens Brüning, Max Planck Society, ou_2149656
3Klinisches PET, Neurologische Abteilung, Max-Planck-Institut für neurologische Forschung, Managing Director: D. Yves von Cramon, Max Planck Institute for Metabolism Research, Managing Director: Jens Brüning, Max Planck Society, ou_2149663
4Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479639
5Gene Structure and Array Design (Stefan Haas), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479640

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Abstract: 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.

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Language(s): eng - English

Dates: Published Online: 2015-01-05

Publication Status: Published online

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Identifiers: DOI: 10.1186/s13059-014-0558-0

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Title: Genome Biology : Biology for the Post-Genomic Era

Source Genre: Journal

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Publ. Info: London : BioMed Central Ltd.

Pages: - Volume / Issue: 16 Sequence Number: 16:7 Start / End Page: - Identifier: ISSN: 1465-6906
CoNE: https://pure.mpg.de/cone/journals/resource/1000000000224390