Fernandez-Cuesta, Lynnette ORCID: 0000-0002-0724-6703, Sun, Ruping, Menon, Roopika, George, Julie, Lorenz, Susanne, Meza-Zepeda, Leonardo A., Peifer, Martin ORCID: 0000-0002-5243-5503, Plenker, Dennis, Heuckmann, Johannes M., Leenders, Frauke, Zander, Thomas, Dahmen, Ilona, Koker, Mirjam, Schoettle, Jakob, Ullrich, Roland T., Altmueller, Janine, Becker, Christian, Nuernberg, Peter, Seidel, Henrik ORCID: 0000-0001-7804-5143, Boehm, Diana, Goeke, Friederike, Ansen, Sascha, Russell, Prudence A., Wright, Gavin M., Wainer, Zoe, Solomon, Benjamin, Petersen, Iver, Clement, Joachim H. ORCID: 0000-0002-6601-2456, Saenger, Joerg, Brustugun, Odd-Terje, Helland, Aslaug ORCID: 0000-0002-5520-0275, Solberg, Steinar, Lund-Iversen, Marius, Buettner, Reinhard, Wolf, Juergen, Brambilla, Elisabeth, Vingron, Martin, Perner, Sven, Haas, Stefan A. and Thomas, Roman K. (2015). Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data. Genome Biol., 16. LONDON: BIOMED CENTRAL LTD. ISSN 1474-760X

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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.

Item Type: Journal Article
Creators:
CreatorsEmailORCIDORCID Put Code
Fernandez-Cuesta, LynnetteUNSPECIFIEDorcid.org/0000-0002-0724-6703UNSPECIFIED
Sun, RupingUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Menon, RoopikaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
George, JulieUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Lorenz, SusanneUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Meza-Zepeda, Leonardo A.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Peifer, MartinUNSPECIFIEDorcid.org/0000-0002-5243-5503UNSPECIFIED
Plenker, DennisUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Heuckmann, Johannes M.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Leenders, FraukeUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Zander, ThomasUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Dahmen, IlonaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Koker, MirjamUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Schoettle, JakobUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Ullrich, Roland T.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Altmueller, JanineUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Becker, ChristianUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Nuernberg, PeterUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Seidel, HenrikUNSPECIFIEDorcid.org/0000-0001-7804-5143UNSPECIFIED
Boehm, DianaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Goeke, FriederikeUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Ansen, SaschaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Russell, Prudence A.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wright, Gavin M.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wainer, ZoeUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Solomon, BenjaminUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Petersen, IverUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Clement, Joachim H.UNSPECIFIEDorcid.org/0000-0002-6601-2456UNSPECIFIED
Saenger, JoergUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Brustugun, Odd-TerjeUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Helland, AslaugUNSPECIFIEDorcid.org/0000-0002-5520-0275UNSPECIFIED
Solberg, SteinarUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Lund-Iversen, MariusUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Buettner, ReinhardUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wolf, JuergenUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Brambilla, ElisabethUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Vingron, MartinUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Perner, SvenUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Haas, Stefan A.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Thomas, Roman K.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
URN: urn:nbn:de:hbz:38-414788
DOI: 10.1186/s13059-014-0558-0
Journal or Publication Title: Genome Biol.
Volume: 16
Date: 2015
Publisher: BIOMED CENTRAL LTD
Place of Publication: LONDON
ISSN: 1474-760X
Language: English
Faculty: Unspecified
Divisions: Unspecified
Subjects: no entry
Uncontrolled Keywords:
KeywordsLanguage
END RNA-SEQ; TUMOR; ALGORITHMS; MUTATIONS; DISCOVERY; RASSF8Multiple languages
Biotechnology & Applied Microbiology; Genetics & HeredityMultiple languages
URI: http://kups.ub.uni-koeln.de/id/eprint/41478

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