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Journal Article

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

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/persons/resource/persons147255

Peifer,  Martin
Funktionelle 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;

/persons/resource/persons147193

Heuckmann,  Johannes M.
Funktionelle 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;

/persons/resource/persons147352

Zander,  Thomas
Klinisches 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;

/persons/resource/persons147213

Koker,  Mirjam
Funktionelle 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;

/persons/resource/persons147290

Schöttle,  Jakob
Klinisches 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;

/persons/resource/persons147322

Ullrich,  Roland T.
Klinisches 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;

/persons/resource/persons50613

Vingron,  Martin
Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

/persons/resource/persons50183

Haas,  Stefan A.
Gene Structure and Array Design (Stefan Haas), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

/persons/resource/persons147315

Thomas,  Roman K.
Funktionelle 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;

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Citation

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.


Cite as: https://hdl.handle.net/11858/00-001M-0000-002A-3ADC-F
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.