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| Item Type: | Article |
|---|---|
| Title: | Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data |
| Creators Name: | Fernandez-Cuesta, L. and Sun, R. and Menon, R. and George, J. and Lorenz, S. and Meza-Zepeda, L.A. and Peifer, M. and Plenker, D. and Heuckmann, J.M. and Leenders, F. and Zander, T. and Dahmen, I. and Koker, M. and Schöttle, J. and Ullrich, R.T. and Altmüller, J. and Becker, C. and Nürnberg, P. and Seidel, H. and Böhm, D. and Göke, F. and Ansén, S. and Russell, P.A. and Wright, G.M. and Wainer, Z. and Solomon, B. and Petersen, I. and Clement, J.H. and Sänger, J. and Brustugun, O.T. and Helland, Å. and Solberg, S. and Lund-Iversen, M. and Buettner, R. and Wolf, J. and Brambilla, E. and Vingron, M. and Perner, S. and Haas, S.A. and Thomas, R.K. |
| 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. |
| Keywords: | Fusion Transcript, Crizotinib, Read Pair, Chimeric Transcript, Fusion Point |
| Source: | Genome Biology |
| ISSN: | 1465-6906 |
| Publisher: | BioMed Central |
| Volume: | 16 |
| Page Range: | 7 |
| Date: | 5 January 2015 |
| Additional Information: | Copyright © 2015 Fernandez-Cuesta et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
| Official Publication: | https://doi.org/10.1186/s13059-014-0558-0 |
| PubMed: | View item in PubMed |
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