Introduction

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.

Publications

  1. Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data.
    Cite this
    Fernandez-Cuesta L, Sun R, Menon R, George J, Lorenz S, Meza-Zepeda LA, Peifer M, Plenker D, Heuckmann JM, Leenders F, Zander T, Dahmen I, Koker M, Schöttle J, Ullrich RT, Altmüller J, Becker C, Nürnberg P, Seidel H, Böhm D, Göke F, Ansén S, Russell PA, Wright GM, Wainer Z, Solomon B, Petersen I, Clement JH, Sänger J, Brustugun OT, Helland Å, Solberg S, Lund-Iversen M, Buettner R, Wolf J, Brambilla E, Vingron M, Perner S, Haas SA, Thomas RK, 2015-01-01 - Genome biology

Credits

  1. Lynnette Fernandez-Cuesta
    Developer

  2. Ruping Sun
    Developer

  3. Roopika Menon
    Developer

  4. Julie George
    Developer

  5. Susanne Lorenz
    Developer

  6. Leonardo A Meza-Zepeda
    Developer

  7. Martin Peifer
    Developer

  8. Dennis Plenker
    Developer

  9. Johannes M Heuckmann
    Developer

  10. Frauke Leenders
    Developer

  11. Thomas Zander
    Developer

  12. Ilona Dahmen
    Developer

  13. Mirjam Koker
    Developer

  14. Jakob Schöttle
    Developer

  15. Roland T Ullrich
    Developer

  16. Janine Altmüller
    Developer

  17. Christian Becker
    Developer

  18. Peter Nürnberg
    Developer

  19. Henrik Seidel
    Developer

  20. Diana Böhm
    Developer

  21. Friederike Göke
    Developer

  22. Sascha Ansén
    Developer

  23. Prudence A Russell
    Developer

  24. Gavin M Wright
    Developer

  25. Zoe Wainer
    Developer

  26. Benjamin Solomon
    Developer

  27. Iver Petersen
    Developer

  28. Joachim H Clement
    Developer

  29. Jörg Sänger
    Developer

  30. Odd-Terje Brustugun
    Developer

  31. Aslaug Helland
    Developer

  32. Steinar Solberg
    Developer

  33. Marius Lund-Iversen
    Developer

  34. Reinhard Buettner
    Developer

  35. Jürgen Wolf
    Developer

  36. Elisabeth Brambilla
    Developer

  37. Martin Vingron
    Developer

  38. Sven Perner
    Developer

  39. Stefan A Haas
    Developer

  40. Roman K Thomas
    Investigator

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Summary
AccessionBT007010
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByRoman K Thomas