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

Genome Biol. 2015 Jan 5;16(1):7. doi: 10.1186/s13059-014-0558-0.


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) (, 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Cell Line, Tumor
  • Chromosome Breakpoints*
  • Cluster Analysis
  • Computational Biology* / methods
  • Gene Silencing
  • Genomics
  • High-Throughput Nucleotide Sequencing*
  • Humans
  • In Situ Hybridization, Fluorescence
  • Lung Neoplasms / genetics
  • Oncogene Fusion*
  • Oncogene Proteins, Fusion / genetics
  • Transcriptome*
  • Translocation, Genetic*
  • Tumor Suppressor Proteins / genetics


  • EML4-ALK fusion protein, human
  • Oncogene Proteins, Fusion
  • RASSF8 protein, human
  • Tumor Suppressor Proteins