Related Experiment Video
Updated: Apr 17, 2026
Oncogenic Gene Fusion Detection Using Anchored Multiplex Polymerase Chain Reaction Followed by Next Generation Sequencing
Published on: July 5, 2019
Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data
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.
Insights
We developed TRUP, a computational tool to identify gene fusions in cancer specimens. TRUP is more sensitive than existing methods for detecting chimeric transcripts and potential therapeutic targets.
Area of Science:
- Genomics
- Bioinformatics
- Cancer Research
Background:
- Genomic translocations drive cancer by creating oncogenic gene fusions.
- Identifying these fusion transcripts is crucial for discovering novel therapeutic targets.
Purpose of the Study:
- To develop a sensitive computational approach for identifying chimeric transcripts in cancer specimens.
- To evaluate the performance of the developed tool against existing methods.
Main Methods:
- Development of TRUP (Tumor-specimen suited RNA-seq Unified Pipeline), a computational pipeline.
- TRUP integrates split-read, read-pair analysis, and de novo assembly.
- Application of TRUP to RNA-sequencing data from various tumor types.
Main Results:
- TRUP demonstrated higher sensitivity in detecting chimeric transcripts compared to alternative tools.
- Identified secondary rearrangements in EML4-ALK-positive lung tumors.
- Detected recurrent inactivating rearrangements affecting RASSF8.
Conclusions:
- TRUP is a sensitive and effective tool for identifying oncogenic gene fusions in cancer.
- The pipeline aids in the discovery of potential therapeutic targets through comprehensive chimeric transcript identification.
