Pegasus – a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer

The extraordinary success of imatinib in the treatment of BCR-ABL1 associated cancers underscores the need to identify novel functional gene fusions in cancer. RNA sequencing offers a genome-wide view of expressed transcripts, uncovering biologically functional gene fusions. Although several bioinformatics tools are already available for the detection of putative fusion transcripts, candidate event lists are plagued with non-functional read-through events, reverse transcriptase template switching events, incorrect mapping, and other systematic errors. Such lists lack any indication of oncogenic relevance, and they are too large for exhaustive experimental validation.

Researchers at Columbia University have designed and implemented a pipeline, Pegasus, for the annotation and prediction of biologically functional gene fusion candidates. Pegasus provides a common interface for various gene fusion detection tools, reconstruction of novel fusion proteins, reading-frame-aware annotation of preserved/lost functional domains, and data-driven classification of oncogenic potential. Pegasus dramatically streamlines the search for oncogenic gene fusions, bridging the gap between raw RNA-Seq data and a final, tractable list of candidates for experimental validation.

rna-seq

Availability and Requirements

Project home page: http://sourceforge.net/p/pegasus-fus.
Operating system: UNIX
Programming language: Java, Perl, Python, BASH

Contact: [email protected].

Abate F, Zairis S, Ficarra E, Acquaviva A, Wiggins CH, Frattini V, Lasorella A, Iavarone A, Inghirami G, Rabadan R. (2014) Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer. BMC Syst Biol 8(1):97. [abstract]