Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript

Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript by Matteo Benelli, Chiara Pescucci, Giuseppina Marseglia, Marco Severgnini, Francesca Torricelli and Alberto Magi published in Bioinformatics October 2012.

Abstract

Motivation: The discovery of novel gene fusions can lead to a better comprehension of cancer progression and development. The emergence of deep sequencing of trancriptome, known as RNAseq, has opened many opportunities for the identification of this class of genomic alterations, leading to the discovery of novel chimeric transcripts in melanomas, breast cancers and lymphomas. Nowadays, few computational approaches have been developed for the detection of chimeric transcripts. Although all of these computational methods show good sensitivity, much work remains to reduce the huge number of false positive calls that arises from this analysis.

Results: We proposed a novel computational framework, named chimEric tranScript detection algorithm (EricScript), for the identification of gene fusion products in paired-end RNA-seq data. Our simulation study on synthetic data demonstrates that EricScript enables to achieve higher sensitivity and specificity than existing methods with noticeably lower running times. We also applied our method to publicly available RNA-seq tumour datasets and we showed its capability in rediscovering known gene fusions.

Availability: The EricScript package is freely available under GPL v3 license at http://ericscript.sourceforge.net.