Fusion Transcript Detection from Short-Read RNA-Seq

Abstract

Fusion proteins have been shown to play an important role in many different cancers and other diseases. While the causal mutation can often be found in the genome as a structural variant (SV), differentiating between normal variation within individuals and somatic variants with functional consequences can be time-consuming as well as expensive since it requires a whole-genome sequencing (WGS) method. RNA Sequencing (RNA-Seq) provides a much cheaper and more straightforward approach to the detection of functional somatic events such as overexpression of proto-oncogenes as well as gene fusion. This chapter aims to discuss the utility of RNA-Seq for fusion detection as well as provide a detailed analysis pipeline for the detection of fusion transcripts.

Keywords: Fusion detection; Gene fusion; RNA-Seq.