FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq.

ABSTRACT:

Background

Gene fusions, which result from abnormal chromosome rearrangements, are a pathogenic factor in cancer development. The emerging RNA-Seq technology enables us to detect gene fusions and profile their features.

Results

In this paper, we proposed a novel fusion detection tool, FusionQ, based on paired-end RNA-Seq data. This tool can detect gene fusions, construct the structures of chimerical transcripts, and estimate their abundances. To confirm the read alignment on both sides of a fusion point, we employed a new approach, "residual sequence extension", which extended the short segments of the reads by aggregating their overlapping reads. We also proposed a list of filters to control the false-positive rate. In addition, we estimated fusion abundance using the Expec

SUBMITTER: Liu C 

PROVIDER: S-EPMC3691734 | biostudies-literature | 2013 Jun

REPOSITORIES: biostudies-literature