Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples.

ABSTRACT:

Background

Readthrough fusions across adjacent genes in the genome, or transcription-induced chimeras (TICs), have been estimated using expressed sequence tag (EST) libraries to involve 4-6% of all genes. Deep transcriptional sequencing (RNA-Seq) now makes it possible to study the occurrence and expression levels of TICs in individual samples across the genome.

Methods

We performed single-end RNA-Seq on three human prostate adenocarcinoma samples and their corresponding normal tissues, as well as brain and universal reference samples. We developed two bioinformatics methods to specifically identify TIC events: a targeted alignment method using artificial exon-exon junctions within 200,000 bp from adjacent genes, and genomic alignment allowing splicing within individual reads

SUBMITTER: Nacu S 

PROVIDER: S-EPMC3041646 | biostudies-literature | 2011 Jan

REPOSITORIES: biostudies-literature