Impact of RNA degradation on fusion detection by RNA-seq.

ABSTRACT:

Background

RNA-seq is a well-established method for studying the transcriptome. Popular methods for library preparation in RNA-seq such as Illumina TruSeq® RNA v2 kit use a poly-A pulldown strategy. Such methods can cause loss of coverage at the 5' end of genes, impacting the ability to detect fusions when used on degraded samples. The goal of this study was to quantify the effects RNA degradation has on fusion detection when using poly-A selected mRNA and to identify the variables involved in this process.

Results

Using both artificially and naturally degraded samples, we found that there is a reduced ability to detect fusions as the distance of the breakpoint from the 3' end of the gene increases. The median transcript coverage decreases exponentially as a function of the

SUBMITTER: Davila JI 

PROVIDER: S-EPMC5072325 | biostudies-literature | 2016 Oct

REPOSITORIES: biostudies-literature