|Bracing against the wind|
Monday, October 28, 2013
We used RNA-Seq to detect viral homologs in tumor sample expression data obtained from The Cancer Genome Atlas (TCGA) 1. We compared normal tissue viral expression to cancer tissue expression using sequence alignment to a repeat-masked virome, quantification and differential expression. We validated the viral homologs using pileup+scaffold assembly and BLAST of high-complexity contigs.
Roughly 30% of lymphoma cancer samples are associated with EBV, and the majority are associated with either EBV, XMRV or SMRV. The use of controls is essential for removing ubiquitous viruses and viral homologs from results. It was difficult obtaining information about public samples. Each TCGA contributor used different processing methods. Many samples (thyroid, ovarian) did not have whole FASTQ’s (an artifact of using BAM as the primary submission format). Although there are often stringent sample submission guidelines for large-scale projects, there appear to be insufficient guidelines for sequencing and bioinformatics.
Link to poster:
[View/Post Comments] [Digg] [Del.icio.us] [Stumble]
| Bloghop: | Blogarama | Technorati | Blogwise