Viral expression associated with gastrointestinal adenocarcinomas in TCGA high-throughput sequencing data.

ABSTRACT:

Background

Up to 20% of cancers worldwide are thought to be associated with microbial pathogens, including bacteria and viruses. The widely used methods of viral infection detection are usually limited to a few a priori suspected viruses in one cancer type. To our knowledge, there have not been many broad screening approaches to address this problem more comprehensively.

Methods

In this study, we performed a comprehensive screening for viruses in nine common cancers using a multistep computational approach. Tumor transcriptome and genome sequencing data were available from The Cancer Genome Atlas (TCGA). Nine hundred fifty eight primary tumors in nine common cancers with poor prognosis were screened against a non-redundant database of virus sequences. DNA sequences from norm

SUBMITTER: Salyakina D 

PROVIDER: S-EPMC3906926 | biostudies-literature | 2013 Nov

REPOSITORIES: biostudies-literature