viGEN: An open source pipeline for the detection and quantification of viral RNA in human tumors

Abstract

ABSTRACTAn estimated 17% of cancers worldwide are associated with infectious causes. The extent and biological significance of viral presence/infection in actual tumor samples is generally unknown but could be measured using human transcriptome (RNA-seq) data from tumor samples.We present an open source bioinformatics pipeline viGEN, which combines existing well-known and novel RNA-seq tools for not only the detection and quantification of viral RNA, but also variants in the viral transcripts.The pipeline includes 4 major modules: The first module allows to align and filter out human RNA sequences; the second module maps and count (remaining un-aligned) reads against reference genomes of all known and sequenced human viruses; the third module quantifies read counts at the individual viral genes level thus allowing for downstream differential expression analysis of viral genes between experimental and controls groups. The fourth module calls variants in these viruses. To the best of our knowledge, there are no publicly available pipelines or packages that would provide this type of complete analysis in one open source package.In this paper, we applied the viGEN pipeline to two case studies. We first demonstrate the working of our pipeline on a large public dataset, the TCGA cervical cancer cohort. We also performed additional in-depth analyses on a small focused study of TCGA liver cancer patients. In this cohort, we perform viral-gene quantification, viral-variant extraction and survival analysis. This allowed us to find differentially expressed viral-transcripts and viral-variants between the groups of patients, and connect them to clinical outcome.From our analyses, we show that we were able to successfully detect the human papilloma virus among the TCGA cervical cancer patients. We compared the viGEN pipeline with two metagenomics tools and demonstrate similar sensitivity/specificity. We were also able to quantify viral-transcripts and extract viral-variants using the liver cancer dataset. The results presented corresponded with published literature in terms of rate of detection, viral gene expression patterns and impact of several known variants of HBV genome. Results also show novel information about distinct patterns of expression and co-expression in Hepatitis B and the Human Endogenous Retrovirus (HERV) K113 viruses.This pipeline is generalizable, and can be used to provide novel biological insights into the significance of viral and other microbial infections in complex diseases, tumorigeneses and cancer immunology. The source code, with example data and tutorial is available at: https://github.com/ICBI/viGEN/.