Jun 10, 2014

Landscape of oncoviral genotype and co-infection via Human papilloma and Hepatitis B viral tumor in-situ profiling

BioRxiv : the Preprint Server for Biology
Peter Acuña CombsBojan Losic

Abstract

Hepatitis B virus (HBV) and human papillomavirus (HPV) infection are known risk factors for developing several cancers. However, the effect of viral genotype and co-infection in actually driving oncogenesis remains unclear. We have developed and deployed a new scalable, high throughput tool (ViralMine) for sensitive and precise oncoviral genotype deconvolution using tumor RNA sequencing data from 537 virally infected liver, cervical, and head and neck tumors. We provide the first comprehensive integrative landscape of tumor-viral gene expression, viral antigen immunogenicity, patient survival, and mutational profiling organized by tumor onco-viral genotype. We find that HBV and HPV genotype, and surprisingly high rates of multi-genotype co-infection, serve as significant predictors of patient survival, tumor immune responsiveness, and APOBEC activity modulation. Finally, we demonstrate that HPV genotype strongly associates with viral onco-gene expression over cancer type, implying expression may be similar across episomal and stochastic integration-based infections.

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Mentioned in this Paper

Study
Sequence Determinations, RNA
Evaluation
Sequencing
Analysis
cDNA Library
Metric
Clinical Protocols
Validation
RNA

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