Background

Certain types of cancers can be initiated by viruses. The co-infection rates for these oncogenic viruses in cancer diagnosed patients are largely unknown and not easily attainable by serotyping (serologic tests allow identification of tumor-free virus. However, they do not provide information on the tumor -viral ecosystem or the co-infection status of the tumor, unless testing for it explicitly). Because the clinical response to therapy can depend on the viruses present in the tumor, it is important to be able to provide a personalized tumor infection status for each patient.

Technology Overview

ViralMine is an algorithm that quantifies tumor viral phenotype (oncoviral genotype, viral gene expression, and co-infection estimation) in human solid tumors. Using tumoral RNA-seq data, ViralMine characterizes the infection in the tumor: viral genotyping, viral abundance calling, and single virus coinfection characterization.

Further Details

Landscape of oncoviral genotype and co-infection via Human papilloma and Hepatitis B viral tumor in-situ profiling. Adrian Bubie, Fabien Zoulim, Barbara Testoni, Brett Miles, MarshallPosner, Augusto Villanueva, Bojan Losic. Published in bioRxiv

Stage of Development

Mount Sinai has developed and deployed a new scalable, high throughput tool (ViralMine) for sensitive and precise oncoviral genotype deconvolution using tumor RNA sequencing data from537 virally infected liver, cervical, and head and neck tumors (TCGA).

The tool is publicly available for research and teaching purposes: https://github.com/LosicLab/ViralMine.

Benefits

This innovative virus detection method is the only available method to date that presents a consensus co-infection call for the patient given multiple viral genotypes present (e.g. HPV18 andHPV45).
Sensitivity and specificity performance of virus detection is on par to other existing viral genotyping bioinformatic tools (e.g. VarScan), with 99% accuracy and precision in a limited validation cohort from the TCGA.
Can be used with existing, standard tumor RNA-Seq data (no special sequencing method required) and has been demonstrated to maintain performance in samples with low coverage and/or low viral burden.

Applications

The tool allows for comprehensive integration of viral phenotype with tumor-viral geneexpression, viral antigen immunogenicity, patient survival, and mutational profiling organized byviral genotyping.

Opportunity

The tool is to be licensed for commercial use.

ViralMine: Oncogenic Viral Genotyper

Seeking