Recently various studies have established role of tumor associated pathogens, including bacteria and viruses, in determining the progression of disease and clinical outcomes of the patients. This demands tools and methodologies for better detection and quantification of pathogens in tumor samples. For systematic detection and quantification of cancer associated pathogens in NGS samples, we have developed Cancer Pathogen Detector (CPD) -- a novel computational tool to detect the presence of 1070 pathogenic strains with high specificity and sensitivity using whole exome, genome, and transcriptome data. CPD comprises of in-built modules to filter low quality reads and reports sample-wise normalized quantification of pathogens along with comprehensive annotation of the pathogen-genes detected in the tumor samples. Using this novel computational methodology we aim to identify novel infectious agent associations with various tumor types and probe for novel putative mechanisms of pathogenesis.
Figure: Cancer Pathogen Detector analytical workflow