Metagenomic Assay for Identification of Microbial Pathogens in Tumor Tissues

Baldwin, Don A.; Feldman, Michael; Alwine, James C.; Robertson, Erle S.

The PathoChip screening assay described here supported faster laboratory and data analysis turnarounds than those for deep sequencing of whole-genome tumor DNA or RNA and coverage of viral and eukaryotic genomes not assayed by 16S rRNA approaches. The Agilent SurePrint platform is relatively economical compared to other microarray formats and is flexible for quick production of customized probe subsets or updated metagenome compilations, as well as being compatible with a variety of upstream sample preparation strategies. The PathoChip metagenomic assay allows for a comprehensive assessment of the frequency of coinfection by multiple organisms and their correlation with driving oncogenic events. These events can lead to proliferation early in the infection process as well as over an extensive period during which the contributions by these agents may vary or have specific effects on the host cell important for disease development. The data analysis workflows will test for statistically significant interactions between these infectious agents. Critically, as these studies unfold, the PathoChip data in combination with patient genotyping, RNA profiling, and clinical data may be used to search for genetic or environmental predispositions that influence the host-pathogen interactions important for initiation and maintenance of the cancer phenotype.