Metagenomic Assay for Identification of Microbial Pathogens in Tumor Tissues

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

These and other array-based tools illustrate the demand for methods to quickly and economically screen sets of samples for broad microbial content, including species beyond bacteria (23) . This report describes development of the PathoChip platform containing probes for all known publicly available virus sequences and hundreds of pathogenic bacteria, fungi, and helminths, providing wide coverage of microbial pathogens in an economical format. Where possible, multiple probes to independent regions of the target genome are used to improve an opportunity for detection. Furthermore, while the PathoChip content was developed from sequences to known targets, the ability to discover new strains or organisms is provided by the inclusion of probes to sequences that are conserved within and between viral families. To this end, a previously unknown virus with homology to a conserved sequence may produce a corresponding hybridization signal from such a probe, if not to a complete probe set. A supporting workflow is described for profiling large collections of tumor samples typically available as formalin-fixed, paraffin-embedded (FFPE) tissue in biobanks and includes simultaneous detection of DNA and RNA to expand the range of targets available for hybridization.