Metagenomic Assay for Identification of Microbial Pathogens in Tumor Tissues

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

Validation of PathoChip HPV16 detection. Inspection of HPV16 probe intensities after PathoChip screening (Fig. 6A) revealed patterns of high and low signal across the probe sets and tumor samples with high, low, or undetectable signal overall. PCR primers were designed to regions with high (f1 Ï© r1) or moderate (f2 Ï© r3) signals and adjacent to regions of low signal (primers r2 and r4) (Fig. 6A) . PCR of genomic DNA from representative samples produced the appropriate amplicons from the high-and moderate-signal regions in tumors positive for HPV16 detection. Importantly, amplicons were not observed from HPV16-negative tumors (Fig. 6B) . Occasional faint bands were observed for amplicons using the r2 or r4 primer as expected, as these had low signals in probe sets identified above.