Metagenomic Assay for Identification of Microbial Pathogens in Tumor Tissues

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

Assay response to positive controls. The limited amounts of tissue available in most tumor archives or obtained from clinical procedures, such as fine needle aspirates and other biopsy specimens, require that metagenomic screening protocols include efficient strategies for nucleic acid extractions combined with an amplification step which allows for genome-or transcriptome-wide representation of microbial agents present in the sample. These methods must additionally be compatible with the degraded DNA and RNA typically produced by formalin tissue fixation. A draft workflow was designed to address these technical hurdles (Fig. 1C) , and pilot experiments were conducted to test the amplification and detection of a number of positive-control viruses.