HPV cell free DNA as a marker of response to chemoradiation for HPV-positive oropharngeal cancers.

6083Background: Circulating cell free plasma DNA(cfDNA) can be a sensitive biomarker of tumor burden that is accessible by simple phlebotomy. Virally induced cancers present unique advantages for cfDNA technologies in that viral genomes present a cancer-specific, broadly applicable target for assessment by quantitative PCR(qPCR) without any additional DNA processing steps that reduce DNA yield. In this pilot study, we hypothesize that qPCR of HPV16 cfDNA can serve as a marker of disease burden after a course of chemoradiation for HPV-associated oropharyngeal cancer(OPC). Methods: Patients were consented and enrolled on MSKCC specimen protocol #06-107. 8-10 mL of blood was collected in EDTA-lined vacutainer tubes before the first fraction of radiation and after the completion of radiation. Within 30 minutes of phlebotomy, samples were centrifuged at 820g for 10 minutes. The upper plasma layer was further centrifuged at 16,000g for 10 minutes to remove any remaining cell debris. DNA was extracted from the u...