Blood and saliva‐derived ctDNA is a marker of residual disease after treatment and correlates with recurrence in human papillomavirus‐associated head and neck cancer

BACKGROUND: There is an alarming increase in human papillomavirus‐associated head and neck cancer (HNC), reaching epidemic levels. While patient prognosis is generally good, off‐target treatment effects are associated with decreased quality of life. Thus, non‐invasive strategies to predict treatment response and risk of recurrence could help de‐escalate treatment. In this study, we tested circulating tumor (ct)DNA in liquid biopsies (blood/saliva) of HPV‐positive HNC patients to assess treatment response and disease progression. METHODS: A total of 235 blood and saliva samples were collected from 60 HPV‐positive and 17 HPV‐negative HNC patients (control group) before and/or after treatment. Samples were analyzed using ddPCR for HPV16/18/31/33/35/45 and correlated with imaging and pathological examination. RESULTS: HPV‐ctDNA detection was significantly higher prior to treatment (91%) than after treatment (8.0%) (χ (2) p < 0.00001), with high concordance between saliva and blood (93%). In matched samples, all patients positive for ctDNA before treatment showed significant reductions in ctDNA levels post treatment (p < 0.0001). All but one patient with persistent ctDNA after treatment showed residual tumor and subsequent recurrence. Finally, fragmentomic analysis revealed shifts in cell‐free DNA fragment size after treatment, suggesting a complementary biomarker for treatment response. CONCLUSIONS: Blood and saliva were found to be good sources of HPV‐ctDNA. The presence of ctDNA strongly correlated with treatment response, demonstrating clinical utility as a non‐invasive biomarker to monitor tumor progression in HPV‐positive HNC. Liquid biopsy based ctDNA testing could be an effective approach to predict recurrence and stratify patients for de‐escalation of treatment, thereby improving quality of life.