New Liquid Biopsy May Detect HPV-Related Cancers 10 Years Before Symptoms: Study Finds

To address this gap, researchers led by Dr. Daniel L. Faden, head and neck surgical oncologist at Mass Eye and Ear, developed HPV-DeepSeek, a tool that uses whole-genome sequencing to identify trace fragments of HPV DNA shed into the bloodstream by early-stage tumors.

The team tested 56 blood samples from the Mass General Brigham Biobank — 28 from individuals who developed HPV-related head and neck cancer years later and 28 from healthy controls. HPV-DeepSeek detected tumor DNA in 22 of the 28 pre-diagnosis samples, with zero false positives among controls. Using machine learning, the test's accuracy improved further, identifying 27 of 28 future cancer cases, including samples collected up to 10 years before diagnosis.

“Our study shows for the first time that we can accurately detect HPV-associated cancers in asymptomatic individuals many years before they are ever diagnosed with cancer,” said Dr. Faden. “We hope tools like HPV-DeepSeek will allow us to catch these cancers at their very earliest stages, which ultimately can improve patient outcomes and quality of life.”

These findings highlight the promise of HPV-DeepSeek as a future screening tool, potentially enabling earlier, less invasive treatment for thousands of at-risk individuals.

Reference: Das, D., et al. (2025). Circulating tumor human papillomavirus DNA whole genome sequencing enables human papillomavirus-associated oropharynx cancer early detection. JNCI: Journal of the National Cancer Institute. doi.org/10.1093/jnci/djaf249