Researchers at Mass General Brigham have developed HPV-DeepSeek, a highly sensitive blood test that identifies HPV-associated head and neck cancers nearly a decade before symptoms appear. The test uses whole-genome sequencing to detect viral DNA fragments in the bloodstream. This advance could enable earlier treatments and improve patient outcomes.
Human papillomavirus (HPV) causes about 70% of head and neck cancers in the United States, which are rising in frequency. Unlike cervical cancer, no routine screening exists for these HPV-linked cancers, leading to diagnoses only after tumors grow large and spread, often to lymph nodes.
A study published in the Journal of the National Cancer Institute introduces HPV-DeepSeek, a liquid biopsy test developed by a team at Mass General Brigham. The test identifies trace HPV DNA from tumors in the blood, achieving 99% sensitivity and specificity in earlier research for detecting cancer at clinical presentation.
To assess early detection potential, researchers analyzed 56 blood samples from the Mass General Brigham Biobank: 28 from individuals who later developed HPV-associated head and neck cancer and 28 from healthy controls. HPV-DeepSeek detected tumor DNA in 22 of the 28 pre-diagnosis samples, with all controls negative. Using machine learning enhancements, detection improved to 27 of 28 cases, including samples up to 10 years before diagnosis. The earliest unaided positive result was 7.8 years prior.
"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 lead author Daniel L. Faden, MD, FACS, a head and neck surgical oncologist at Mass Eye and Ear. He noted that late diagnoses often require treatments with lifelong side effects, and early detection via tools like HPV-DeepSeek could reduce aggressive interventions and enhance quality of life.
The findings are being validated in a National Institutes of Health-funded blinded study using hundreds of samples from the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial.