Blood Test Identifies HPV-Associated Head and Neck Cancers 10 Years Before Symptoms

Human papillomavirus (HPV) causes around 70% of head and neck cancers in the United States, and cases are rising each year. Unlike cervical cancers linked to HPV, there is currently no screening test for HPV-associated head and neck cancers. This often means patients are only diagnosed once tumors are large and have already spread, requiring treatments with severe long-term side effects. Now, a new blood-based tool has demonstrated the ability to detect these cancers up to 10 years before symptoms appear.

Researchers at Mass General Brigham (Wellesley, MA, USA) have developed the HPV-DeepSeek test, a liquid biopsy that uses whole-genome sequencing to find microscopic fragments of HPV DNA shed from tumors into the bloodstream. Previous work demonstrated the test’s ability to achieve 99% sensitivity and 99% specificity for diagnosing cancer at first clinical presentation. The new study sought to determine if it could also identify cancer years before diagnosis.

In the trial, investigators analyzed 56 biobank samples, half from individuals who later developed HPV-associated head and neck cancer and half from healthy controls. Results, published in the Journal of the National Cancer Institute, show that the test detected HPV tumor DNA in 22 of 28 future cancer cases, while all controls tested negative. With machine learning enhancements, HPV-DeepSeek identified 27 of 28 cases, including blood samples collected up to 10 years prior.

By identifying cancers earlier, the test could enable less intensive treatments and improve patient quality of life. Validation is already underway in a larger blinded study funded by the National Institutes of Health (NIH), involving hundreds of samples from the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO). If confirmed, the test could provide the first screening method for HPV-associated head and neck cancers.

“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 study author Daniel L. Faden, MD, FACS. “By the time patients enter our clinics with symptoms from the cancer, they require treatments that cause significant, life-long side effects. 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.”

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