A Better Blood Test for Cancers Caused by HPV
Within just a few months of becoming sexually active, nearly everyone is infected with human papillomavirus (HPV). About half of these infections are with a high-risk type of HPV that increases the risk of developing certain cancers, including cervical cancer and oropharyngeal (throat) cancer. While the number of cervical cancer cases has been going down in the U.S. thanks to the HPV vaccine and effective screening methods, cases of throat cancer are increasing.
“HPV-associated throat cancer has increased over 200% and it's projected to continue increasing for about the next 10 years or so,” says Daniel Faden, MD, a Mass General Brigham head and neck surgical oncologist who cares for patients at Mass Eye and Ear, and principal investigator in the Mike Toth Head and Neck Cancer Research Center. “We hope later on we'll start to see the impact of HPV vaccination in decreasing those rates. But that's not projected to occur for many years.”
An effective screening method for all HPV-associated cancers could save lives in the meantime. To address this need, Dr. Faden and his colleagues have developed a new test, HPV-DeepSeek, to detect these cancers.
Cancers caused by HPV
Most people who contract HPV clear the virus within a year or two. In others, their immune system does not fight off the virus and, sometimes, it can causes cancers of the throat, cervix, anus, penis, vulva, or vagina.
Cervical and anal Pap smears can detect these cancers before symptoms arise, but there are no tests to detect other cancers caused by HPV in early stages, including the most common HPV cancer — throat cancer. Providers often diagnose HPV-related throat cancer many years after it starts developing, at a later and more difficult-to-treat stage, once it has spread to lymph nodes in the neck.
HPV-DeepSeek: more accurate than other tests
With funding from the National Institutes of Health (NIH), Dr. Faden and colleagues developed a new blood test, HPV-DeepSeek, to diagnose cancers caused by HPV much earlier. HPV-DeepSeek identifies pieces of the HPV genome and nine other factors in a blood sample. Other blood tests for HPV-related cancers only look for one or two pieces of the HPV genome, making it harder to find signs of cancer. But by looking at the whole genome, HPV-DeepSeek has more opportunity to detect cancer much earlier.
Dr. Faden’s team used HPV-DeepSeek to test blood samples taken from people with and without throat cancer. They found the test offers 99% accuracy.
In a study published in May 2025, they compared HPV-DeepSeek to other blood tests that detect cancers caused by HPV and to tissue biopsy. HPV-DeepSeek correctly identified people with or without throat cancer 99% of the time, while other methods had accuracies ranging from 82% to 90%.
The future of early detection
While HPV-DeepSeek is still being studied, Dr. Faden believes that this blood test for cancer detection will have many beneficial uses. An effective screening method that diagnoses HPV-related cancers early is critical for effective treatment.
For people who received treatment for these cancers, follow-up involves testing to quickly detect cancer that comes back. According to Dr. Faden, this intensive regimen, “does not work very well. So, there's a lot of interest in trying to replace the existing approaches with a less invasive, less time-intensive approach like [HPV-DeepSeek]. This is something we, and others, are studying in clinical trials.”
Dr. Faden and the team are now evaluating how well the test works in other types of cancers caused by HPV and improving HPV-DeepSeek to make it even more sensitive.
“This approach has significantly higher sensitivity than what's currently available, and therefore means earlier, more accurate detection than what we can do right now,” he says. “We hope in the future HPV-DeepSeek will become available for patients, and we can start to use it to improve their care.”
