New Blood Test Outperforms Standard Diagnostic Methods for Detecting HPV-associated Oropharyngeal Cancer

Researchers at the Mass General Brigham health care system have developed a blood-based test for HPV-associated cancer detection and early diagnosis. This novel test, called HPV-DeepSeek, demonstrates a 99% diagnostic accuracy — a significant improvement over existing detection methods — in blood samples taken from patients with human papillomavirus (HPV)-head and neck squamous cell carcinoma (HNSCC).

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“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,” notes the study’s lead author, Daniel Faden, MD, a principal investigator in the Mike Toth Head and Neck Cancer Research Center and surgical oncologist at Mass Eye and Ear.

A More Thorough Blood Test for HPV-associated Cancer

Cervical cancer is the only HPV-associated cancer with a routine screening method. Other HPV-associated cancers, such as oropharyngeal cancer, are typically discovered through imaging after symptoms arise and the disease has progressed to become symptomatic. In addition, for patients with oropharyngeal cancer, there are no effective tests to accurately determine early on if or when cancer has recured.

To address this unmet need, Dr. Faden, with funding from the National Institutes of Health (NIH), began developing some of the first liquid biopsy tools for HPV-associated cancer detection in his lab about five years ago. These blood tests used Droplet Digital PCR (ddPCR) to detect circulating tumor HPV DNA (ctHPVDNA) by targeting one to two pieces of the HPV genome.

“We did many studies with those original first-generation assays, and what we learned is that those tools work relatively well when patients have a large tumor burden,” says Dr. Faden. “But they don't work very well when we're looking for very small amounts of tumor, such as after surgery or in screening, when you expect the tumor to be extremely small.”

HPV-DeepSeek, developed by Dr. Faden and a team of collaborators across Mass Eye and Ear, the Massachusetts General Hospital Department of Pathology, and the Broad Institute of MIT, uses whole-genome sequencing of the entire genome to detect HPV genome fragments, as well as ctHPVDNA quantity and size, high-risk HPV16 single nucleotide polymorphisms (SNPs), integration events of the HPV genome into the host cell DNA, and mutations in the cancer-driving gene PIK3CA, in a blood sample. This thorough analysis allows for highly accurate HPV-associated cancer detection and diagnosis early in the progression of the disease.

“We look at many other features as well, in addition to HPV DNA, so we get a bunch of other prognostic information at the same time, in addition to the sensitivity boost,” says Dr. Faden.

Effectiveness in Oropharyngeal Cancer

In the study, published in Clinical Cancer Research, blood samples from 304 patients were tested using HPV-DeepSeek, three other blood tests, and standard-of-care tissue biopsy. Half the population had untreated HPV-associated HNSCC in various stages. The researchers found that HPV-DeepSeek had:

• A diagnostic accuracy of 99% compared to the other tests, which had accuracies ranging from 82%-90%
• Maintained its accuracy, even for the earliest stages of disease, before the cancer had metastasized, suggesting it may be effective as a screening tool as well

To further explore HPV-DeepSeek’s potential in screening for HPV-associated cancer detection, the researchers conducted another study that they presented at the 2024 AACR Special Conference in Cancer Research: Liquid Biopsy: From Discovery to Clinical Implementation, currently in preprint. This study analyzed plasma samples of 28 patients who were later diagnosed with HPV-associated HNSCC. HPV-DeepSeek correctly identified cancer:

• 80% of the time in samples taken eight years before clinical diagnoses
• 100% of the time in samples taken four years before diagnosis

Early diagnosis could provide a significant advantage for patients with oropharyngeal cancer, as it’s estimated that diagnosis currently takes place 10 to 15 years after the cancer starts developing, when symptoms such as a noticeable tumor in the neck, throat pain, or difficulty swallowing occur. At this metastatic stage, patients often require multiple types of treatment, increasing their risk of significant side effects.

In addition to screening, HPV-DeepSeek could help physicians provide personalized patient care after surgery by identifying which patients clear ctHPVDNA and thus don’t require further treatment. This kind of blood testing could also replace current time-consuming and invasive monitoring procedures needed every three to four months after treatment. Findings from a study investigating HPV-DeepSeek as a tool for minimal residual disease (MRD) detection after surgery were presented at ASCO and showed high promise.

The Future of Early Detection

Dr. Faden and his colleagues have several studies underway, including:

• Evaluating the performance of their novel blood test in other types of HPV-associated cancers, with preliminary data suggesting it performs similarly to the oropharyngeal cancer studies
• Working with multiple cancer modeling experts to examine how early detection impacts patient care and survival

Through their work, they continually improve HPV-DeepSeek to make it even more useful in detecting HPV-associated cancers. Dr. Faden says, “We continue to iterate on the technology and make it more and more sensitive, and to address more questions and get more data out of the assay.”

Learn more about the Mike Toth Head and Neck Cancer Research Center

Refer a patient to Mass Eye and Ear/Mass General Brigham