Rapid Biopsy Approach Shortens Time Required to Diagnose HPV-linked Head and Neck Cancers

A non-invasive, liquid biopsy approach for the diagnosis of head and neck squamous cell carcinomas caused by human papilloma virus (HPV+HNSCC) demonstrated improved accuracy, reduced cost, and a shorter time to diagnosis compared to the current clinical workup and could become the method of choice in the future.

HNSCC constitute 3–5% of all malignancies worldwide and there are approximately 600,000 newly diagnosed cases annually. The majority of patients with HNSCC present with locally and/or regionally advanced disease at diagnosis. Despite the rising incidence of HPV+HNSCC, treatment of metastatic disease remains palliative rather than curative. Even with new treatments such as immunotherapy, response rates are low and can be delayed, while even mild tumor progression in the face of an ineffective therapy can lead to rapid death.


Current diagnostic approaches for HPV+HNSCC rely on tissue biopsy followed by histomorphologic assessment and detection of HPV indirectly by p16 immunohistochemistry. Such approaches are invasive and have variable sensitivity. While determination of cell-free DNA poses difficulties for detection of some cancers, HPV-associated cancers offer a major advantage, as they release HPV DNA, which is only found in the bloodstream in conjunction with an HPV-associated cancer.

To improve the current diagnostic picture by incorporating determination of circulating HPV DNA, investigators at the Massachusetts Eye And Ear Infirmary (Boston, USA) turned to a sensitive liquid biopsy-based digital PCR test.

The classical PCR test carries out one reaction per single sample. The digital PCR (dPCR) method also carries out a single reaction within a sample, however the sample is separated into a large number of partitions and the reaction is carried out in each partition individually. This separation allows a more reliable collection and sensitive measurement of nucleic acid amounts. The dPCR method has been demonstrated as useful for studying variations in gene sequences - such as copy number variants and point mutations - and it is routinely used for clonal amplification of samples for next-generation sequencing. Droplet digital PCR (ddPCR) is a variation of dPCR in which a 20 microliter sample reaction including assay primers and either Taqman probes or an intercalating dye, is divided into about 20,000 nanoliter-sized oil droplets through a water-oil emulsion technique, thermocycled to endpoint in a 96-well PCR plate, and fluorescence amplitude read for all droplets in each sample well in a droplet flow cytometer.

In a recent paper, the investigators described a prospective observational study on 140 subjects (70 cases and 70 controls) that tested a non-invasive diagnostic approach for HPV+HNSCC designed to improve diagnostic accuracy, lower cost, and shorter diagnostic interval compared to standard approaches. Blood was collected, processed for circulating tumor HPV DNA (ctHPVDNA) and analyzed with custom ddPCR assays for HPV genotypes. Diagnostic performance, cost, and diagnostic interval were calculated for standard clinical work up and compared to the non-invasive approach using ctHPVDNA combined with cross-sectional imaging and physical exam findings.

Results revealed that the liquid biopsy was significantly more accurate than the current diagnostic procedure, with 98.4% sensitivity for identifying a positive result and 98.6% specificity for detecting a negative result. When liquid biopsy was combined with routine imaging and physical exam findings, diagnostic sensitivity was 95.1% and diagnostic specificity was 98.6%. The average time from first presentation to a health care provider to diagnosis was 15 days, 63% less than typical methods (41 days). Costs of the liquid biopsy were also significantly lower than conventional methods with an average estimated savings of over $6,000 per patient.

“Current diagnostic approaches for HPV-associated head and neck cancers are imperfect and invasive, which means patients often need repeat biopsies to get to the diagnosis, thereby delaying care and increasing uncertainty, not to mention the discomfort of the procedures,” said senior author Dr. Daniel L. Faden, assistant professor of otolaryngology–head and neck surgery at Harvard Medical School’s Massachusetts Eye And Ear Infirmary. “Our results show strong proof of principle and suggest that in the future, a fully integrated liquid biopsy approach to diagnose and monitor disease could be possible.”

The study was published in the December 2, 2021, online edition of the journal Clinical Cancer Research.

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