Blood Test Could Detect HPV-Associated Cancers 10 Years before Clinical Diagnosis

Human papilloma virus (HPV) is known to cause various cancers, including those of the genitals, anus, mouth, throat, and cervix. HPV-associated oropharyngeal cancer (HPV+OPSCC) is the most common HPV-associated cancer in the United States but currently lacks an effective screening method. It is thought that HPV+OPSCC may begin to develop 10-15 years before it is clinically diagnosed, indicating a window for early detection. Circulating tumor HPV DNA (ctHPVDNA) has emerged as a highly sensitive and specific biomarker for HPV+OPSCC. Taken together, blood-based screening for HPV+OPSCC could enable detection years before the disease is diagnosed.

Investigators from Harvard Medical School (Boston, MA, USA) and partner institutions have developed HPV-DeepSeek, an HPV whole genome sequencing assay with 99% sensitivity and specificity at clinical diagnosis. For their study, they analyzed 28 plasma samples from patients with HPV+OPSCC, collected between 1.3 and 10.8 years prior to their diagnosis, alongside an equal number of age and gender-matched controls. The HPV-DeepSeek and an HPV serology assay identified 22 out of 28 patient samples (79%) as positive for HPV+OPSCC, achieving 100% detection within four years of diagnosis and a maximum lead time of 7.8 years. Furthermore, a machine learning model successfully classified 27 of the 28 cases (96%), with 100% detection within 10 years.

The team used plasma-based PIK3CA gene mutations, viral genome integration events, and HPV serology to orthogonally validate cancer detection with 68% (19/28) of the cohort with multiple cancer signals being detected. Molecular fingerprinting of the HPV genomes confirmed the uniqueness of each viral genome within the cohort, effectively ruling out the possibility of contamination. In cases where tumor blocks from the diagnosis were available (15/28), molecular fingerprinting performed within patients confirmed the same viral genome across time. This groundbreaking study showcases the potential of ctDNA-based screening to detect HPV-associated cancers up to a decade before clinical diagnosis becomes possible, paving the way for potentially transformative advancements in cancer screening.

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