HPV detection and genotyping of FFPE head and neck cancer biopsies by molecular testing to address new oropharyngeal squamous cell carcinoma classification based on HPV status

Recently, both the WHO/IARC (World Health Organisation/International Agency for Research on Cancer) and the American Joint Committee on Cancer (AJCC) have classified the oropharyngeal squamous cell carcinoma (OPSCC) on the basis of HPV status. For this purpose, the WHO/IARC recommended direct molecular HPV testing. In practice, formalin-fixed, paraffin-embedded (FFPE) biopsy specimens are frequently the only available samples. We herein compared in parallel two commercially available molecular assays that were firstly designed for cervical HPV detection and genotyping: Inno-Lipa ® HPV genotyping extra II assay (Fujirebio, Gent, Belgium) (IL) and Anyplex TM II HPV 28 (Seegene, Seoul, South Korea) (AP28). Both assays were carried out on the same DNA extracts obtained from prospectively collected FFPE biopsies from OPSCC origin and results were compared. A total of 55 samples were tested. By IL assay, chosen as reference assay, 27 (49.1%) biopsies were positive for HPV16, 10 (18.2%) were positive for HPV but negative for HPV16, and 18 (32.7%) were negative for HPV. A valid result with AP28 was obtained for 51 biopsy samples (92.7%). Among 37 HPV-positive samples by IL, 33 (89.2%) were positive by AP28. The agreement between both assays was good (Cohen’s κ = 0.78). Among the six discrepancies between assays, always associated with low HPV16 viral load, four biopsies positive for HPV16 by IL could not be detected by AP28. Taken together, these observations demonstrate that both assays could be used in routine for HPV detection and genotyping on FFPE-biopsy samples of head and neck tumour.