Detection and Genotyping of Human Papillomavirus in Hypopharyngeal Carcinoma Samples

The incidence of hypopharyngeal cancer globally is about 0.8 per 100 000. Globally, approximately 38 000 cases of head and neck cancer are considered yearly to be high-risk human papillomavirus (HR-HPV) related. Biopsy material fixation in formalin and embedding in paraffin (FFPE) creates many challenges. The extraction of nucleic acid material requires a more complicated approach, and often the extracted DNA is fragmented. The aim of the study was to compare several HR-HPV detection methods in nucleic acid material extracted from FFPE samples. The extracted DNA was analysed with different molecular biology methods to assess DNA quality and to determine the presence of HPV DNA with various HPV detection systems. The results were compared and statistically analysed. There was good agreement between two real-time PCR methods — Anyplex II HPV28 and Sacace HPV High-Risk Screen Real-TM Quant. We failed to reach a conclusion on agreement between real-time PCR methods and HPV16 type-specific primer PCR. There was moderate positive correlation between Anyplex II HPV28 semiquantitative results and Sacace quantitative results. We suggest that real-time PCR assays detecting smaller DNA amplicons are good and reliable methods for detecting HPV genetic material in FFPE samples.