Detection and genotyping of human papillomavirus in hypopharyngeal carcinoma samples

To compare several HPV detection methods in nucleic acid material extracted from FFPE samples. Extracted DNA was analyzed with different molecular biology methods to assess DNA quality and analyze it for presence of HPV DNA with various HPV detection systems.  Used HPV detection methods - GP5+/6+ and My09/11 consensus primers, Anyplex II HPV28 multiplex RT PCR, Sacace HPV High-Risk Screen Real-TM Quant, HPV16 and HPV18 specific primers.  Results were compared and statistically analyzed.  There was good agreement between two rea-time PCR methods – Anyplex II HPV28 and Sacace HPV High-Risk Screen Real-TM Quant. We failed to conclude upon agreement between real-time PCR methods and HPV16 type-specific primers’ PCR. There was a moderate positive correlation between Anyplex II HPV28 semiquantitative results and Sacace quantitative results. We suggest real-time PCR assays detecting smaller DNA amplicons are good and reliable methods for detecting HPV genetic material in FFPE samples.