Comparison of molecular methods for detection of HPV in oral and oropharyngeal squamous cell carcinoma.

Substantial molecular evidence exists to implicate human papillomavirus (HPV) in the pathogenesis of a subset of oral and oropharyngeal squamous cell carcinomas. Several studies have shown that HPV-associated oral/oropharyngeal tumors differ etiologically, biologically, and clinically from those that lack the virus. HPV infection confers a significant survival benefit; therefore, HPV detection in tumors could be used to risk-stratify patients and drive optimum treatment strategies. We explored the clinical utility of 6 polymerase chain reaction (PCR)-based or signal amplification-based methods in the detection of HPV in 68 invasive oral/oropharyngeal SSCs and 10 reactive tonsil specimens. Agreement for HPV16 results among the 5 different assays capable of detecting this genotype was substantial (multirater κ=0.72). Only moderate agreement was noted for the 3 assays capable of detecting HPV18 (multirater κ=0.43). HPV results for each assay were evaluated relative to a "majority" HPV result derived from the results of all the detection methods. An HPV16 E6 PCR assay showed the highest concordance with adjudicated consensus HPV16 results (98.7%; κ=0.97), followed by the TaqMan (93.4%; κ=0.87), Linear Array (92.1%; κ=0.84), and E7 PCR (92.1%; κ=0.84) assays, all of which had agreements exceeding 90%, whereas the HPV16/18 Invader assay was lower (85.5%; κ=0.71). The presence of high-risk HPV in a minority of "normal" tonsillar tissues may confound assessment of the virus in oral/oropharyngeal squamous cell carcinoma biopsies using in vitro amplification methods.