Evaluation of an E6/E7 PCR‐capillary electrophoresis fragment analysis in the genotyping of human papillomavirus in archival FFPE samples of oropharyngeal cancer

Abstract Accumulating evidence has demonstrated that high‐risk human papillomaviruses (HR‐HPVs) are involved in the etiology of a subset of oropharyngeal squamous cell carcinoma (OPSCC). In this regard, the International Agency for Research on Cancer (IARC) has recommended direct molecular HPV testing. So far, there is no agreement on the most appropriate method for HPV detection on OPSCC formalin‐fixed paraffin‐embedded (FFPE) materials. In this study, we aimed to evaluate the performance of the high‐sensitive SureX HPV assay in OPSCC FFPE tissues compared with LiPA‐25 and p16 ink4a immunostaining. A retrospective series of FFPE primary OPSCC cases were diagnosed between 2008 and 2019 and provided by the Henan Cancer Hospital, China. The level of agreement of two assays was determined using Cohen's Kappa (κ) statistics. A total of 230 FFPE OPSCC samples from tumor resections ( n = 160) and diagnostic biopsies ( n = 70) were detected. Sixty‐six (28.7%) and 70 (30.4%) samples were identified as HPV‐DNA‐positive by LiPA‐25 and SureX, respectively, of which HPV16 was largely the most common type (95.5% vs 94.3%). We found a perfect concordance between LiPA‐25 and SureX for HPV‐DNA status ( κ = 0.906, 95% CI: 0.875–0.937) and for HPV16 ( κ = 0.925, 95% CI: 0.897–0.953). In addition, SureX and p16 ink4a immunostaining had a perfect concordance ( κ = 0.917, 95% CI: 0.888‐0.946). Moreover, the HPV‐driven fraction, based on double positivity for HPV‐DNA and p16 ink4a , was similar between SureX (63 of 230, 27.4%) and LiPA‐25 (60 of 230, 26.1%). Similar results were found in samples from resections and biopsies. SureX and LiPA‐25 are comparable. SureX could be used for routine HPV‐DNA detection and genotyping on archival OPSCC FFPE tissues.