Testing for high-risk HPV in cervical and tonsillar paraffin-embedded tissue using a cartridge-based assay ELINA VIRTANEN, 1 PEKKA LAURILA, 2 JAANA HAGSTR € OM, 2 PEKKA NIEMINEN 3 and EEVA AUVINEN 1 Departments of 1 Virology; 2 Pathology; and 3 Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland Virtanen E, Laurila P, Hagstr€ om J, Nieminen P, Auvinen E. Testing for high-risk HPV in cervical and tonsillar paraffin-embedded tissue using a cartridge-based assay. APMIS 2017. This study evaluates the suitability of Xpert HPV (Cepheid, Sunnyvale, CA, USA) test for cervical and tonsillar forma- lin-fixed paraffin-embedded (FFPE) tissue samples as compared to the tests currently used in diagnostics. Cervical biop- sies and liquid cytology (LC) samples were collected from 48 women attending colposcopy. Biopsies were processed for histology and tested for hrHPV using Xpert HPV. LC samples were tested using Xpert and Hybrid Capture 2 (HC2; Qiagen, Hilden, Germany) tests. Also 29 archived tonsillar carcinoma samples were tested using Xpert, and the results were compared with histology and immunohistochemical p16INK4a (p16) staining. Among valid cervical LC samples 46.8% were hrHPV positive using Xpert test and 55.3% with HC2. The sensitivity of Xpert was 84.6% as compared to HC2, and overall test concordance was 91.5%. Test concordance between valid Xpert results from biopsies and LC samples was 84.6%. Among valid tonsillar samples 70.4% were hrHPV positive, and concordance of 96.3% was found between Xpert and p16 staining. To conclude, Xpert HPV test cartridge provides a convenient platform to test individ- ual samples, including FFPE samples. Further studies are needed to establish whether test sensitivity is sufficient to reli- ably differentiate between hrHPV positive and hrHPV negative head and neck carcinomas. Key words: HPV; FFPE; cervical; head and neck; Xpert. Elina Virtanen, Department of Virology, Faculty of Medicine, POB 21, 00014 University of Helsinki, Finland. e-mail: elina.i.virtanen@helsinki.fi High-risk human papillomavirus (hrHPV) testing has shown great potential in screening of cervical cancer, whose established cause is hrHPV infection (1,2). Head and neck squamous cell carcinomas (HNSCC) differ from cervical cancer in that they consist of two distinct, histologically indistinguish- able subsets of disease: HPV positive and HPV neg- ative cancers (3). Cancers causally associated with HPV infection respond considerably better to chemotherapy and irradiation, and have an alto- gether better prognosis than HPV negative cancers (4,5). Especially among oropharyngeal cancer the proportion of HPV positive cases is on the rise, presumably due to the changes in sexual practices (6). Among HPV negative cancer patients, male gender and habits of heavy smoking and drinking are frequent (3,7). A number of high-throughput test platforms are available to manage high num- bers of cell swab samples in cancer screening. An option is needed for testing of individual samples such as formalin-fixed paraffin-embedded (FFPE) samples, which are routinely available from cancer patients. We wanted to assess the feasibility of the car- tridge-based Xpert HPV test (Cepheid, Sunnyvale, CA, USA) for hrHPV testing of tonsillar and cervi- cal lesions, with the emphasis on FFPE tissue sam- ples. The test has been validated for cervical samples collected in PreservCyt Solution (Hologic, Marlborough, MA, USA), and the performance of the test in this sample material has been assessed (8–10). To our knowledge only one study has previ- ously evaluated the test for FFPE samples (11). In the present study, both cervical lesions and tonsillar carcinomas were assessed, because the hrHPV geno- types found in head and neck cancers are essentially identical to those found in anogenital lesions (12), and the HPV genotypes included in the Xpert test thus cover the genotypes found in both anatomical regions. Validated diagnostic tests currently Received 4 January 2017. Accepted 3 May 2017 1 APMIS © 2017 APMIS. Published by John Wiley & Sons Ltd. DOI 10.1111/apm.12727