Formalin fixed paraffin embedded (FFPE) material is amenable to HPV detection by the Xpert® HPV assay

Daniel Guerendiain*, Catherine Moore, Lucy Wells, Brendan Conn, Kate Cuschieri

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

9 Citations (Scopus)


Background: The Xpert® HPV Assay (Cepheid®, Sunnyvale, USA) is a rapid, cartridge-based HPV test validated for use on cervical cytology samples. However, there is an increasing demand for HPV annotation of formalin fixed paraffin embedded (FFPE) material. 

Objectives: The aim of this study was to determine the suitability of the Xpert HPV assay for the detection of nucleic acid (NA) derived from FFPE samples. 

Study design: A total of 88, 10 μm sections derived from FFPE tissue blocks were assessed, 74 originated from oropharyngeal squamous cell carcinomas (OPSCC) and 14 from a range of other sites. All had previously been tested with a sensitive Luminex® based assay with a component also tested with p16 immunohistochemistry (IHC). NA was extracted from samples using the easyMag® platform and after dilution was added directly to the Xpert cartridge.Agreement between assays was assessed. 

Results: Overall agreement between the assays was 92%; with a Kappa for HR-HPV detection of 0.833 (95% CI 0.725-0.953). In the 50 samples that had been annotated for p16 status overall agreement between the Xpert assay and the p16 IHC was 90%. 

Conclusions: These data indicate that FFPE material is amenable to HPV detection by the Xpert assay. To our knowledge, this is the first study to interrogate the use of the Xpert® HPV assay for this application.

Original languageEnglish
Pages (from-to)55-59
Number of pages5
JournalJournal of Clinical Virology
Early online date11 Feb 2016
Publication statusPublished - Apr 2016


  • Biopsy
  • FFPE
  • HPV
  • Oropharyngeal
  • p16
  • Squamous cell carcinoma


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