title: Formalin fixed paraffin embedded (FFPE) material is amenable to HPV detection by the Xpert(®) HPV assay.
abstract: 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.
  
  
  OBJECTIVE
  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.
  
  
  METHODS
  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.
authors.affiliation: Scottish HPV Reference Lab (SHPVRL), Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh EH16 4SA, UK. Electronic address: Daniel.Guerendiain@nhslothian.scot.nhs.uk.
authors.forename: Daniel
authors.initials: D
authors.lastname: Guerendiain
authors.affiliation: Scottish HPV Reference Lab (SHPVRL), Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh EH16 4SA, UK. Electronic address: Catherine.Moore@nhslothian.scot.nhs.uk.
authors.forename: Catherine
authors.initials: C
authors.lastname: Moore
authors.affiliation: Department of Oncology, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK. Electronic address: Lucy.Wells@nhslothian.scot.nhs.uk.
authors.forename: Lucy
authors.initials: L
authors.lastname: Wells
authors.affiliation: Department of Pathology, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh EH16 4SA, UK. Electronic address: Brendan.Conn@nhslothian.scot.nhs.uk.
authors.forename: Brendan
authors.initials: B
authors.lastname: Conn
authors.affiliation: Scottish HPV Reference Lab (SHPVRL), Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh EH16 4SA, UK. Electronic address: Kate.Cuschieri@luht.scot.nhs.uk.
authors.forename: Kate
authors.initials: K
authors.lastname: Cuschieri
mesh_terms: D002294:Carcinoma, Squamous Cell / Q000175:diagnosis / Q000209:etiology; D004279:DNA, Viral; D006652:Histological Techniques; D006801:Humans; D009959:Oropharyngeal Neoplasms / Q000175:diagnosis* / Q000209:etiology*; D027383:Papillomaviridae / Q000235:genetics*; D030361:Papillomavirus Infections / Q000150:complications* / Q000175:diagnosis / Q000821:virology*; D011933:Reagent Kits, Diagnostic; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity
chemical_list: D004279:DNA, Viral; D011933:Reagent Kits, Diagnostic
keywords: Biopsy; FFPE; HPV; Oropharyngeal; Squamous cell carcinoma; p16