title: Automated Extraction of Formalin-Fixed, Paraffin-Embedded Tissue for High-Risk Human Papillomavirus Testing of Head and Neck Squamous Cell Carcinomas Using the Roche Cobas 4800 System.
abstract: BACKGROUND
  -Testing for high-risk human papillomavirus (HR-HPV) in head and neck squamous cell carcinomas (HNSCCs) is important for both prognostication and clinical management. Several testing platforms are available for HR-HPV; however, effective alternative automated approaches are needed.
  
  
  OBJECTIVE
  -To assess the performance of the automated Roche cobas 4800 HPV real-time polymerase chain reaction-based system on formalin-fixed, paraffin-embedded HNSCC specimens and compare results with standard methods of in situ hybridization (ISH) and p16 immunohistochemistry.
  
  
  METHODS
  -Formalin-fixed, paraffin-embedded samples of HNSCC were collected from archival specimens in the Department of Pathology, Massachusetts General Hospital (Boston), and prepared using the automated system by deparaffinization and dehydration followed by tissue lysis. Samples were integrated into routine cervical cytology testing runs by cobas. Corresponding formalin-fixed, paraffin-embedded samples were evaluated for HR-HPV by ISH and p16 by immunohistochemistry. Discrepant cases were adjudicated by polymerase chain reaction.
  
  
  RESULTS
  -Sixty-two HNSCC samples were analyzed using the automated cobas system, ISH, and immunohistochemistry. Fifty-two percent (n = 32 of 62) of formalin-fixed, paraffin-embedded tumors were positive for HR-HPV by cobas. Eighty-eight percent (n = 28 of 32) of cases were the HPV 16 subtype and 12% (n = 4 of 32) were other HR-HPV subtypes. Corresponding testing with ISH was concordant in 92% (n = 57 of 62) of cases. Compared with the adjudication polymerase chain reaction standard, there were 3 false-positive cases by cobas.
  
  
  CONCLUSIONS
  -Concordance in HNSCC HR-HPV status between cobas and ISH was more than 90%. The cobas demonstrated a sensitivity of 100% and a specificity of 91% for detection of HR-HPV. Advantages favoring cobas include its automation, cost efficiency, objective results, and ease of performance.
authors.forename: Darcy A
authors.initials: DA
authors.lastname: Kerr
authors.forename: Brenda
authors.initials: B
authors.lastname: Sweeney
authors.forename: Ronald N
authors.initials: RN
authors.lastname: Arpin
authors.forename: Melissa
authors.initials: M
authors.lastname: Ring
authors.forename: Martha B
authors.initials: MB
authors.lastname: Pitman
authors.forename: David C
authors.initials: DC
authors.lastname: Wilbur
authors.affiliation: From the Department of Pathology, Massachusetts General Hospital, Boston; and Harvard Medical School, Boston, Massachusetts. Dr Kerr and Ms Sweeney contributed equally as first authors on this manuscript.
authors.forename: William C
authors.initials: WC
authors.lastname: Faquin
mesh_terms: D057205:Automation, Laboratory / Q000295:instrumentation / Q000379:methods; D002294:Carcinoma, Squamous Cell / Q000175:diagnosis / Q000378:metabolism / Q000821:virology*; D019941:Cyclin-Dependent Kinase Inhibitor p16 / Q000378:metabolism; D004279:DNA, Viral / Q000235:genetics / Q000302:isolation & purification*; D005404:Fixatives; D005557:Formaldehyde; D006258:Head and Neck Neoplasms / Q000175:diagnosis / Q000378:metabolism / Q000821:virology*; D054884:Host-Pathogen Interactions; D052162:Human papillomavirus 16 / Q000235:genetics / Q000502:physiology*; D006801:Humans; D007150:Immunohistochemistry; D017403:In Situ Hybridization; D009856:Oncogene Proteins, Viral / Q000235:genetics; D050725:Papillomavirus E7 Proteins / Q000235:genetics; D030361:Papillomavirus Infections / Q000175:diagnosis / Q000378:metabolism / Q000821:virology*; D016612:Paraffin Embedding; D016133:Polymerase Chain Reaction; D012097:Repressor Proteins / Q000235:genetics; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016707:Tissue Fixation
chemical_list: C000614131:CDKN2A protein, human; D019941:Cyclin-Dependent Kinase Inhibitor p16; D004279:DNA, Viral; C068651:E6 protein, Human papillomavirus type 16; D005404:Fixatives; D009856:Oncogene Proteins, Viral; D050725:Papillomavirus E7 Proteins; D012097:Repressor Proteins; C059731:oncogene protein E7, Human papillomavirus type 16; D005557:Formaldehyde