title: Evaluation of the HPV typing INNO-LiPA EXTRA assay on formalin-fixed paraffin-embedded cervical biopsy samples.
abstract: BACKGROUND
  The HPV genotyping line probe assay INNO-LiPA EXTRA allows the detection of a wider spectrum of viral types compared to the earlier V2 version of the assay. Its performance in formalin-fixed paraffin-embedded tissues is unknown.
  
  
  OBJECTIVE
  To test the EXTRA assay in HPV genotyping of paired cervical scrapings and corresponding FFPE biopsy specimens.
  
  
  METHODS
  Paired samples from 188 women with abnormal cytology were examined using the INNO-LiPA HPV genotyping assay, version EXTRA. The assay can simultaneously detect 18 high-risk, 7 low-risk, and 2 unclassified HPV types. Kappa statistics were used to measure interrater agreement between groups.
  
  
  RESULTS
  The evaluation of paired cervical scraping and biopsy samples gave a 100% overall agreement for HPV status and of 72.9% (kappa 0.6554) for the number of infecting HPVs. 392 out of 507 individual HPV types were concordant, corresponding to a positive agreement rate of 87.2% (95% CI 84.1-90.3). As to the individual genotypes, the agreement was absolute for HPV 45, 68, 73 (kappa 1), excellent for HPV 6, 11, 16, 18, 31, 35, 39, 44, 51, 52, 53, 54, 56, 69/71 and 82 (kappa 0.7796-0.9714), good for HPV26, 33, 43, 58, 66 and 74 (kappa 0.6768-0.7449), and poor for HPV 59 and 40. These agreement values were comparable to those obtained with the V2 assay.
  
  
  CONCLUSIONS
  The EXTRA assay provided excellent performance in HPV typing on FFPE samples comparable to the earlier version of the test despite higher complexity and increased coverage of types.
authors.affiliation: Department of Pathology, IRCCS-Fondazione Policlinico San Matteo and University of Pavia, Pavia, Italy.
authors.forename: Paola
authors.initials: P
authors.lastname: Alberizzi
authors.affiliation: Department of Obstetrics and Gynaecology, IRCCS-Fondazione Policlinico San Matteo and University of Pavia, Pavia, Italy.
authors.forename: Arsenio
authors.initials: A
authors.lastname: Spinillo
authors.affiliation: Department of Obstetrics and Gynaecology, IRCCS-Fondazione Policlinico San Matteo and University of Pavia, Pavia, Italy.
authors.forename: Barbara
authors.initials: B
authors.lastname: Gardella
authors.affiliation: Department of Pathology, IRCCS-Fondazione Policlinico San Matteo and University of Pavia, Pavia, Italy.
authors.forename: Stefania
authors.initials: S
authors.lastname: Cesari
authors.affiliation: Unit of Surgical Pathology and Centre for Molecular and Translational Oncology (COMT), University of Parma, Parma, Italy. Electronic address: enricomaria.silini@unipr.it.
authors.forename: Enrico Maria
authors.initials: EM
authors.lastname: Silini
mesh_terms: D000328:Adult; D015331:Cohort Studies; D005260:Female; D005557:Formaldehyde; D060005:Genotyping Techniques / Q000379:methods*; D006801:Humans; D027383:Papillomaviridae / Q000145:classification* / Q000235:genetics*; D010232:Paraffin; D057089:Pathology, Molecular / Q000379:methods*; D016610:Tissue Embedding; D016707:Tissue Fixation; D002583:Uterine Cervical Neoplasms / Q000473:pathology* / Q000821:virology*
chemical_list: D005557:Formaldehyde; D010232:Paraffin
keywords: CIN; Cervix; Genotypes; Molecular epidemiology; SIL