title: Detection of HPV DNA in paraffin-embedded cervical samples: a comparison of four genotyping methods.
abstract: BACKGROUND
  Identification of human papillomavirus (HPV) DNA in cervical tissue is important for understanding cervical carcinogenesis and for evaluating cervical cancer prevention approaches. However, HPV genotyping using formalin-fixed, paraffin-embedded (FFPE) tissues is technically challenging. We evaluated the performance of four commonly used genotyping methods on FFPE cervical specimens conducted in different laboratories and compared to genotyping results from cytological samples.
  
  
  METHODS
  We included 60 pairs of exfoliated-cell and FFPE specimens from women with histologically confirmed cervical intraepithelial lesions grade 2 or 3. Cytology specimens were genotyped using the Linear Array assay. Four expert laboratories processed tissue specimens using different preparation methods and then genotyped the resultant sample preparations using four different HPV genotyping methods: SPF10-PCR DEIA LiPA25 (version 1), Inno-LiPA, Linear Array and the Onclarity assay. Percentage agreement, kappa statistics and McNemar's chi-square were calculated for each comparison of different methods and specimen types.
  
  
  RESULTS
  Overall agreement with respect to carcinogenic HPV status for FFPE samples between different methods was: 81.7, 86.7 and 91.7% for Onclarity versus Inno-LiPA, Linear Array and SPF-LiPA25, respectively; 81.7 and 85.0% for Linear Array versus Inno-LiPA and SPF-LiPA25, respectively; and 86.7% for SPF-LiPA25 versus Inno-LiPA. Type-specific agreement was >88.3% for all pair-wise comparisons. Comparisons with cytology specimens resulted in overall agreements from 80 to 95% depending on the method and type-specific agreement was >90% for most comparisons.
  
  
  CONCLUSIONS
  Our data demonstrate that the four genotyping methods run by expert laboratories reliably detect HPV DNA in FFPE specimens with some variation in genotype-specific detection.
authors.affiliation: Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA. f.castro@Dkfz-Heidelberg.de.
authors.forename: Felipe A
authors.initials: FA
authors.lastname: Castro
authors.affiliation: Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA. koshiolj@mail.nih.gov.
authors.forename: Jill
authors.initials: J
authors.lastname: Koshiol
authors.affiliation: DDL, Diagnostic Laboratory, Rijswijk, The Netherlands. wim.quint@ddl.nl.
authors.forename: Wim
authors.initials: W
authors.lastname: Quint
authors.affiliation: Department of Pathology, School of Medicine, University of New Mexico, Albuquerque, NM, USA. CWheeler@salud.unm.edu.
authors.forename: Cosette M
authors.initials: CM
authors.lastname: Wheeler
authors.affiliation: Viral Oncology Program, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA. Maura.Gillison@osumc.edu.
authors.forename: Maura L
authors.initials: ML
authors.lastname: Gillison
authors.affiliation: BD Diagnostics, Sparks, MD, USA. laurence_vaughan@bd.com.
authors.forename: Laurence M
authors.initials: LM
authors.lastname: Vaughan
authors.affiliation: DDL, Diagnostic Laboratory, Rijswijk, The Netherlands. Bernhard.Kleter@ddl.nl.
authors.forename: Bernhard
authors.initials: B
authors.lastname: Kleter
authors.affiliation: DDL, Diagnostic Laboratory, Rijswijk, The Netherlands. L.J.van.Doorn@ddl.nl.
authors.forename: Leen-Jan
authors.initials: LJ
authors.lastname: van Doorn
authors.affiliation: Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA. chaturva@mail.nih.gov.
authors.forename: Anil K
authors.initials: AK
authors.lastname: Chaturvedi
authors.affiliation: Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA. hildesha@exchange.nih.gov.
authors.forename: Allan
authors.initials: A
authors.lastname: Hildesheim
authors.affiliation: Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA. schiffmm@exchange.nih.gov.
authors.forename: Mark
authors.initials: M
authors.lastname: Schiffman
authors.affiliation: Division of Cancer Etiology, Department of Population Sciences, Beckman Research Institute and the City of Hope, Duarte, CA, USA. sowang@coh.org.
authors.forename: Sophia S
authors.initials: SS
authors.lastname: Wang
authors.affiliation: Departments of Pathology and Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA. rosemary-zuna@ouhsc.edu.
authors.forename: Rosemary E
authors.initials: RE
authors.lastname: Zuna
authors.affiliation: Departments of Pathology and Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA. joan-walker@ouhsc.edu.
authors.forename: Joan L
authors.initials: JL
authors.lastname: Walker
authors.affiliation: Departments of Pathology and Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA. Terence-Dunn@ouhsc.edu.
authors.forename: S Terence
authors.initials: ST
authors.lastname: Dunn
authors.affiliation: Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA. wentzenn@mail.nih.gov.|Division of Cancer Epidemiology & Genetics, NCI Shady Grove, 9609 Medical Center Drive 7E114, Rockville, MD, 20850, USA. wentzenn@mail.nih.gov.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Wentzensen
mesh_terms: D000328:Adult; D002584:Cervix Uteri / Q000473:pathology* / Q000821:virology*; D004279:DNA, Viral / Q000302:isolation & purification*; D005260:Female; D005838:Genotype; D060005:Genotyping Techniques; D006801:Humans; D008875:Middle Aged; D058889:Molecular Typing / Q000379:methods; D027383:Papillomaviridae / Q000235:genetics* / Q000302:isolation & purification; D016612:Paraffin Embedding; D016133:Polymerase Chain Reaction / Q000379:methods; D013048:Specimen Handling / Q000379:methods / Q000592:standards; D002583:Uterine Cervical Neoplasms / Q000473:pathology / Q000821:virology; D002578:Uterine Cervical Dysplasia / Q000473:pathology / Q000821:virology
chemical_list: D004279:DNA, Viral