title: Clinical evaluation of polymerase chain reaction reverse hybridization assay for detection and identification of human papillomavirus type 16 variants.
abstract: BACKGROUND
  Isolates of HPV16 comprise six variants: European (Eu), Asian (As), Asian-American (AA), North American (NA), African-1 (AF1), and African-2 (AF2) with different carcinogenic potentials. Highly reliable automatable techniques for HPV variant genotyping would be helpful to confirm the role of variants in cervical cancer in large epidemiological studies.
  
  
  OBJECTIVE
  To validate the performance of a novel assay for identification of HPV16 variants.
  
  
  METHODS
  The test is a multiplex PCR amplifying four small fragments from the E6 open reading frame (ORF). Variants are identified in a reverse hybridization assay with variant specific probes. The novel assay was compared to sequence analysis of the E6 ORF in 68 clinical samples. In addition, HPV16 variant distribution was studied in 218 cervical samples from women with normal cytology, squamous cell carcinoma (SCC) and adenocarcinoma of countries in Africa, Asia and South-America.
  
  
  RESULTS
  There was 95.6% agreement between the test and sequencing. Analysis of the clinical panel including 218 positive samples revealed worldwide distribution patterns of HPV16 variants. Finally, a threefold increased risk for SCC with grouped Eu and As variants in South-American countries as compared to controls was found, although the association was not statistically significant.
  
  
  CONCLUSIONS
  The novel assay is a reliable and simple technique, distribution patterns of HPV16 variants in different world regions and disease associations could be established and it may be useful in further epidemiological studies investigating the role of HPV16 variants in cervical carcinogenesis.
authors.affiliation: Group Infection and Cancer, Cra 51 D No. 62-29, Lab 283, School of Medicine, University of Antioquia, Medellin, Colombia. sanchezg@medicina.udea.edu.co
authors.forename: Gloria I
authors.initials: GI
authors.lastname: Sanchez
authors.forename: Bernhard
authors.initials: B
authors.lastname: Kleter
authors.forename: Tarik
authors.initials: T
authors.lastname: Gheit
authors.forename: Leen-Jan
authors.initials: LJ
authors.lastname: van Doorn
authors.forename: Maurits N C
authors.initials: MN
authors.lastname: de Koning
authors.forename: Silvia
authors.initials: S
authors.lastname: de Sanjosé
authors.forename: Laia
authors.initials: L
authors.lastname: Alemany
authors.forename: Xavier F
authors.initials: XF
authors.lastname: Bosch
authors.forename: Massimo
authors.initials: M
authors.lastname: Tommasino
authors.forename: Nubia
authors.initials: N
authors.lastname: Muñoz
authors.forename: Wim G V
authors.initials: WG
authors.lastname: Quint
mesh_terms: D002584:Cervix Uteri / Q000821:virology; D017931:DNA Primers / Q000235:genetics; D005260:Female; D005838:Genotype; D052162:Human papillomavirus 16 / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D006801:Humans; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D009693:Nucleic Acid Hybridization / Q000379:methods*; D009856:Oncogene Proteins, Viral / Q000235:genetics; D030361:Papillomavirus Infections / Q000175:diagnosis* / Q000821:virology; D016133:Polymerase Chain Reaction / Q000379:methods*; D012097:Repressor Proteins / Q000235:genetics; D014773:Virology / Q000379:methods*
chemical_list: D017931:DNA Primers; C068651:E6 protein, Human papillomavirus type 16; D009856:Oncogene Proteins, Viral; D012097:Repressor Proteins