title: HPV Genotyping of Modified General Primer-Amplicons Is More Analytically Sensitive and Specific by Sequencing than by Hybridization.
abstract: Sensitive and specific genotyping of human papillomaviruses (HPVs) is important for population-based surveillance of carcinogenic HPV types and for monitoring vaccine effectiveness. Here we compare HPV genotyping by Next Generation Sequencing (NGS) to an established DNA hybridization method. In DNA isolated from urine, the overall analytical sensitivity of NGS was found to be 22% higher than that of hybridization. NGS was also found to be the most specific method and expanded the detection repertoire beyond the 37 types of the DNA hybridization assay. Furthermore, NGS provided an increased resolution by identifying genetic variants of individual HPV types. The same Modified General Primers (MGP)-amplicon was used in both methods. The NGS method is described in detail to facilitate implementation in the clinical microbiology laboratory and includes suggestions for new standards for detection and calling of types and variants with improved resolution.
authors.affiliation: Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway.
authors.forename: Roger
authors.initials: R
authors.lastname: Meisal
authors.affiliation: Department of Research, Cancer Registry of Norway, Oslo, Norway.
authors.forename: Trine Ballestad
authors.initials: TB
authors.lastname: Rounge
authors.affiliation: Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway.
authors.forename: Irene Kraus
authors.initials: IK
authors.lastname: Christiansen
authors.affiliation: Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway.
authors.forename: Alexander Kirkeby
authors.initials: AK
authors.lastname: Eieland
authors.affiliation: Bioinformatics Core Facility, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.
authors.forename: Merete Molton
authors.initials: MM
authors.lastname: Worren
authors.affiliation: Department of Vaccines, Norwegian Institute of Public Health, Oslo, Norway.
authors.forename: Tor Faksvaag
authors.initials: TF
authors.lastname: Molden
authors.affiliation: Department of Microbiology, Haukeland University Hospital, Bergen, Norway.
authors.forename: Øyvind
authors.initials: Ø
authors.lastname: Kommedal
authors.affiliation: Department of Informatics, University of Oslo, Oslo, Norway.|Department of Tumor Biology, Institute of Cancer Research and Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.
authors.forename: Eivind
authors.initials: E
authors.lastname: Hovig
authors.affiliation: Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway.|Division of Medicine and Laboratory Sciences, University of Oslo, Oslo Norway.
authors.forename: Truls Michael
authors.initials: TM
authors.lastname: Leegaard
authors.affiliation: Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway.|Department of Life Sciences and Health, Oslo and Akershus University College of Applied Sciences, Oslo, Norway.
authors.forename: Ole Herman
authors.identifier: http://orcid.org/0000-0001-9870-6375
authors.initials: OH
authors.lastname: Ambur
mesh_terms: D000293:Adolescent; D000328:Adult; D002690:Chlamydia Infections; D017931:DNA Primers / Q000235:genetics*; D004279:DNA, Viral / Q000235:genetics; D005260:Female; D014644:Genetic Variation; D060005:Genotyping Techniques / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D006824:Hybridization, Genetic; D009693:Nucleic Acid Hybridization; D027383:Papillomaviridae / Q000235:genetics*; D030361:Papillomavirus Infections / Q000175:diagnosis / Q000821:virology*; D012680:Sensitivity and Specificity; D002583:Uterine Cervical Neoplasms / Q000175:diagnosis / Q000821:virology*; D055815:Young Adult
chemical_list: D017931:DNA Primers; D004279:DNA, Viral