title: Comparative evaluation of different DNA extraction methods for HPV genotyping by linear array and INNO-LiPA.
abstract: In order to investigate the influence of DNA extraction on two PCR-based HPV genotyping tests (Linear Array, Roche and INNO-LiPA Extra, Innogenetics), three different procedures were used to purify DNA from 28 cervico-vaginal samples tested previously by the Hybrid Capture 2: the AmpliLute Liquid Media Extraction kit (Roche), the QIAamp DNA Blood mini kit (QIAGEN), and the NucliSENS EasyMAG automated platform (bioMérieux). All HC2-positive samples were found positive by both assays, independently of the extract used. Type-specific concordance (i.e., identical HPV type-specific profile in all the extracts of the same sample) was observed in 55% and 75% of the cases testing samples by the Linear Array and the INNO-LiPA, respectively. Using the DNA extracted with the two manual methods the results were concordant in 75% of the cases both for the Linear Array and the INNO-LiPA. When comparing the Linear Array results obtained on either of the two manual extracts with those obtained following automated extraction, 65% of the samples showed type-specific concordance in both cases. The INNO-LiPA results were concordant in 80% of the cases comparing the AmpliLute versus the automated extract, while concordant results were observed in 90% of the cases when comparing the QIAGEN versus the automated extract. In conclusion, the Linear Array and INNO-LiPA results are affected by the method of DNA extraction. Consequently, different HPV type-specific profiles may be observed using different extracts of the same sample. The use of consistent protocols for DNA purification is a priority to guarantee intra-assay reproducibility over time.
authors.affiliation: Sexually Transmitted Infections (STI) Unit, San Gallicano Dermatological Institute, Rome, Italy. dona@ifo.it
authors.forename: Maria Gabriella
authors.initials: MG
authors.lastname: Donà
authors.forename: Maria
authors.initials: M
authors.lastname: Benevolo
authors.forename: Fulvia
authors.initials: F
authors.lastname: Pimpinelli
authors.forename: Mara
authors.initials: M
authors.lastname: Battista
authors.forename: Francesca
authors.initials: F
authors.lastname: Rollo
authors.forename: Francesca
authors.initials: F
authors.lastname: Stivali
authors.forename: Antonella
authors.initials: A
authors.lastname: Moscarelli
authors.forename: Massimo
authors.initials: M
authors.lastname: Giuliani
authors.forename: Aldo
authors.initials: A
authors.lastname: Di Carlo
authors.forename: Amina
authors.initials: A
authors.lastname: Vocaturo
mesh_terms: D052685:Alphapapillomavirus / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D002584:Cervix Uteri / Q000821:virology; D004279:DNA, Viral / Q000235:genetics / Q000302:isolation & purification*; D005260:Female; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods* / Q000592:standards; D006801:Humans; D030361:Papillomavirus Infections / Q000235:genetics / Q000821:virology*; D016133:Polymerase Chain Reaction / Q000379:methods; D011247:Pregnancy; D011251:Pregnancy Complications, Infectious / Q000235:genetics / Q000821:virology; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D014412:Tumor Virus Infections / Q000235:genetics / Q000821:virology*; D014621:Vagina / Q000821:virology; D014626:Vaginal Smears / Q000379:methods
chemical_list: D004279:DNA, Viral