Comparative evaluation of different DNA extraction methods for HPV genotyping by Linear Array and INNO-LiPA

Maria Gabriella Dona' (1) , Maria Benevolo (2) , Fulvia Pimpinelli (3) , Mara Battista (3) , Francesca Rollo (2) , Francesca Stivali (3) , Antonella Moscarelli (3) , Massimo Giuliani (1) , Aldo Di Carlo (1) , Amina Vocaturo (2)

1 Dermatologia Infettiva
2 Pathology
3 Clinical Pathology and Microbiology

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 vs. the automated extract, while concordant results were observed in 90% of the cases when comparing the QIAGEN vs. 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.

Mots clés: Medicine

Maria Gabriella Dona', Maria Benevolo, Fulvia Pimpinelli, Mara Battista, Francesca Rollo, et al.. Comparative evaluation of different DNA extraction methods for HPV genotyping by Linear Array and INNO-LiPA. Journal of Medical Virology, 2011, 83 (6), pp.1042. ⟨10.1002/jmv.22088⟩. ⟨hal-00633209⟩