Comparative evaluation of different DNA extraction methods for HPV genotyping by linear array and INNO-LiPA

Area of Science:

• Molecular diagnostics
• Virology
• Biotechnology

Background:

• Human Papillomavirus (HPV) is a major cause of cervical cancer.
• Accurate HPV genotyping is essential for effective screening and management.
• Different DNA extraction methods may influence the performance of HPV detection assays.

Purpose of the Study:

• To evaluate the impact of three distinct DNA extraction procedures on two PCR-based HPV genotyping tests.
• To compare the concordance of HPV genotyping results obtained using different DNA purification methods.

Main Methods:

• Three DNA extraction kits were used: AmpliLute Liquid Media Extraction, QIAamp DNA Blood mini kit, and NucliSENS EasyMAG automated platform.
• 28 cervico-vaginal samples, previously tested by Hybrid Capture 2 (HC2), were analyzed.
• HPV genotyping was performed using Linear Array (Roche) and INNO-LiPA Extra (Innogenetics) assays.

Main Results:

• All HC2-positive samples were correctly identified by both genotyping assays, irrespective of the DNA extract.
• Type-specific concordance varied: 55% for Linear Array and 75% for INNO-LiPA.
• Manual extraction methods showed 75% concordance for both assays. Comparing manual vs. automated extraction yielded 65% (Linear Array) and 80-90% (INNO-LiPA) concordance.

Conclusions:

• The choice of DNA extraction method significantly affects HPV genotyping results obtained with Linear Array and INNO-LiPA assays.
• Variations in HPV type-specific profiles can occur due to different DNA extracts from the same sample.
• Standardized DNA purification protocols are essential for ensuring intra-assay reproducibility and reliable HPV testing.