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Abstract Objective: To evaluate the functional performance of a new Human Papillomaviruses (HPV) genotyping assay based on semiconductor NextGen sequencing methodology and to discuss the clinical value in HPV prognostics, diagnostics, and disease control. Methods: Used the new sequencingbased HPV genotyping assay to analyze 30 national standardized reference samples classified by the HPV L1 gene types, 9 national standardized reference samples classified by HPV whole genome typing and 500 clinical cervical exfoliated cell DNA samples which were tested by known and registered HPV genotyping assay kits, and evaluated the analytical performance of the new HPV genotyping assay and its clinical relevance. Results: The new sequencingbased HPV genotyping assay could accurately detect the 16 HPV genotypes (HPV 6、11、16、18、31、33、35、39、45、51、52、56、58、59、66、68) without any crossreactivities between the 16 subtype of HPV, and toward other types of HPV and human genome DNA fragments as host DNA/genome. The detection limit of this assay is 10 copies/μL (50 copies/reaction). The positive coincidence rate, negative coincidence rate, total coincidence rate and consistency coefficient (Kappa) value of this new assay with the clinical HPV genotyping result were 99.33% (298/300), 100% (200/200), 99.60% (498/500) and 0.99, respectively. Conclusions: The new sequencingbased HPV genotyping assay has many advantages,such as , highaccuracy, highspecificity, highsensitivity, highthroughput in clinical applications, especially for HPV potential highthroughput screenings ,and so it has an excellent clinical value.
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