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Evaluation of human papillomavirus (HPV) genotyping assays using type-specific HPV L1 reference DNA

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Abstract

Background

Human papillomaviruses (HPV) are known to play a central etiological role in the development of cervical cancer. General HPV genotyping methods consist of PCR with consensus primers combined with various detection methods.

Objective

The aim was to develop HPV L1 DNA reference materials to evaluate the sensitivity, specificity, and accuracy of genotyping results obtained from the HPV DNA Genotyping Chip (HPV CHIP) and RFMP assays.

Methods

In this study, the Ministry of Food and Drug Safety (MFDS) established reference DNA materials for the L1 gene from 41 subtypes of anogenital HPV to aid in genotyping human papillomavirus (HPV) strains. Of these, 22 subtypes were obtained from cervical scrape samples of Korean women and 19 subtypes were synthesized. These reference materials include 13 high-risk types (HPV-16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, and 68), 3 probable high-risk types (HPV-26, 53, and 66), 16 low-risk types (HPV-6, 10, 11, 27, 34, 40, 42, 43, 44, 54, 55, 61, 70, 72, 73, and 81), and 8 undetermined-risk types (HPV-3, 57, 62, 67, 69, 71, 74, and 84). After confirming the sequences by standard methods, these HPV L1 DNA reference materials were then used to compare results from the HPV DNA Genotyping Chip (HPV CHIP) and restriction fragment mass polymorphism (RFMP) assays.

Results

Data collected from the HPV CHIP and RFMP assay showed comparably high sensitivity and accuracy. Both assays could detect 102 or more copies/μl of HPV L1 DNA from 39 types of HPV, with higher accuracy in detecting samples with mixed types of HPV.

Conclusion

The present study confirms the HPV L1 DNA reference materials developed by MFDS are reliable and useful for the evaluation of HPV genotyping assays.

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Acknowledgements

The author thanks Britni M. Arlian (Scripps Research Institute), TaeJeong Oh (GenomicTree) for scientific discussions.

Funding

This research was supported by the National Research Foundation of Korea (NRF) grant (NRF-2019R1I1A1A01043181) and Korea Innovation Foundation grant (2020-DD-RD-0735) funded by the Korea government.

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Authors and Affiliations

  1. Department of Biological Sciences and Biotechnology, Hannam University, 1646 Yuseongdaero, Yuseong-gu, Daejeon, 34054, Korea

    Kyung Ho Han

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  1. Kyung Ho Han
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Correspondence to Kyung Ho Han.

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Author Kyung Ho Han declares that he has no conflict of interest.

Ethical approval

Informed consent and pertinent patient information for each sample was obtained under approval and guidance of the Institutional Review Board of the School of Medicine at ChungNam National University.

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Informed consent was obtained from all individual participants included in the study.

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Han, K.H. Evaluation of human papillomavirus (HPV) genotyping assays using type-specific HPV L1 reference DNA. Genes Genom 43, 775–781 (2021). https://doi.org/10.1007/s13258-021-01100-4

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