HPV Genotyping of Modified General Primer-Amplicons Is More Analytically Sensitive and Specific by Sequencing than by Hybridization

Meisal, Roger; Rounge, Trine B.; Christiansen, Irene Kraus; Eieland, Alexander Kirkeby; Worren, Merete Molton; Molden, Tor; Kommedal, Øyvind; Hovig, Eivind; Leegaard, Truls Michael; Ambur, Ole Herman

doi:10.1371/journal.pone.0169074

Cited by 11 publications

(18 citation statements)

References 47 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Further data cleaning and statistical analyses were performed on R (v3.6.0). A final cut-off of 500 mapped read pairs or more were considered as positive [35][36][37]. Choice of cutoff was based on the mean reads of CCAS and SCAS.…”

Section: Bioinformatics and Statisticsmentioning

confidence: 99%

Self-collected and clinician-collected anal swabs show modest agreement for HPV genotyping

et al. 2021

Self Cite

View full text Add to dashboard Cite

Background & aim Women with HIV/HPV coinfection and cervical lesions are at increased risk of developing HPV related anal cancer. Self-collection of anal swabs may facilitate HPV molecular testing in anal cancer screening, especially in high-risk groups, and yet it is not adequately studied. We evaluated level of agreement between self-collected anal swabs (SCAS) and clinician-collected anal swabs (CCAS) when used for HPV genotyping. We also described the anal HPV genotype distribution and HIV/HPV coinfection. Methods We performed a cross sectional study with participants from a visual-inspection-with-acetic-acid and cervicography (VIAC) clinic, in Harare, Zimbabwe. In a clinic setting, the women aged ≥18 years provided anal swabs in duplicate; first CCAS and then SCAS immediately after. HPV detection and genotyping were performed using next generation amplicon sequencing of a 450bp region of the HPV L1 gene. Level of agreement of HPV genotypes between CCAS and SCAS was calculated using the kappa statistic. McNemar tests were used to evaluate agreement in the proportion of genotypes detected by either method. Results Three-hundred women provided 600 samples for HPV genotyping. HPV genotypes were detected in 25% of SCAS and in 22% of CCAS. The most common genotypes with CCAS were HPV52, HPV62 and HPV70 and with SCAS were HPV62, HPV44, HPV52, HPV53 and HPV68. Total HPV genotypes detected in CCAS were more than those detected in SCAS, 32 versus 27. The agreement of HPV genotypes between the two methods was 0.55 in kappa value (k). The test of proportions using McNemar gave a Chi-square value of 0.75 (p = 0.39). Multiple HPV infections were detected in 28/75 and 29/67 women for CCAS and SCAS respectively. Conclusions SCAS and CCAS anal swabs showed moderate agreement, with no statistically significant difference in the proportion of genotypes detected by either methods. Although the differences between the two methods were not statistically significant, CCAS detected more HPV genotypes than SCAS and more HPV infections were detected in SCAS than in CCAS. Our data suggest that self-collected anal swabs can be used as an alternative to clinician-collected anal swabs for HPV genotyping.

show abstract

Section: Bioinformatics and Statisticsmentioning

confidence: 99%

Self-collected and clinician-collected anal swabs show modest agreement for HPV genotyping

et al. 2021

Self Cite

View full text Add to dashboard Cite

show abstract

“…The QPLEX™ HPV genotyping kit can detect a total of 32 HPV genotypes including 19 high-risk HPV genotypes (16,18,26,31,32,33,35,39,45,51,52,56,58,59, 66, 68, 69, 70 and 73), and 13 low-risk HPV genotypes (6,11,34,40,42,43,44,53,54,55,61, 62 and 81). However, due to the difference in categorization of carcinogenicity between literatures or manufacturer's claims [4,9,10], we classified HPV genotypes according to the carcinogen classification of the International Agency for Research on Cancer [10,11] as follows: group 1 (carcinogenic to humans), group 2A (probably carcinogenic to humans), group 2B (possibly carcinogenic to humans), group 3 (not classifiable as to its carcinogenicity to humans) and unclassified group.…”

Section: Qplex™ Hpv Genotyping Kitmentioning

confidence: 99%

Analytical evaluation of a new Microdisk™ technology-based multiplex HPV genotyping system – the QPLEX™ HPV genotyping kit

Lim

Kweon

Choi

et al. 2019

Journal of Laboratory Medicine

View full text Add to dashboard Cite

Abstract Background Recently, the QPLEX™ human papillomavirus (HPV) genotyping kit (QuantaMatrix, Seoul, Korea), a Microdisk™ technology-based multiplex system, was developed to detect 32 HPV genotypes. We evaluated the analytical performance of this kit by conducting a comparison study, precision evaluation and interference testing. Methods A total of 1594 cervical swab specimens were used to compare the QPLEX™ HPV genotyping kit with other commercially available kits (GeneFinder HPV Liquid Bead MicroArray Genotype polymerase chain reaction [PCR] kit, Infopia, Seoul, Korea; PANArray™ HPV Genotyping Chip, PANAGENE, Daejeon, Korea). For the determination of precision, we evaluated four types of precision profiles: repeatability, lot-to-lot variability, operator-to-operator variability and site-to-site variability. In addition, interference tests were performed with various interferents. Results The results of the QPLEX™ HPV genotyping kit showed almost perfect agreement with the other commercially available HPV genotyping assays. The combined precision was acceptable. In addition, there was no tested interferent that affected the results of the QPLEX™ HPV genotyping kit. Conclusions The QPLEX™ HPV genotyping kit showed acceptable analytical performance in our study. This assay could be a suitable option for HPV genotyping in routine and follow-up tests.

show abstract

“…HPV-PCR (polymerase chain reaction) protocols use specific primers, especially MY09/MY11 and GP5+/GP6+ primers, which amplify conserved regions of the HPV genome, such as the L1 gene that allow the detection of the presence of HPV 32 . After amplification, HPV genotypes can be determined separately using techniques such as restriction fragment length polymorphism (PCR-RFLP), multiplex PCR, real time PCR (RT-qPCR), nucleic acid hybridization assays, direct sequencing, among others 33 .…”

Section: Polymerase Chain Reaction Techniquesmentioning

confidence: 99%

Potential Diagnostic Techniques for Cervical Cancer Prevention - Review

Melo¹,

Ribeiro²,

Canevari³

2018

J Cancer Treat & Diagnosis

View full text Add to dashboard Cite

Human papillomavirus (HPV) infection is the most common sexually transmitted disease worldwide and several studies have proven the close relationship between HPV and the development of cervical cancer. Several tests are currently performed for early and reliable diagnosis, in which the cervical cytology evaluation by the Papanicolaou method is highlighted. However, errors in the collection and misinterpretation of cell differentiation degree in smear by the pathologist result in incorrect or inaccurate results. Considering these points, it is of utmost importance to develop new technologies that perform accurate and reliable diagnosis and that present financial advantages and accessibility. Currently, molecular biology assays are excellent detectors of viral DNA, but it presents disadvantages, such as the need for high financial resources to gain access. Therefore, this review has the objective of highlighting the main diagnostic techniques that are already being used, such as specific kits for the detection of high-risk HPVs, or methodologies that are still in the study phase, but which already present good results, such as the application of physical FTIR spectroscopy principles and ultrasensitive biosensors.

show abstract

HPV Genotyping of Modified General Primer-Amplicons Is More Analytically Sensitive and Specific by Sequencing than by Hybridization

Cited by 11 publications

References 47 publications

Self-collected and clinician-collected anal swabs show modest agreement for HPV genotyping

Self-collected and clinician-collected anal swabs show modest agreement for HPV genotyping

Analytical evaluation of a new Microdisk™ technology-based multiplex HPV genotyping system – the QPLEX™ HPV genotyping kit

Potential Diagnostic Techniques for Cervical Cancer Prevention - Review

Contact Info

Product

Resources

About