Comparison of the performance of different HPV genotyping methods for detecting genital HPV types
ABSTRACT Classification of high-risk HPV types for cervical cancer screening depends on epidemiological studies defining HPV type-specific risk. The genotyping tests that are used, are however, not uniform with regard to type-specific detection rates making comparisons between different studies difficult. To overcome the lack of a "gold standard" four tests were evaluated crosswise using 824 cervical smears pretested by HC2. The tests evaluated were the L1-PCR-based assays PGMY09/11 LBA, HPV DNA Chip and SPF LiPA and an E1 consensus PCR followed by cycle sequencing (E1-PCR). A subset of 265 samples was tested in addition with the GP5+/6+ reverse line blot assay. Differences were noted in the sensitivity and range for specific HPV types, e.g. with detection rates for HPV53 ranging from 2.3% to 11.6%. HPV16 was the most prevalent type detected by all tests except for the SPF-10 LiPa, which detected HPV31 more often. Kappa values calculated ranged from poor (k=0.20) to intermediate (k=0.54) for HPV positivity, but were higher for high-risk type positivity (k=0.31-0.61) and best for recognition of HPV16 (k=0.53-0.72). The analytical sensitivity of the tests ranged between 15% and 97% for individual types and specificity was highly dependent on which test system was used as "gold standard" for the analysis. The results of histology were used for calculation of clinical sensitivity and specificity. E1-PCR, PGMY09/11 LBA and SPF-10 LiPA had a high clinical sensitivity (>95%) for the detection of cervical intraepithelial neoplasia 2 or higher, whereas the HPV DNA Chip reached only 84.1%.
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ABSTRACT: Objective: The aetiology of Focal Cortical Dysplasia Type IIb (FCDIIb) remains enigmatic in patients suffering from drug-resistant epilepsy, and an aberrant activation of the mammalian target of rapamycin complex 1 signalling pathway (mTORC1) was detectedin this developmental brain malformation. Recently, the human papillomavirus (HPV) oncoprotein E6 has been identified as a potent activator of mTORC1, and HPV16 E6 described to persist in balloon cells obtained from surgical FCDIIb specimens. Although this observation was replicated by an independent second report, it contradicts current knowledge of HPV biology. HPV infects the squamous or mucocutaneous epithelium; haematogenic spread into other tissues has not been observed. In addition, brain carcinogenesis has never been reported in FCDIIb patients. Herein, we have tried to confirm two previous reports of HPV16 E6 infection using an independent series of 14 surgical specimens with histopathologically confirmed FCDIIb. Methods: Snap-frozen FCDIIb specimens were tested for HPV DNA using the primer set for amplification of the complete E6 reading frame of HPV16 and three other sets of primers (two consensus primer sets detecting multiple HPV genotypes, and another primer set specifically used for HPV16). Furthermore, formalin-fixed and paraffin-embedded (FFPE) histopathological preparations were immunohistochemically analysed using previously described antibodies directed against the HPV E6 oncoprotein. Results: All 14 FCDIIb specimens were negative for HPV DNA with all four primer sets. Antibodies directed against the HPV E6 epitope showed weak labelling of cytoplasm in balloon cells, as previously described in FCDIIb, but also in other cell populations. Interpretation: Our data did not confirm previously reported evidence for HPV16 detection in FCDIIb. This article is protected by copyright. All rights reserved. © 2014 American Neurological Association.Annals of Neurology 02/2015; 77(2). DOI:10.1002/ana.24328 · 11.91 Impact Factor
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ABSTRACT: Background: Researchers often group various HPV types into composite measures based on vaccine subtypes, oncogenic potential, or phylogenetic position. Composite prevalence estimates based on various genotyping assay results have been calculated to assess the burden of HPV infections and to monitor HPV vaccine effectiveness. While these prevalence estimates have been used to assist development of prevention strategies, research on how well these estimates measure the true underlying infection burden is limited. Methods: A simulation study was conducted to evaluate use of composite genotyping assay results to monitor HPV infections when underlying infection rates change or assays with different performance are used. Data were generated based on mathematical algorithms with pre-specified type-specific infection rates, assay sensitivity and specificity, and correlations between various HPV types. Estimated-to-true infection rate ratios and percent reduction of vaccine types were calculated. Results: When the true underlying type-specific prevalence was specified as the reported prevalence between 2003-2006 in the US and genotyping assays with high sensitivity and specificity (0.95, 0.95) were used, estimated-to-true rate ratios were 2.31, 2.17, 2.12 and 1.62, for composite measures with 2 vaccine high-risk types, 4 vaccine types, 14 high-risk types and 37 HPV types, respectively. For a given composite measure, estimated-to-true rate ratios increased when the true underlying infection rates or assay specificity declined. When underlying type-specific infection rates were reduced by 50%, the true composite infection rate of any of the 4 vaccine types decreased by 47%, but the estimated rate only decreased by 15%. Conclusions: Composite infection rate estimates calculated based on panels of genotyping assay results generally over-estimate the true infection burden and could under-estimate effectiveness. The impact of assay specificity is as or more important than sensitivity and should be considered in selecting a genotyping assay to monitor HPV.National STD Prevention Conference 2014 Centers for Disease Control and Prevention; 06/2014
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ABSTRACT: The HPV genotyping line probe assay INNO-LiPA EXTRA allows the detection of a wider spectrum of viral types compared to the earlier V2 version of the assay. Its performance in formalin-fixed paraffin-embedded tissues is unknown.Objectives To test the EXTRA assay in HPV genotyping of paired cervical scrapings and corresponding FFPE biopsy specimens.Study designPaired samples from 188 women with abnormal cytology were examined using the INNO-LiPA HPV genotyping assay, version EXTRA. The assay can simultaneously detect 18 high-risk, 7 low-risk, and 2 unclassified HPV types. Kappa statistics were used to measure interrater agreement between groups.ResultsThe evaluation of paired cervical scraping and biopsy samples gave a 100% overall agreement for HPV status and of 72.9% (kappa 0.6554) for the number of infecting HPVs. 392 out of 507 individual HPV types were concordant, corresponding to a positive agreement rate of 87.2% (95% CI 84.1–90.3). As to the individual genotypes, the agreement was absolute for HPV 45, 68, 73 (kappa 1), excellent for HPV 6, 11, 16, 18, 31, 35, 39, 44, 51, 52, 53, 54, 56, 69/71 and 82 (kappa 0.7796–0.9714), good for HPV26, 33, 43, 58, 66 and 74 (kappa 0.6768–0.7449), and poor for HPV 59 and 40. These agreement values were comparable to those obtained with the V2 assay.Conclusions The EXTRA assay provided excellent performance in HPV typing on FFPE samples comparable to the earlier version of the test despite higher complexity and increased coverage of types.Journal of Clinical Virology 11/2014; 61(4). DOI:10.1016/j.jcv.2014.10.016 · 3.47 Impact Factor