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Yin J, Peng S, Zhang C, Li X, Hu F, Chen W, Qiao Y. Head-to-head comparison of genotyping of human papillomavirus by real-time multiplex PCR assay using type-specific primers and SPF10-PCR-based line probe assay. J Med Virol 2023; 95:e28579. [PMID: 36786174 DOI: 10.1002/jmv.28579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 02/15/2023]
Abstract
The SPF10-polymerase chain reaction (PCR)-based line probe assay (LiPA-25) with high analytical sensitivity and specificity for human papillomavirus (HPV) genotyping in clinical samples has been widely used in vaccine and epidemiologic studies. A real-time multiplex PCR assay using type-specific primers (Hybribio-23) with low workload and cost has been developed recently. The study aimed to compare the performance of LiPA-25 and Hybribio-23 in selected 1731 cervical swab and 117 tissue samples, with a focus on 20 common HPV types (14 high-risk: 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, and 68/73; 6 low-risk: 6, 11, 42, 43, 44, and 53). The level of agreement of two assays was determined using Cohen's Kappa (κ) statistics. A total of 1296 (74.9%) swab samples were identified as HPV-positive by Hybribio-23 or LiPA-25, of which 814 (62.8%) samples exhibited concordant, 358 (27.6%) showed additional or fewer types (compatible), and 124 (9.6%) were discordant. In addition, the two assays showed a perfect agreement for 20 HPV-combined detection (κ = 0.838) and 17 individual HPV types (all κ > 0.800), a good agreement for HPV31 (κ = 0.792) and 43 (κ = 0.696), and a moderate agreement for HPV42 (κ = 0.504). Hybribio-23 was significantly more sensitive for HPV58, 59, 68/73, 42, 43, and 44, and less sensitive for HPV35 and 66 than LiPA-25 (McNemar's test: all p < 0.05). For 117 HPV-positive tissue specimens, the identification of genotypes was 85.2% identical, 12.2% compatible, and only 2.6% discordant. The agreement for HPV31 (κ = 0.786), 68/73 (κ = 0.742), and HPV53 (κ = 0.742) was good, while for other types (all κ > 0.853) and 20 HPV-combined detection (κ = 0.936) was perfect (all p > 0.05). In conclusion, Hybribio-23 and LiPA-25 are comparable. Hybribio-23 could be used for the detection and genotyping of HPV in cervical samples for epidemiological and vaccine studies worldwide.
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Affiliation(s)
- Jian Yin
- School of Population Medicine and Public Health, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Department of Cancer Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Siying Peng
- Department of Cancer Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,The State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, Fujian, China
| | - Changning Zhang
- Department of Cancer Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,College of Life Sciences, Hebei University, Baoding, China
| | - Xinyue Li
- Department of Cancer Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,College of Life Sciences, Hebei University, Baoding, China
| | - Fangfang Hu
- Department of Cancer Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,The State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, Fujian, China
| | - Wen Chen
- Department of Cancer Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Youlin Qiao
- School of Population Medicine and Public Health, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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2
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Kir G, Gunel H, Olgun ZC, McCluggage WG. High-risk human papillomavirus (HPV) detection in formalin-fixed paraffin-embedded cervical tissues: performances of Aptima HPV assay and Beckton Dickinson (BD) Onclarity assay. J Clin Pathol 2023; 76:40-46. [PMID: 34376567 DOI: 10.1136/jclinpath-2021-207657] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 08/01/2021] [Indexed: 12/27/2022]
Abstract
AIM There are many scenarios where high-risk human papillomavirus (HPV) detection in formalin-fixed paraffin-embedded (FFPE) specimens is important. However, there is no Food and Drug Administration (FDA)-approved and clinically validated technique for detecting high-risk HPV in FFPE tissues. In this study, we evaluated two commercially available HPV assays which are FDA-approved for use on cytology specimens, the Aptima HPV assay and the Beckton Dickinson (BD) Onclarity assay, to detect high-risk HPV in FFPE tissues of cervical high-grade squamous intraepithelial lesion (HSIL) and squamous cell carcinoma (SCC). METHODS A total of 189 cases (46 SCC, 107 HSIL and 36 benign/normal) were tested for high-risk HPV with the Aptima HPV assay and a subset of cases (n=97) with the BD Onclarity assay. RESULTS The sensitivities of the Aptima and BD Onclarity HPV assays were 99.4% (95% CI 96.46% to 99.98%) and 75.9% (95% CI 65.27% to 84.62%), respectively; the specificity and positive predictive value (PPV) of the two assays were 100%. Negative predictive values of the Aptima and BD Onclarity HPV assays were 97.3% (95% CI 83.61% to 99.61%) and 67.7% (95% CI 58.91% to 75.47%), respectively. The kappa value (0.96) for comparison of the distribution of high-risk HPV types between the two assays was high. HPV 16 was the most common high-risk HPV type for HSIL and SCC cases. However, SCC cases had higher percentages of HPV 16 and HPV 18/45 and lower percentages of other high-risk HPV types compared with HSIL cases. CONCLUSION Both assays are reliable methods for high-risk HPV detection and genotype determination in FFPE specimens, with high PPV and specificity. The Aptima HPV assay has the advantage of higher sensitivity. As far as we are aware, this is the first study comparing the Aptima HPV assay and the BD Onclarity assay in FFPE tissues. Our study results should be tested and confirmed in larger cohorts.
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Affiliation(s)
- Gozde Kir
- Department of Pathology, Medeniyet University Goztepe Training and Research Hospital, Istanbul, Turkey
| | - Humeyra Gunel
- Department of Pathology, Medeniyet University Goztepe Training and Research Hospital, Istanbul, Turkey
| | - Zeynep Cagla Olgun
- Department of Pathology, Medeniyet University Goztepe Training and Research Hospital, Istanbul, Turkey
| | - W Glenn McCluggage
- Department of Pathology, Royal Group of Hospitals and Dental Hospital Health and Social Services Trust, Belfast, UK
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3
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Pimenoff VN, Tous S, Benavente Y, Alemany L, Quint W, Bosch FX, Bravo IG, de Sanjosé S. Distinct geographic clustering of oncogenic human papillomaviruses multiple infections in cervical cancers: Results from a worldwide cross-sectional study. Int J Cancer 2018; 144:2478-2488. [PMID: 30387873 DOI: 10.1002/ijc.31964] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 10/01/2018] [Accepted: 10/16/2018] [Indexed: 01/10/2023]
Abstract
Coinfections by multiple Human Papillomaviruses (HPVs) are observed in approximately 6-8% of invasive cervical cancer (ICC) cases worldwide. But neither the presence of persistent HPVs coinfections nor their etiological role in the development of ICC is well understood. Cervical HPVs coinfections have been observed randomly, mostly in women with preneoplastic lesions, and only few studies have globally analyzed ICC cases. Here we explored the HPVs multiple infection patterns in a large worldwide sample of cross-sectional ICC cases. Paraffin-embedded ICC biopsy samples were tested using stringent HPV genotyping. Logistic regression models were used to identify the most likely pairwise HPV types in multiple infections. Multivariate analysis was applied to detect significant HPV coinfection patterns beyond pairwise HPVs comparison. Among 8780 HPV DNA-positive ICC cases worldwide, 6.7% (N = 587) contained multiple HPVs. Pairwise analysis revealed that HPV16|74, HPV31|33, HPV31|44, HPV33|44 and HPV45|70 pairs were significantly more frequently found together in multiple infections compared to any other HPV type combination, which supports the occasional role of Alpha-10 LR-HPVs in cervical cancers. In contrast, HPV16|31, HPV16|45, HPV16|51 and HPV18|HPV45 pairs were significantly less frequently found together than with any other HPV pair combination. Multivariate analysis sustained the results and revealed for the first time a distinct coinfection pattern in African ICCs stemming from the clustering of oncogenic HPV51/35/18/52 coinfections in African women. We suggest that the differential geographic HPVs coinfections clustering observed might be compatible with a specific modulation of the natural history/oncogenic potential of particular HPVs multiple infections and warrant monitoring for post-vaccinated.
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Affiliation(s)
- Ville N Pimenoff
- Unit of Biomarkers and Susceptibility, Bellvitge Institute of Biomedical Research (IDIBELL), Catalan Institute of Oncology (ICO), L'Hospitalet de Llobregat, Barcelona, Spain.,Department of Epidemiology, University of Tampere, Tampere, Finland
| | - Sara Tous
- Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), IDIBELL. L'Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Yolanda Benavente
- Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), IDIBELL. L'Hospitalet de Llobregat, Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Laia Alemany
- Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), IDIBELL. L'Hospitalet de Llobregat, Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Wim Quint
- DDL Diagnostic Laboratory, Rijswijk, The Netherlands
| | - Francesc Xavier Bosch
- Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), IDIBELL. L'Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Ignacio G Bravo
- National Center for Scientific Research (CNRS), Laboratory MIVEGEC (UMR CNRS, IRD, UM), Montpellier, France
| | - Silvia de Sanjosé
- Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), IDIBELL. L'Hospitalet de Llobregat, Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,PATH, Reproductive Health Global Program, Seattle, USA
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4
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Castro FA, Koshiol J, Quint W, Wheeler CM, Gillison ML, Vaughan LM, Kleter B, van Doorn LJ, Chaturvedi AK, Hildesheim A, Schiffman M, Wang SS, Zuna RE, Walker JL, Dunn ST, Wentzensen N. Detection of HPV DNA in paraffin-embedded cervical samples: a comparison of four genotyping methods. BMC Infect Dis 2015; 15:544. [PMID: 26607224 PMCID: PMC4660657 DOI: 10.1186/s12879-015-1281-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 11/17/2015] [Indexed: 11/23/2022] Open
Abstract
Background Identification of human papillomavirus (HPV) DNA in cervical tissue is important for understanding cervical carcinogenesis and for evaluating cervical cancer prevention approaches. However, HPV genotyping using formalin-fixed, paraffin-embedded (FFPE) tissues is technically challenging. We evaluated the performance of four commonly used genotyping methods on FFPE cervical specimens conducted in different laboratories and compared to genotyping results from cytological samples. Methods We included 60 pairs of exfoliated-cell and FFPE specimens from women with histologically confirmed cervical intraepithelial lesions grade 2 or 3. Cytology specimens were genotyped using the Linear Array assay. Four expert laboratories processed tissue specimens using different preparation methods and then genotyped the resultant sample preparations using four different HPV genotyping methods: SPF10-PCR DEIA LiPA25 (version 1), Inno-LiPA, Linear Array and the Onclarity assay. Percentage agreement, kappa statistics and McNemar’s chi-square were calculated for each comparison of different methods and specimen types. Results Overall agreement with respect to carcinogenic HPV status for FFPE samples between different methods was: 81.7, 86.7 and 91.7 % for Onclarity versus Inno-LiPA, Linear Array and SPF-LiPA25, respectively; 81.7 and 85.0 % for Linear Array versus Inno-LiPA and SPF-LiPA25, respectively; and 86.7 % for SPF-LiPA25 versus Inno-LiPA. Type-specific agreement was >88.3 % for all pair-wise comparisons. Comparisons with cytology specimens resulted in overall agreements from 80 to 95 % depending on the method and type-specific agreement was >90 % for most comparisons. Conclusions Our data demonstrate that the four genotyping methods run by expert laboratories reliably detect HPV DNA in FFPE specimens with some variation in genotype-specific detection. Electronic supplementary material The online version of this article (doi:10.1186/s12879-015-1281-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Felipe A Castro
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA.
| | - Jill Koshiol
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA.
| | - Wim Quint
- DDL, Diagnostic Laboratory, Rijswijk, The Netherlands.
| | - Cosette M Wheeler
- Department of Pathology, School of Medicine, University of New Mexico, Albuquerque, NM, USA.
| | - Maura L Gillison
- Viral Oncology Program, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
| | | | | | | | - Anil K Chaturvedi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA.
| | - Allan Hildesheim
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA.
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA.
| | - Sophia S Wang
- Division of Cancer Etiology, Department of Population Sciences, Beckman Research Institute and the City of Hope, Duarte, CA, USA.
| | - Rosemary E Zuna
- Departments of Pathology and Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
| | - Joan L Walker
- Departments of Pathology and Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
| | - S Terence Dunn
- Departments of Pathology and Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA. .,Division of Cancer Epidemiology & Genetics, NCI Shady Grove, 9609 Medical Center Drive 7E114, Rockville, MD, 20850, USA.
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5
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Kocjan BJ, Hošnjak L, Poljak M. Detection of alpha human papillomaviruses in archival formalin-fixed, paraffin-embedded (FFPE) tissue specimens. J Clin Virol 2015; 76 Suppl 1:S88-S97. [PMID: 26514313 DOI: 10.1016/j.jcv.2015.10.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Revised: 10/05/2015] [Accepted: 10/10/2015] [Indexed: 01/14/2023]
Abstract
Formalin-fixed, paraffin-embedded (FFPE) tissue specimens stored in pathology departments worldwide are an invaluable source for diagnostic purposes when fresh clinical material is unavailable as well as for retrospective molecular and epidemiological studies, especially when dealing with rare clinical conditions for which prospective collection is not feasible. Accurate detection of HPV infection in these specimens is particularly challenging because nucleic acids are often degraded and therefore, not suitable for amplification of larger fragments of the viral genome or viral gene transcripts. This review provides a brief summary of molecular methods for detecting alpha-HPV DNA/RNA in FFPE tissue specimens. We specifically address the key procedural and environmental factors that have the greatest impact on the quality of nucleic acids extracted from FFPE tissue specimens, and describe some solutions that can be used to increase their integrity and/or amplifiability. Moreover, commonly used methods for HPV DNA/RNA detection in FFPE tissue specimens are presented and discussed, focusing on studies using polymerase chain reaction as an HPV detection method and published after 1999. Finally, we briefly summarize our 22 years of experience with HPV detection in FFPE tissue specimens.
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Affiliation(s)
- Boštjan J Kocjan
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Lea Hošnjak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia; European Society of Clinical Microbiology and Infectious Diseases (ESCMID), Study Group for Forensic and Postmortem Microbiology (ESGFOR), Basel, Switzerland.
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6
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Ejegod DM, Rebolj M, Bonde J. Comparison of analytical and clinical performance of CLART HPV2 genotyping assay to Linear Array and Hybrid Capture 2: a split-sample study. BMC Cancer 2015; 15:216. [PMID: 25886410 PMCID: PMC4391531 DOI: 10.1186/s12885-015-1223-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 03/19/2015] [Indexed: 01/21/2023] Open
Abstract
Background Human Papillomavirus (HPV) genotyping has an increasingly important role in cervical cancer screening and vaccination monitoring, however, without an internationally agreed standard reference assay. The test results from the most widely used genotyping assays are read manually and hence prone to inter-observer variability. The reading of test results on the CLART HPV2 genotyping assay is, on the other hand, automated. The aim of our study was to directly compare the detection of HPV genotypes and high-grade cervical intraepithelial neoplasia (CIN) by CLART, Linear Array (LA), and Hybrid Capture 2 (HC2) using samples stored in SurePath. Methods Residual material from 401 routine samples from women with abnormal cytology was tested by CLART, LA, and HC2 (ClinicalTrial.gov: NCT01671462, Ethical Committee approval: H-2012-070). Histological outcomes were ascertained by linkage to the Danish nation-wide Pathology Data Bank. For comparison of CLART and LA in terms of genotype detection, we calculated κ-coefficients, and proportions of overall and positive agreement. For comparison of CIN detection between CLART, LA, and HC2, we calculated the relative sensitivity and specificity for high-grade CIN. Results The κ-coefficient for agreement in detection of genotypes 16, 18, 31, 33, 35, and 51 was ≥0.90 (overall agreement: 98-99%, positive agreement: 84-95%). The values were slightly lower, but still in the “substantial” range for genotypes 39, 45, 52, 56, 58, 59, and several low-risk genotypes. The relative sensitivity of CLART for ≥ CIN2 and ≥ CIN3 was not significantly lower than that of LA and HC2, although CLART showed a higher specificity than HC2. Conclusions In Danish women with abnormal SurePath cytology, CLART and LA were highly comparable for detection of most high-risk and low-risk genotypes; and CLART’s sensitivity for high-grade CIN was comparable to that of both LA and HC2.
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Affiliation(s)
- Ditte Møller Ejegod
- Department of Pathology, Copenhagen University Hospital, Allé 30, 2650, Hvidovre, Denmark.
| | - Matejka Rebolj
- Department of Public Health, University of Copenhagen, Copenhagen, Denmark.
| | - Jesper Bonde
- Department of Pathology, Copenhagen University Hospital, Allé 30, 2650, Hvidovre, Denmark. .,Clinical Research Center, Copenhagen University Hospital, Hvidovre, Denmark.
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Hardt AL, Schildgen V, Tillmann RL, Brockmann M, Schildgen O. Utility of the QIAGEN/ artus PCR assays and Meningofinder™ for the detection of human herpes virus genomes in formalin-fixed paraffin-embedded clinical samples. Future Virol 2014. [DOI: 10.2217/fvl.14.7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ABSTRACT: Aim: The aim of the study was to analyze whether human herpes viruses can be detected from formalin-fixed paraffin-embedded (FFPE) tissues with two commercial methods. Materials & methods: In total, 91 clinical FFPE samples were analyzed with QIAGEN/artus (Hilden, Germany) qPCRs and the Meningofinder™ assay from PathoFinder (Maastricht, The Netherlands). Results: A total of 27 out of 91 samples were tested for HSV-1 and HSV-2. Three of these 27 samples (11.1%) were positive for HSV-1 and one sample was positive for HSV-2. Out of 91 samples, 50 were tested for CMV, of which six samples were positive (12%). In total, 12 out of 91 samples were tested for the presence of Varizella zoster virus DNA, revealing one as positive (8%). Finally, two samples were tested negative for EBV. Conclusion: Minor differences were identified between both assays, making them a reliable tool for detection of herpes viruses from FFPE material, although this is an off-label use for both assays.
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Affiliation(s)
- Anna-Lena Hardt
- Kliniken der Stadt Köln gGmbH, Krankenhaus Merheim, Institut für Pathologie, Klinikum der Privaten Universität Witten/Herdecke mit Sitz in Köln, Ostmerheimer Str. 200, D-51109 Cologne, Germany
| | - Verena Schildgen
- Kliniken der Stadt Köln gGmbH, Krankenhaus Merheim, Institut für Pathologie, Klinikum der Privaten Universität Witten/Herdecke mit Sitz in Köln, Ostmerheimer Str. 200, D-51109 Cologne, Germany
| | - Ramona-Liza Tillmann
- Kliniken der Stadt Köln gGmbH, Krankenhaus Merheim, Institut für Pathologie, Klinikum der Privaten Universität Witten/Herdecke mit Sitz in Köln, Ostmerheimer Str. 200, D-51109 Cologne, Germany
| | - Michael Brockmann
- Kliniken der Stadt Köln gGmbH, Krankenhaus Merheim, Institut für Pathologie, Klinikum der Privaten Universität Witten/Herdecke mit Sitz in Köln, Ostmerheimer Str. 200, D-51109 Cologne, Germany
| | - Oliver Schildgen
- Kliniken der Stadt Köln gGmbH, Krankenhaus Merheim, Institut für Pathologie, Klinikum der Privaten Universität Witten/Herdecke mit Sitz in Köln, Ostmerheimer Str. 200, D-51109 Cologne, Germany
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8
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Herraez-Hernandez E, Preda O, Alonso S, Pardo RS, Olmo A. Detection and Genotyping of Human Papillomavirus DNA in Formalin-Fixed Paraffin-Embedded Specimens with the HPV Direct Flow CHIP System. Open Virol J 2013; 7:91-5. [PMID: 24222806 PMCID: PMC3821083 DOI: 10.2174/1874357920130927004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 09/14/2013] [Accepted: 09/20/2013] [Indexed: 11/29/2022] Open
Abstract
The novel HPV Direct Flow CHIP commercial system for Human Papillomavirus (HPV) genotyping is based on rapid PCR and automatic reverse dot blot hybridization to genotype-specific probes, allowing the detection of 36 HPV genotypes. This study examined the performance of HPV Direct Flow CHIP in formalin-fixed paraffin-embedded (FFPE) samples (n= 99). Each sample was analyzed both by Direct PCR, using crude cell extracts without DNA purification, and by conventional PCR, using purified DNA. Pair-wise analysis of the results demonstrated strong concordance between the results obtained with the two protocols, although a slightly higher rate of multiple infections was detected by conventional PCR. In summary, HPV Direct Flow CHIP achieves effective HPV detection from FFPE samples with both Direct PCR and Conventional PCR protocols.
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Affiliation(s)
- Elsa Herraez-Hernandez
- R&D Department, Master Diagnóstica, Avenida del Conocimiento 100, Parque Tecnológico de Ciencias de la Salud, 18016, Granada, Spain
| | - Ovidiu Preda
- R&D Department, Master Diagnóstica, Avenida del Conocimiento 100, Parque Tecnológico de Ciencias de la Salud, 18016, Granada, Spain
| | - Sonia Alonso
- Pathology Department, Elda General Hospital. Carretera Elda-Sax, La Torreta s/n, 03600, Elda, Alicante, Spain
| | | | - Asuncion Olmo
- R&D Department, Master Diagnóstica, Avenida del Conocimiento 100, Parque Tecnológico de Ciencias de la Salud, 18016, Granada, Spain
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9
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Herraez-Hernandez E, Alvarez-Perez M, Navarro-Bustos G, Esquivias J, Alonso S, Aneiros-Fernandez J, Lacruz-Pelea C, Sanchez-Aguera M, Santamaria JS, de Antonio JC, Rodriguez-Peralto JL. HPV Direct Flow CHIP: A new human papillomavirus genotyping method based on direct PCR from crude-cell extracts. J Virol Methods 2013; 193:9-17. [DOI: 10.1016/j.jviromet.2013.04.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Revised: 03/26/2013] [Accepted: 04/29/2013] [Indexed: 11/28/2022]
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10
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Micalessi MI, Boulet GA, Pillet S, Jacquet J, Pozzetto B, Bogers JJ, Bourlet T. Comparison of SPF10 real-time PCR and conventional PCR in combination with the INNO-LiPA HPV Genotyping Extra assay for the detection and typing of human papillomavirus in cervical samples. J Virol Methods 2013; 194:113-7. [PMID: 23978605 DOI: 10.1016/j.jviromet.2013.08.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2013] [Revised: 08/12/2013] [Accepted: 08/15/2013] [Indexed: 11/18/2022]
Abstract
The novel SPF10 real-time PCR assay allows the simultaneous amplification and detection of the HPV target. That way, LiPA analysis of the HPV-negative samples can be avoided, reducing workload and cost. This study aims to evaluate the performance of the SPF10 real-time PCR in combination with the LiPA assay for HPV detection and typing in cervical samples. Thirty-nine cervical samples were subjected to the SPF10 conventional PCR in combination with the LiPA assay. Subsequently, the SPF10 real-time PCR was performed to enable the comparison between the SPF10 conventional and the real-time PCR results. In case of discrepancy, the samples were subjected to the CLART HPV2 assay. As a result, 27 out of 39 samples were identified as HPV-positive by the SPF10 real-time PCR and were genotyped further by the LiPA assay. Twenty samples (74.1%) showed an absolute agreement between the conventional and real-time SPF10 PCR (concordant), three (11.1%) displayed additional or fewer types (compatible), two (7.4%) did not show any similarity between both assays (discordant) and the remaining two (7.4%) were LiPA-negative. The two assays showed an excellent strength of agreement for individual (κ=0.932) and multiple genotype detection (κ=0.834). In conclusion, the two SPF10 PCR methods are comparable. Therefore, the SPF10 real-time PCR with subsequent LiPA could be used for the detection and genotyping of HPV in cervical samples.
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Affiliation(s)
- M I Micalessi
- Applied Molecular Biology Research (AMBIOR) Group, Laboratory of Cell Biology and Histology, University of Antwerp, Groenenborgerlaan 171, B2020 Antwerp, Belgium; Vaccine & Infectious Diseases Institute (VAXINFECTIO), University of Antwerp, Universiteitsplein 1, B2610 Antwerp, Belgium.
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