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Mudhigeti N, Kalawat U, Hulikal N, Racherla RG. E6-E7 based nested multiplex PCR assay for genital HPV detection and simultaneous typing of 15 high and low-risk HPV types. Indian J Med Microbiol 2021; 40:18-23. [PMID: 34871707 DOI: 10.1016/j.ijmmb.2021.11.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 11/12/2021] [Accepted: 11/24/2021] [Indexed: 12/26/2022]
Abstract
PURPOSE Due to a wide range of Human Papillomavirus (HPV) types associated with genital cancers; HPV genotyping remains important for the introduction of an appropriate vaccine, disease diagnosis, follow-up and epidemiological surveys. Currently, available molecular genotyping assays are not only expensive but also requires dedicated and expensive equipment which is not feasible in the majority of low-and-middle-socioeconomic countries. The purpose of the study was to develop and evaluated a cost-effective nested-multiplex polymerase chain reaction (NM-PCR) assay for HPV genotyping. METHODS HPV-DNA containing plasmids and cervical scrapings from histologically confirmed cervical cancer cases were used to evaluate the NM-PCR. In the first round PCR, a set of consensus primers were used to amplify 38 mucosal HPV types. HPV Type-specific primers were used in the second-round polymerase chain reaction (PCR) to amplify 15 HPV types in three multiplex cocktails. The assay sensitivity was determined with the control panel containing one to 1010genome equivalents (GE). DNA sequencing was done to confirm the PCR results. RESULTS The assay was able to amplify all HPV types and detected as few as 50GE per reaction. A total of 23 endo-cervical samples obtained from healthy, HPV negative subjects and 52 histologically confirmed cervical scrapings were processed for HPV genotyping by NM-PCR. HPV DNA was detected in all histologically confirmed samples. DNA sequencing results showed complete concordance with PCR results. CONCLUSIONS The designed nested PCR based assay had good concordance with clinical histology and sequencing results and appears to be a promising tool for HPV genotyping especially in resource-constrained settings.
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Affiliation(s)
- Nagaraja Mudhigeti
- VRDL, Department of Microbiology, Sri Venkateswara Institute of Medical Sciences, Tirupati, 517 507, Andhra Pradesh, India.
| | - Usha Kalawat
- Department of Microbiology, Sri Venkateswara Institute of Medical Sciences, Tirupati, 517 507, Andhra Pradesh, India.
| | - Narendra Hulikal
- Department of Surgical Oncology, Sri Venkateswara Institute of Medical Sciences, Tirupati, 517 507, Andhra Pradesh, India.
| | - Rishi Gowtham Racherla
- Department of Microbiology, Sri Venkateswara Institute of Medical Sciences, Tirupati, 517 507, Andhra Pradesh, India.
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2
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Grace VMB, B L, Wilson DD. The Effect of Indian Fig Fruit Extract on Human Papilloma Virus containing Cervical Cancer Cells (HeLa) by Decreasing the HPV18 L1 Gene Load. Asian Pac J Cancer Prev 2021; 22:785-791. [PMID: 33773542 PMCID: PMC8286670 DOI: 10.31557/apjcp.2021.22.3.785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Indexed: 12/14/2022] Open
Abstract
Background: Global trend is moving towards the use of natural phytochemicals to fight against pathogens. Human cervical cancer is directly associated with onco-potent type of Human Papilloma Virus (HPV). There is no known medicine for clearance of HPV type whose persistence is the cause of occurrence and re-occurrence of cervical cancer. The different species of fig fruit and their latex are reported to have HPV associated genital warts clearance capability. Methods: In the current investigation, the effect of the methanol extract of Ficus benghalensis L. fruits on HPV type18 viral load in HeLa cell line was tested by doing PCR using HPV L1 primers (MY09/My011) and the cytotoxicity was also analysed by MTT assay. The induction of apoptotic activity in terms of DNA fragmentation and hyper-chromic effects of DNA was analysed. Results: The PCR results showed a reduction in the HPV18 DNA and also the treatment exhibited a promising cytotoxicity with IC50 value at 211.86 μg/ml. The DNA samples from treated HeLa cells showed DNA shearing and laddering as a mark of apoptotic DNA fragmentation (Fig. 2) and the UV absorbance value at 260 nm was found to be significantly (P<0.01) higher in the DNA sample treated with fruit extract compared to the untreated DNA sample. Conclusion: The Ficus benghalensis L. fruit extract reduced the HPV viral load in HPV18 containing HeLa cells and showed an effective cytotoxicity on HeLa cell line. It also could induce the apoptotic activity in HeLa cell line and this study results suggest that the Ficus benghalensis L. fruits can be used to fight against cervical carcinoma, acting on HPV load.
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Affiliation(s)
- V M Berlin Grace
- Department of Biotechnology & Health Sciences, Karunya Institute of Technology and Sciences, Karunya Nagar, Coimbatore-641 114, Tamil Nadu, India
| | - Lydia B
- Department of Biotechnology & Health Sciences, Karunya Institute of Technology and Sciences, Karunya Nagar, Coimbatore-641 114, Tamil Nadu, India
| | - D David Wilson
- School of Science, Arts, Media and Management (SSAMM), Karunya Institute of Technology and Sciences, Karunya Nagar, Coimbatore-641 114, Tamil Nadu, India
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3
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Gautam A, Gedda MR, Rai M, Sundar S, Chakravarty J. Human Papillomavirus Genome based Detection and Typing: A Holistic Molecular Approach. Curr Mol Med 2020; 19:237-246. [PMID: 30950352 DOI: 10.2174/1566524019666190405120441] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 03/20/2019] [Accepted: 03/27/2019] [Indexed: 11/22/2022]
Abstract
Human Papillomavirus (HPV) is a species specific double-stranded DNA virus infecting human cutaneous or mucosal tissues. The genome structure of HPV is extremely polymorphic hence making it difficult to discriminate between them. HPV exhibits numerous dissimilar types that can be subdivided into high-risk (HR), probably high-risk and low-risk (LR), causing numerous types of cancers and warts around the genital organs in humans. Several screening methods are performed in order to detect cytological abnormalities and presence or absence of HPV genome. Currently available commercial kits and methods are designed to detect only a few HR/LR-HPV types, which are expensive adding to the economic burden of the affected individual and are not freely available. These gaps could be minimized through Polymerase Chain reaction (PCR) method, which is a gold standard and a cost-effective technique for the detection of most HPV (both known and unknown) types by using specific consensus primers in minimal lab setup. In this context, numerous studies have validated the effectiveness of different sets of consensus primers in the screening of HPVs. Numerous consensus primers, such as E6, E6/E7, GP-E6/E7, MY09/11, GP5+/GP6+, SPF10, and PGMY09/11 have been developed to detect the presence of HPV DNA. In addition, HPV detection sensitivity could be achieved through consensus primer sets targeting specific ORF regions like L1 and E6, which may finally assist in better diagnosis of several unknown HR-HPVs. The present review, provides a summary of the available methods, kits and consensus primer sets for HPV genome based detection, their advantages and limitations along with future goals to be set for HPV detection.
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Affiliation(s)
- Abhilasha Gautam
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi-221005, India
| | - Mallikarjuna R Gedda
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi-221005, India
| | - Madhukar Rai
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi-221005, India
| | - Shyam Sundar
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi-221005, India
| | - Jaya Chakravarty
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi-221005, India
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4
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Fan Z, Feng X, Zhang W, Zhang X, Lin JM. Rapid detection of high-risk HPV16 and HPV18 based on microchip electrophoresis. J Pharm Anal 2020; 10:329-333. [PMID: 32923006 PMCID: PMC7474136 DOI: 10.1016/j.jpha.2020.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/23/2020] [Accepted: 04/13/2020] [Indexed: 11/30/2022] Open
Abstract
Researches on detection of human papillomavirus (HPV) high-risk samples were carried out by polymerase chain reaction (PCR) coupled with microchip electrophoresis (MCE). Herein, we introduced a simple, rapid, automated method for detecting high-risk samples HPV16 and HPV18. In this research, general primers were initially selected to obtain sufficient detectable yield by PCR to verify feasibility of MCM method for HPV detection, then type-specific primers were further used to evaluate the specificity of MCE method. The results indicated MCE method was capable of specifically detecting high-risk HPV16 and HPV18, and also enabled simultaneous detection of multiplex samples. This MCE method described here has been successfully applied to HPV detection and displayed excellent reliability demonstrating by sequencing results. The inherent capability of MCE facilitated HPV detection conducted in a small chip with automated, high throughput, massive parallelized analysis. We envision that MCE method will definitely pave a way for clinical diagnosis, and even on-site screening of cervical cancer. A rapid, automatic assay was established for HPV detection. The described method exhibited the advantages of facile operation mode. The proposed method is of high sensitivity, specificity and reproducibility.
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Affiliation(s)
- Zhaoxuan Fan
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, PR China.,Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, PR China
| | - Xiao Feng
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, PR China.,State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, 100029, PR China
| | - Weifei Zhang
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, PR China
| | - Xueji Zhang
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, PR China.,School of Biomedical Engineering, Shenzhen University, Shenzhen, Guangdong 518060, PR China
| | - Jin-Ming Lin
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, PR China
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5
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Nilyanimit P, Chansaenroj J, Poomipak W, Praianantathavorn K, Payungporn S, Poovorawan Y. Comparison of Four Human Papillomavirus Genotyping Methods: Next-generation Sequencing, INNO-LiPA, Electrochemical DNA Chip, and Nested-PCR. Ann Lab Med 2018; 38:139-146. [PMID: 29214758 PMCID: PMC5736673 DOI: 10.3343/alm.2018.38.2.139] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 06/09/2017] [Accepted: 11/02/2017] [Indexed: 11/19/2022] Open
Abstract
Background Human papillomavirus (HPV) infection causes cervical cancer, thus necessitating early detection by screening. Rapid and accurate HPV genotyping is crucial both for the assessment of patients with HPV infection and for surveillance studies. Methods Fifty-eight cervicovaginal samples were tested for HPV genotypes using four methods in parallel: nested-PCR followed by conventional sequencing, INNO-LiPA, electrochemical DNA chip, and next-generation sequencing (NGS). Results Seven HPV genotypes (16, 18, 31, 33, 45, 56, and 58) were identified by all four methods. Nineteen HPV genotypes were detected by NGS, but not by nested-PCR, INNO-LiPA, or electrochemical DNA chip. Conclusions Although NGS is relatively expensive and complex, it may serve as a sensitive HPV genotyping method. Because of its highly sensitive detection of multiple HPV genotypes, NGS may serve as an alternative for diagnostic HPV genotyping in certain situations.
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Affiliation(s)
- Pornjarim Nilyanimit
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok
| | - Jira Chansaenroj
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok
| | - Witthaya Poomipak
- Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok
| | | | - Sunchai Payungporn
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok.
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Cortés-Alaguero C, González-Mirasol E, Morales-Roselló J, Poblet-Martinez E. Do clinical data and human papilloma virus genotype influence spontaneous regression in grade I cervical intraepithelial neoplasia? J Turk Ger Gynecol Assoc 2017; 18:1-8. [PMID: 28506943 PMCID: PMC5450204 DOI: 10.4274/jtgga.2016.0138] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 12/05/2016] [Indexed: 01/19/2023] Open
Abstract
OBJECTIVE To determine whether medical history, clinical examination and human papilloma virus (HPV) genotype influence spontaneous regression in cervical intraepithelial neoplasia grade I (CIN-I). MATERIAL AND METHODS We retrospectively evaluated 232 women who were histologically diagnosed as have CIN-I by means of Kaplan-Meier curves, the pattern of spontaneous regression according to the medical history, clinical examination, and HPV genotype. RESULTS Spontaneous regression occurred in most patients and was influenced by the presence of multiple HPV genotypes but not by the HPV genotype itself. In addition, regression frequency was diminished when more than 50% of the cervix surface was affected or when an abnormal cytology was present at the beginning of follow-up. CONCLUSION The frequency of regression in CIN-I is high, making long-term follow-up and conservative management advisable. Data from clinical examination and HPV genotyping might help to anticipate which lesions will regress.
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Affiliation(s)
- Caterina Cortés-Alaguero
- Department of Obstetrics and Gynecology, Complex Hospital of Albacete University, Albacete, Spain
| | - Esteban González-Mirasol
- Department of Obstetrics and Gynecology, Complex Hospital of Albacete University, Albacete, Spain
| | - José Morales-Roselló
- Department of Obstetrics and Gynecology, La Fe University and Polytechnic Hospital, Valencia, Spain
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Alberizzi P, Spinillo A, Gardella B, Cesari S, Silini EM. Evaluation of the HPV typing INNO-LiPA EXTRA assay on formalin-fixed paraffin-embedded cervical biopsy samples. J Clin Virol 2014; 61:535-9. [PMID: 25464970 DOI: 10.1016/j.jcv.2014.10.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 07/12/2014] [Accepted: 10/25/2014] [Indexed: 11/17/2022]
Abstract
BACKGROUND 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 DESIGN Paired 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. RESULTS The 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.
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Affiliation(s)
- Paola Alberizzi
- Department of Pathology, IRCCS-Fondazione Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Arsenio Spinillo
- Department of Obstetrics and Gynaecology, IRCCS-Fondazione Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Barbara Gardella
- Department of Obstetrics and Gynaecology, IRCCS-Fondazione Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Stefania Cesari
- Department of Pathology, IRCCS-Fondazione Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Enrico Maria Silini
- Unit of Surgical Pathology and Centre for Molecular and Translational Oncology (COMT), University of Parma, Parma, Italy.
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8
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Murao K, Yoshioka R, Kubo Y. Human papillomavirus infection in Bowen disease: Negative p53 expression, not p16INK4aoverexpression, is correlated with human papillomavirus-associated Bowen disease. J Dermatol 2014; 41:878-84. [DOI: 10.1111/1346-8138.12613] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 07/31/2014] [Indexed: 01/10/2023]
Affiliation(s)
- Kazutoshi Murao
- Department of Dermatology; Institute of Health Biosciences; University of Tokushima Graduate School; Tokushima Japan
| | - Rika Yoshioka
- Department of Dermatology; Institute of Health Biosciences; University of Tokushima Graduate School; Tokushima Japan
| | - Yoshiaki Kubo
- Department of Dermatology; Institute of Health Biosciences; University of Tokushima Graduate School; Tokushima Japan
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Zhao FH, Zhu FC, Chen W, Li J, Hu YM, Hong Y, Zhang YJ, Pan QJ, Zhu JH, Zhang X, Chen Y, Tang H, Zhang H, Durand C, Datta SK, Struyf F, Bi D. Baseline prevalence and type distribution of human papillomavirus in healthy Chinese women aged 18-25 years enrolled in a clinical trial. Int J Cancer 2014; 135:2604-11. [PMID: 24740547 PMCID: PMC4277334 DOI: 10.1002/ijc.28896] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Revised: 02/24/2014] [Accepted: 02/25/2014] [Indexed: 12/05/2022]
Abstract
Baseline human papillomavirus (HPV) prevalence and type distribution were evaluated in young Chinese women enrolled in a clinical trial of an HPV vaccine (ClinicalTrials.gov registration NCT00779766). Cervical specimens and blood samples were collected at baseline from women aged 18–25 years (n = 6,051) from four sites across Jiangsu province. Cervical specimens were tested for HPV DNA by SPF10 PCR-DEIA-LiPA25 version 1, and HPV-16/18 type-specific polymerase chain reaction. Anti-HPV-16 and anti-HPV-18 antibody titres were quantified by enzyme-linked immunosorbent assay. At baseline, 15.3% of women were DNA positive for any of 14 HPV high-risk (hr) types (HPV-16/18/31/33/35/39/45/51/52/56/58/59/66/68). The most commonly detected hrHPV types in cervical specimens were HPV-52 (4.0%) and HPV-16 (3.7%). High-risk HPV DNA-positivity increased with severity of cytological abnormalities: 39.3% in atypical squamous cells of undetermined significance, 85.0% in low-grade squamous intraepithelial lesions and 97.8% in high-grade squamous intraepithelial lesions (HSIL). The hrHPV types most frequently detected in HSIL were HPV-16 (63.0%), HPV-18 (17.4%), HPV-52 (17.4%), HPV-58 (15.2%) and HPV-33 (15.2%). The hrHPV types most frequently detected in cervical intraepithelial neoplasia 2+ were HPV-16 (66.1%), HPV-33 (16.1%), HPV-52 (16.1%), HPV-58 (14.5%) and HPV-51 (11.3%). Multiple hrHPV infections were reported for 24.4% of hrHPV DNA positive women. Regardless of baseline HPV DNA status, 30.5% and 16.0% of subjects were initially seropositive for anti-HPV-16 and anti-HPV-18, respectively. In conclusion, the high baseline seropositivity rate and intermediate prevalence of cervical hrHPV types in Chinese women aged 18–25 years underlines the importance of early HPV vaccination in this population.
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Affiliation(s)
- Fang-Hui Zhao
- Cancer Institute and Hospital, Chinese Academy of Medical Sciences (CICAMS) and Peking Union Medical College, Beijing, China
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10
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Bharti AC, Shukla S, Mahata S, Hedau S, Das BC. Human papillomavirus and control of cervical cancer in India. ACTA ACUST UNITED AC 2014. [DOI: 10.1586/eog.10.23] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Tjalma WAA, Depuydt CE. Cervical cancer screening: which HPV test should be used--L1 or E6/E7? Eur J Obstet Gynecol Reprod Biol 2013; 170:45-6. [PMID: 23932300 DOI: 10.1016/j.ejogrb.2013.06.027] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Revised: 06/19/2013] [Accepted: 06/23/2013] [Indexed: 12/16/2022]
Abstract
Cervical cancer can and should be a historical disease. The reality, however, is that every year more than half a million women are diagnosed with cervical cancer and a quarter of a million die of this disease. The causal factor for cervical cancer is a persistent HPV infection and therefore a vaccine was developed: prophylactic HPV vaccination will reduce cervical cancer by 70%. Screening based on cytology will miss more than 40% of the abnormalities. The introduction of vaccination should lead to the reintroduction of cervical cancer screening based on HPV detection. Primary HPV screening followed by cytology will detect almost all abnormalities. Not all HPV tests, however, are the same! Clinicians are generally not aware that there is a huge difference among HPV tests. If a low grade lesion progresses to a high grade or invasive cancer, their HPV is likely to integrate. During integration L1 expression can be lost, but E6/E7 expression will always remain present. If the viral HPV is completely integrated then a L1 test looking for only L1 expression will miss this (pre)cancer, while the E6/E7 test will not miss it. HPV tests used in cervical cancer screening should be based on the early (E) and the late (L) genes in order not to miss the abnormality.
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Affiliation(s)
- W A A Tjalma
- Department of Gynecology, Multidisciplinary Breast and Gynecologic Oncology Clinic, Antwerp University - Hospital, University of Antwerp, Antwerpen, Belgium.
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12
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Barbieri D, Nocera M, Gallinella G, Gentilomi GA, Plazzi M, Costa S, Santini D, Venturoli S. Comparison of HPV sign genotyping test with INNO-LiPA HPV genotyping extra assay on histologic and cytologic cervical specimens. Diagn Microbiol Infect Dis 2012; 74:43-8. [PMID: 22717156 DOI: 10.1016/j.diagmicrobio.2012.05.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Revised: 05/11/2012] [Accepted: 05/13/2012] [Indexed: 11/25/2022]
Abstract
An accurate tool for viral typing is important for management of patients with human papillomavirus (HPV) infection and to monitor HPV vaccine efficacy. This study evaluated the performance of the HPV sign® Genotyping Test by analyzing 87 archival cervical specimens and compared results with historical data by INNO-LiPA HPV Genotyping Extra assay. There was a substantial concordance for HPV detection in clinical samples (k 0.66), with an overall agreement rate of 85.1%. The genotyping overall agreement, considering one by one the HPV infection detected, was 95.7%. The HPV sign test showed, however, lower sensitivity than INNO-LiPA for HPV 31, 53, and 66. On the other hand, The HPV16 sensitivity was higher for HPV sign (90.0%, confidence interval [CI] 0.79-1.01) than for INNO-LiPA (83.3%, CI 0.70-0.97). Furthermore, HPV sign allowed identifying the presence of HPV16 intratype variants. In conclusion, HPV sign is a promising method for HPV genotyping and has revealed advantages in detecting a broad spectrum of HPV types and variants.
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Affiliation(s)
- Daniela Barbieri
- Department of Haematology and Oncological Sciences L. and A. Seragnoli, Division of Microbiology, University of Bologna, 40138 Bologna, Italy
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13
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Detection of human papillomaviruses by polymerase chain reaction and ligation reaction on universal microarray. PLoS One 2012; 7:e34211. [PMID: 22457826 PMCID: PMC3311614 DOI: 10.1371/journal.pone.0034211] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 02/28/2012] [Indexed: 12/02/2022] Open
Abstract
Sensitive and specific detection of human papillomaviruses (HPV) in cervical samples is a useful tool for the early diagnosis of epithelial neoplasia and anogenital lesions. Recent studies support the feasibility of HPV DNA testing instead of cytology (Pap smear) as a primary test in population screening for cervical cancer. This is likely to be an option in the near future in many countries, and it would increase the efficiency of screening for cervical abnormalities. We present here a microarray test for the detection and typing of 15 most important high-risk HPV types and two low risk types. The method is based on type specific multiplex PCR amplification of the L1 viral genomic region followed by ligation detection reaction where two specific ssDNA probes, one containing a fluorescent label and the other a flanking ZipCode sequence, are joined by enzymatic ligation in the presence of the correct HPV PCR product. Human beta-globin is amplified in the same reaction to control for sample quality and adequacy. The genotyping capacity of our approach was evaluated against Linear Array test using cervical samples collected in transport medium. Altogether 14 out of 15 valid samples (93%) gave concordant results between our test and Linear Array. One sample was HPV56 positive in our test and high-risk positive in Hybrid Capture 2 but remained negative in Linear Array. The preliminary results suggest that our test has accurate multiple HPV genotyping capability with the additional advantages of generic detection format, and potential for high-throughput screening.
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14
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Yi X, Li J, Yu S, Zhang A, Xu J, Yi J, Zou J, Nie X, Huang J, Wang J. A new PCR-based mass spectrometry system for high-risk HPV, part I: methods. Am J Clin Pathol 2011; 136:913-9. [PMID: 22095377 DOI: 10.1309/ajcpwtzdt0q7dovi] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022] Open
Abstract
Infection with high-risk (HR) human papillomaviruses (HPVs) has been confirmed as the necessary cause of cervical cancer. There are many studies that have established and confirmed the relationship of specific HPV types and the risk of invasive cervical cancer. We have developed a novel genotyping method for detecting 14 HR-HPV genotypes simultaneously with MassARRAY (Sequenom, San Diego, CA) technique based on the matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). All 14 HPVs showed high specificities and high sensitivities in the plasmid test; lower detection limits for each genotype were from 10 to 100 copies. Furthermore, the MS system has high-throughput capacities, capable of processing, with type-specific output, 4,500 samples in 24 hours. The MS HPV assay is a sensitive and useful tool for HPV genotyping. It has the potential to be suitable for large-scale epidemiologic studies and routine diagnostic clinical applications owing to its high-throughput capacity, high sensitivity, and low cost per case.
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Affiliation(s)
- Xin Yi
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy Sciences, Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Jingjing Li
- BGI-Shenzhen, Shenzhen, China
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Laboratory of Genetics, Peking University School of Oncology, Beijing Cancer Hospital and Institute, Beijing
| | - Shuang Yu
- BGI-Shenzhen, Shenzhen, China
- Department of Endocrinology of the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Aipeng Zhang
- Department of Obstetrics and Gynecology, General Hospital of Chinese People’s Liberation Army, Beijing
| | - Jiajia Xu
- BGI-Shenzhen, Shenzhen, China
- Genome Research Institute, Shenzhen University Medical School, Shenzhen
| | - Ji Yi
- BGI-Shenzhen, Shenzhen, China
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15
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Performance evaluation of manual and automated (MagNA pure) nucleic acid isolation in HPV detection and genotyping using Roche Linear Array HPV Test. Infect Dis Obstet Gynecol 2011; 2011:931281. [PMID: 21785558 PMCID: PMC3139135 DOI: 10.1155/2011/931281] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 04/20/2011] [Indexed: 12/29/2022] Open
Abstract
Nucleic acids of human papillomavirus (HPV) isolated by manual extraction method (AmpliLute) and automated MagNA pure system were compared and evaluated with cytohistological findings in 253 women. The concordance level between AmpliLute and MagNA was very good 93.3% (κ = 0.864, P < .0001). Overall HPVpositivity detected by AmpliLute was 57.3% (30.4% as single and 27% as multiple infections) in contrast to MagNA 54.5% (32% and 23%, resp.). Discrepant results observed in 25 cases: 11 MagNA(−)/AmpliLute(+), 10 of which had positive histology; 5 MagNA(+)/AmpliLute(−) with negative histology; 8 MagNA(+)/AmpliLute(+): in 7 of which AmpliLute detected extra HPV genotypes and 1 MagNA(invalid)/AmpliLute(+) with positive histology. Both methods performed well when compared against cytological (area under curve (AUC) of AmpliLute 0.712 versus 0.672 of MagNA) and histological diagnoses (AUC of AmpliLute 0.935 versus 0.877 of MagNA), with AmpliLute showing a slightly predominance over MagNA. However, higher sensitivities, specificities, and positive/negative predictive values were obtained by AmpliLute.
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16
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Gheit T, Tommasino M. Detection of high-risk mucosal human papillomavirus DNA in human specimens by a novel and sensitive multiplex PCR method combined with DNA microarray. Methods Mol Biol 2011; 665:195-212. [PMID: 21116803 DOI: 10.1007/978-1-60761-817-1_12] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Epidemiological and functional studies have clearly demonstrated that certain types of human papillomavirus (HPV) from the genus alpha of the HPV phylogenetic tree, referred to as high-risk (HR) types, are the etiological cause of cervical cancer. Several methods for HPV detection and typing have been developed, and their importance in clinical and epidemiological studies has been well demonstrated. However, comparative studies have shown that several assays have different sensitivities for the detection of specific HPV types, particularly in the case of multiple infections. In this chapter, we describe a novel one-shot method for the detection and typing of 19 mucosal HR HPV types (types 16, 18, 26, 31, 33, 35, 39, 45, 51, 52, 53, 56, 58, 59, 66, 68, 70, 73, and 82). The assay combines the advantages of the multiplex PCR methods, i.e., high sensitivity and the possibility to perform multiple amplifications in a single reaction, with an array primer extension (APEX) assay. The latter method offers the benefits of Sanger dideoxy sequencing with the high-throughput potential of the microarray. Initial studies have revealed that the assay is very sensitive in detecting multiple HPV infections.
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Affiliation(s)
- Tarik Gheit
- Infections and Cancer Biology Group, International Agency for Research on Cancer, Lyon, France
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17
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Lack of association between extramammary Paget's disease and human papillomavirus infection. J Dermatol Sci 2010; 59:209-10. [DOI: 10.1016/j.jdermsci.2010.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 06/24/2010] [Accepted: 07/06/2010] [Indexed: 12/12/2022]
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18
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Dinc B, Rota S, Onan A, Bozdayi G, Taskiran C, Biri A, Güner H. Prevalence of human papillomavirus (HPV) and HPV-16 genotyping by real-time PCR in patients with several cervical pathologies. Braz J Infect Dis 2010. [DOI: 10.1016/s1413-8670(10)70005-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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19
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Hong JH, Lee JK, Song ES, Lee JM, Kim MK. Evaluation of the compatibility of the Digene media when performing the Roche linear array human papillomavirus genotyping test. Arch Gynecol Obstet 2009; 280:613-8. [DOI: 10.1007/s00404-009-0974-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Accepted: 01/30/2009] [Indexed: 11/25/2022]
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20
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Hong JH, Song SH, Kim JK, Han JH, Lee JK. Comparison of the novel human papillomavirus 4 auto-capillary electrophoresis test with the hybrid capture 2 assay and with the PCR HPV typing set test in the detection of high-risk HPV including HPV 16 and 18 genotypes in cervical specimens. J Korean Med Sci 2009; 24:579-84. [PMID: 19654936 PMCID: PMC2719217 DOI: 10.3346/jkms.2009.24.4.579] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2008] [Accepted: 03/14/2009] [Indexed: 11/20/2022] Open
Abstract
The aim of this study was to compare the novel human papillomavirus (HPV) detection method, the HPV 4 Auto-capillary Electrophoresis (ACE) test with the hybrid capture (HC) 2 assay for the detection of high-risk HPVs. In addition, we compared the HPV 4 ACE test with the polymerase chain reaction HPV Typing Set test for the detection of HPV 16 and HPV 18 genotypes. One hundred ninety-nine cervical swab samples obtained from women with previous abnormal Pap smears were subjected to testing with the three HPV tests. The HPV 4 ACE test and the HC 2 assay showed substantial agreement for detection of high-risk HPVs (85.4%, kappa=0.71). The HPV 4 ACE test also showed substantial agreement with the PCR HPV Typing Set test in the detection of HPV 16 and HP V 18 genotypes (89.9%, kappa=0.65). In correlation with cytologic results, the sensitivities and specificities of the HPV 4 ACE test and HC 2 assay were 92.9% vs. 92.9% and 48.1% vs. 50.8%, respectively, when high-grade squamous intraepithelial lesions were regarded as abnormal cytologies. The novel HPV 4 ACE test is a valuable tool for the detection of high-risk HPVs and for genotyping of HPV 16 and HPV 18.
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Affiliation(s)
- Jin Hwa Hong
- Department of Obstetrics and Gynecology, Guro Hospital, College of Medicine, Korea University, Seoul, Korea
| | - Seung Hun Song
- Department of Obstetrics and Gynecology, Guro Hospital, College of Medicine, Korea University, Seoul, Korea
| | | | | | - Jae Kwan Lee
- Department of Obstetrics and Gynecology, Guro Hospital, College of Medicine, Korea University, Seoul, Korea
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21
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Sz-Hau Chen, Kun-I Lin, Chuan-Yi Tang, Sheng-Lung Peng, Yao-Chen Chuang, Yi-Rou Lin, Jui-Ping Wang, Chih-Sheng Lin. Optical Detection of Human Papillomavirus Type 16 and Type 18 by Sequence Sandwich Hybridization With Oligonucleotide-Functionalized Au Nanoparticles. IEEE Trans Nanobioscience 2009; 8:120-31. [DOI: 10.1109/tnb.2008.2011733] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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22
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Miyashita M, Agdamag DM, Sasagawa T, Matsushita K, Salud LM, Salud CO, Saikawa K, Leano PS, Pagcaliwagan T, Acuna J, Ishizaki A, Kageyama S, Ichimura H. High-risk HPV types in lesions of the uterine cervix of female commercial sex workers in the Philippines. J Med Virol 2009; 81:545-51. [DOI: 10.1002/jmv.21416] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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23
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Milutin Gasperov N, Sabol I, Matovina M, Spaventi S, Grce M. Detection and typing of human papillomaviruses combining different methods: polymerase chain reaction, restriction fragment length polymorphism, line probe assay and sequencing. Pathol Oncol Res 2008; 14:355-63. [PMID: 18752054 DOI: 10.1007/s12253-008-9084-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2008] [Accepted: 07/07/2008] [Indexed: 11/25/2022]
Abstract
The identification of the etiological factor of many cervical precancerous lesions and cervical cancer, the human papillomavirus (HPV) is widely used. In this study, we evaluated the consensus and type-specific (TS) polymerase chain reaction (PCR), restriction fragment length polymorphism (RFLP), line probe assay (LiPA, Innogenetics) and sequencing to determine the HPV types in cervical specimens. Out of 690 High-grade Squamous Intraepithelial Lesion (HSIL) samples, 86.7% were HPV positive and 13.3% HPV negative by consensus primers (MY09/MY11, L1C1/L1C2-1/L1C2-2 and/or GP5/6) directed PCR. Out of 598 HPV positive samples, 85.3% were typed by TS-PCR being HPV 6/11, 16, 18, 31 and/or 33, while 14.7% remained untyped. The most prevalent HPV type in the study group was HPV 16, identified in 35.5% cases, while HPV 31 was the second most frequent HPV type with a prevalence of 10.5%. They were followed by HPV types 6/11, 33 and 18 with a prevalence of 7.4%, 6.2% and 4.9%, respectively. Multiple HPV infections with two or more HPV types (6/11, 16, 18, 31 and/or 33) were found in 9.4% cases. A subset of 88 samples was further typed by RFLP and LiPA to determine the rare HPV types in HSIL samples. The most frequent low abundant HPV types in single infections in decreasing order were HPV 53, 58, 66, 56 and 52, while HPV 51 was the most frequent low abundant HPV type found in multiple HPV infections. Multiple HPV infections were mostly found by LiPA in 27.3% cases versus 14.8% cases found by RFLP. The perfect agreement between RFLP and LiPA assay pair was observed only for HPV types 16, 18, 34 and 59 (kappa value of 1). For other HPV types, the inter-assay agreement ranged from very good to no agreement indicating that neither assay is perfect. Sequencing was performed for 33 samples in cases where both RFLP and LiPA were inconclusive. Sequencing was shown to be a very good method in case of single HPV infection but not applicable in case of multiple HPV infections. Both RFLP and LiPA are good assays for epidemiological studies, although RFLP being cumbersome and time-consuming is less applicable than LiPA. Careful consideration has to be made before the implementation of either HPV typing methods in clinical laboratories.
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24
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Boulet GAV, Horvath CAJ, Berghmans S, Bogers J. Human papillomavirus in cervical cancer screening: important role as biomarker. Cancer Epidemiol Biomarkers Prev 2008; 17:810-7. [PMID: 18398022 DOI: 10.1158/1055-9965.epi-07-2865] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Cervical cytology screening has reduced cervical cancer morbidity and mortality but shows important shortcomings in terms of sensitivity and specificity. Infection with distinct types of human papillomavirus (HPV) is the primary etiologic factor in cervical carcinogenesis. This causal relationship has been exploited for the development of molecular technologies for viral detection to overcome limitations linked to cytologic cervical screening. HPV testing has been suggested for primary screening, triage of equivocal Pap smears or low-grade lesions and follow-up after treatment for cervical intraepithelial neoplasia. Determination of HPV genotype, viral load, integration status and RNA expression could further improve the effectiveness of HPV-based screening and triage strategies. The prospect of prophylactic HPV vaccination stresses the importance of modification of the current cytology-based screening approach.
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Affiliation(s)
- Gaëlle A V Boulet
- AMBIOR, Laboratory of Cell Biology and Histology, University of Antwerp Groenenborgerlaan 171, Antwerp, Belgium.
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25
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Del Prete R, Di Taranto AM, Lipsi MR, Nirchio V, Antonetti R, Miragliotta G. Prevalence and genotypes identification of human papillomavirus infection in a population of South Italy. J Clin Virol 2008; 42:211-4. [PMID: 18339580 DOI: 10.1016/j.jcv.2008.01.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Revised: 01/22/2008] [Accepted: 01/23/2008] [Indexed: 11/28/2022]
Abstract
BACKGROUND A limited number of human papillomavirus (HPV) types account for the majority of invasive cervical cancer cases. OBJECTIVES To assess, in a southern Italian region, where HPV infection had not yet been investigated, the prevalence of type-specific HPV infection. STUDY DESIGN Multiplex PCR was used to test cervical specimens from 871 asymptomatic women. RESULTS The HPV infection rate was 23.1%, with the highest prevalence being observed in women aged 20-30 years (32.6%). Type 16 was the most frequent HPV type detected either in mono-infected (39.8%) or in multi-infected (46.3%) women. CONCLUSIONS The HPV infection rate was higher than reported from other Italian areas. Our results further emphasise the importance of vaccinations to immunize females before they acquire HPV infection.
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Affiliation(s)
- Raffaele Del Prete
- Section of Microbiology, Department of Clinical Medicine, Immunology, Infectious Diseases, University of Bari, Piazza Giulio Cesare, 70124 Bari, Italy
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26
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van Hamont D, Bulten J, Shirango H, Melchers WJG, Massuger LFAG, de Wilde PCM. Biological behavior of CIN lesions is predictable by multiple parameter logistic regression models. Carcinogenesis 2008; 29:840-5. [PMID: 18310095 DOI: 10.1093/carcin/bgm287] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES Progression and regression of premalignant cervical lesions cannot be predicted using conventional cytomorphological or histomorphological parameters. However, markers such as human papillomavirus (HPV) or makers indicating proliferation, genetic instability and chromosomal aberration may be of predictive value assessing short-term biological behavior of cervical intraepithelial neoplasia. In this paper, we have studied the usage of logistic regression models with Ki-67 labeling index (LI), chromosome index for chromosome 1 (CI#1) and aneusomy for chromosome 1 in cervical smears to predict progressive and regressive behavior of premalignant cervical lesions. METHODS Retrospectively, the intake smears of 42 women showing regression in follow-up and of 31 women showing progression in follow-up were assessed. RESULTS A multiparameter logistic regression model containing the parameters Ki-67 LI, CI#1 and the fraction of cells with four copies of chromosome 1 per nucleus appeared to be the best predicting model, overall correct classification of 93.2% (area under the receiver operating characteristic curve 0.96 +/- 0.02). After cross-validation, the model correctly classified 66 of 73 samples (90.4%). Moreover, the model predicted biological behavior perfectly assessing the smear taken subsequently to the intake smear of 46 women. CONCLUSION Although measuring parameters indicating proliferation and chromosome 1 aberration is laborious, this study demonstrates that short-term progressive and regressive behavior is highly predictable using a model combing these parameters. We also showed that in the triage management of high-risk human papillomavirus-positive women with minimally abnormal smears applying a model as such can be useful.
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Affiliation(s)
- D van Hamont
- Department of Medical Microbiology, Nijmegen University Centre for Infectious Diseases, Nijmegen, The Netherlands.
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27
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Campos EA, Simões JA, Rabelo-Santos SH, Sarian LO, Pitta DR, Levi JE, Derchain S. Recovery of DNA for the detection and genotyping of human papillomavirus from clinical cervical specimens stored for up to 2 years in a universal collection medium with denaturing reagent. J Virol Methods 2007; 147:333-7. [PMID: 17976831 DOI: 10.1016/j.jviromet.2007.09.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2007] [Revised: 09/18/2007] [Accepted: 09/20/2007] [Indexed: 11/24/2022]
Abstract
The recovery and stability of DNA for the detection and genotyping of HPV in UCM-containing specimens, after exposure to denaturing reagents and stored for up to 2 years were evaluated. Samples were collected from 60 women who had cervical cytology specimens harboring cervical intraepithelial neoplasia (CIN) 2 or 3. All samples were stored in UCM and had been frozen at -20 degrees C following the addition of the denaturing reagent (sodium hydroxide) and the removal of the aliquot required for Hybrid Capture 2 testing for the identification of HPV DNA. The samples had been stored for 6, 12 and 24 months (20 samples for each storage time). HPV DNA extraction was performed according to a protocol designed specifically and the presence and quality of DNA was confirmed by human beta-globin detection using the consensus primers G73 and G74. HPV DNA was amplified using the consensus primers PGMY09 and PGMY11, and reverse line-blot hybridization was used to detect type-specific amplicons for 37 HPV types. The DNA extracted from the denatured specimen was recovered in 57/60 (95%) of the samples. HPV DNA was detected in 56/57 (98%) of the recovered samples. Twenty-six of the 56 samples recovered (48%) were genotyped successfully.
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Affiliation(s)
- Elisabete A Campos
- Department of Obstetrics and Gynecology, Universidade Estadual de Campinas (UNICAMP), São Paulo, Brazil
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28
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Dunn ST, Allen RA, Wang S, Walker J, Schiffman M. DNA extraction: An understudied and important aspect of HPV genotyping using PCR-based methods. J Virol Methods 2007; 143:45-54. [PMID: 17399803 DOI: 10.1016/j.jviromet.2007.02.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2006] [Revised: 02/13/2007] [Accepted: 02/16/2007] [Indexed: 11/24/2022]
Abstract
Testing for the group of approximately 15 carcinogenic human papillomavirus (HPV) genotypes is an important adjunct to cytology. Because carcinogenic strengths of HPV types differ greatly, assays that permit identification of individual HPV genotypes are being introduced. Most HPV genotyping systems proposed for clinical use are PCR-based, depending heavily for validity on careful attention to numerous details. One understudied detail is the effect of different sample preparation methods including DNA extraction. This study examines the influence of DNA extraction on performance of a new PCR-based genotyping kit, the Roche LINEAR ARRAY HPV assay. When volume of sample extracted, DNA extraction methods and/or amount of DNA tested were varied, the HPV type results were reproducible for strong viral bands but not weak ones. Moreover, although the experiments were not comprehensive, they showed that the manufacturer-approved DNA extraction method might not be the best method for use in this assay. Because different "front end" protocols introduce variability into genotyping results, the authors urge laboratories not to vary methods for this assay without due consideration. The results suggest that companies carefully optimize DNA extraction methods prior to commercial introduction of their PCR-based genotyping assays destined for widespread clinical use.
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Affiliation(s)
- S Terence Dunn
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73190, USA.
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29
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Stevens MP, Garland SM, Rudland E, Tan J, Quinn MA, Tabrizi SN. Comparison of the Digene Hybrid Capture 2 assay and Roche AMPLICOR and LINEAR ARRAY human papillomavirus (HPV) tests in detecting high-risk HPV genotypes in specimens from women with previous abnormal Pap smear results. J Clin Microbiol 2007; 45:2130-7. [PMID: 17494721 PMCID: PMC1933009 DOI: 10.1128/jcm.02438-06] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The development of cervical cancer is strongly associated with the presence of persistent high-risk (HR) human papillomavirus (HPV) infection. Recently, the commercially manufactured PCR-based Roche AMPLICOR (AMP) and LINEAR ARRAY (LA) HPV tests have become available for HPV detection. However, knowledge of their clinical performance compared to the U.S. Food and Drug Administration-approved Hybrid Capture 2 (HC2) assay is limited. This study evaluated the concordance between the HC2, AMP, and LA tests in detecting HR-HPV among a cohort of 1,679 women with previous abnormal Pap smear results. Overall, 1,393 specimens (81.3%) generated concordant results for HR-HPV presence or absence by the three assays. The concordance levels were substantial between the HC2 and AMP tests (84.4%, kappa = 0.6419) and between the HC2 and LA tests (84.0%, kappa = 0.6341) and nearly perfect between the AMP and LA tests (97.8%, kappa = 0.9441). HR-HPV prevalence, as detected by the AMP or LA tests, was significantly higher among women with cytological or histological high-grade disease (CIN2 or greater) than that detected by HC2 (P < 0.0001). The AMP and LA tests exhibited greater sensitivity, but lower specificity, than HC2 for detecting HR-HPV among this cohort of women with underlying cervical abnormalities, particularly among subjects with histologically proven high-grade disease. Both PCR-based HPV tests may be valuable in the management of care for women with underlying cervical abnormalities, in predicting treatment success, and in studying the clearance or acquisition of new infections.
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Affiliation(s)
- Matthew P Stevens
- Department of Microbiology, The Royal Women's Hospital, 132 Grattan Street, Carlton, Victoria 3053, Australia.
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30
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Lee EH, Chung HJ, Oh HB, Chi HS, Jee MS, Park SN, Hong SP, Yoo W, Kim SO. Human Papilloma Virus Genotyping Assay using Restriction Fragment Mass Polymorphism Analysis, and Its Comparison with Sequencing and Hybrid Capture Assays. Ann Lab Med 2007; 27:62-8. [DOI: 10.3343/kjlm.2007.27.1.62] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Eun Hee Lee
- Green Cross Reference Laboratory, Yongin, Seoul, Korea
| | | | - Heung Bum Oh
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, Korea
| | - Hyun Sook Chi
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, Korea
| | - Mi Sun Jee
- Green Cross Reference Laboratory, Yongin, Seoul, Korea
| | - Sun Nie Park
- Korea Food and Drug Administration, National Institute of Toxicology Research, Seoul, Korea
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31
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Stevens MP, Rudland E, Garland SM, Tabrizi SN. Assessment of MagNA pure LC extraction system for detection of human papillomavirus (HPV) DNA in PreservCyt samples by the Roche AMPLICOR and LINEAR ARRAY HPV tests. J Clin Microbiol 2006; 44:2428-33. [PMID: 16825360 PMCID: PMC1489532 DOI: 10.1128/jcm.02608-05] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Roche Molecular Systems recently released two PCR-based assays, AMPLICOR and LINEAR ARRAY (LA), for the detection and genotyping, respectively, of human papillomaviruses (HPVs). The manual specimen processing method recommended for use with both assays, AmpliLute, can be time-consuming and labor-intensive and is open to potential specimen cross-contamination. We evaluated the Roche MagNA Pure LC (MP) as an alternative for specimen processing prior to use with either assay. DNA was extracted from cervical brushings, collected in PreservCyt media, by AmpliLute and MP using DNA-I and Total Nucleic Acid (TNA) kits, from 150 patients with histologically confirmed cervical abnormalities. DNA was amplified and detected by AMPLICOR and the LA HPV test. Concordances of 96.5% (139 of 144) (kappa=0.93) and 95.1% (135 of 142) (kappa=0.90) were generated by AMPLICOR when we compared DNA extracts from AmpliLute to MP DNA-I and TNA, respectively. The HPV genotype profiles were identical in 78.7 and 74.7% of samples between AmpliLute and DNA-I or TNA, respectively. To improve LA concordance, all 150 specimens were extracted by MP DNA-I protocol after the centrifugation of 1-ml PreservCyt samples. This modified approach improved HPV genotype concordance levels between AmpliLute and MP DNA-I to 88.0% (P=0.043) without affecting AMPLICOR sensitivity. Laboratories that have an automated MP extraction system would find this procedure more feasible and easier to handle than the recommended manual extraction method and could substitute such extractions for AMPLICOR and LA HPV tests once internally validated.
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Affiliation(s)
- Matthew P Stevens
- Department of Microbiology, The Royal Women's Hospital, and Department of Obstetrics and Gynaecology, University of Melbourne, Victoria, Australia.
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32
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Gheit T, Landi S, Gemignani F, Snijders PJF, Vaccarella S, Franceschi S, Canzian F, Tommasino M. Development of a sensitive and specific assay combining multiplex PCR and DNA microarray primer extension to detect high-risk mucosal human papillomavirus types. J Clin Microbiol 2006; 44:2025-31. [PMID: 16757593 PMCID: PMC1489390 DOI: 10.1128/jcm.02305-05] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The importance of assays for the detection and typing of human papillomaviruses (HPVs) in clinical and epidemiological studies has been well demonstrated. Several accurate methods for HPV detection and typing have been developed. However, comparative studies showed that several assays have different sensitivities for the detection of specific HPV types, particularly in the case of multiple infections. Here, we describe a novel one-shot method for the detection and typing of 19 mucosal high-risk (HR) HPV types (types 16, 18, 26, 31, 33, 35, 39, 45, 51, 52, 53, 56, 58, 59, 66, 68, 70, 73, and 82). This assay combines two different techniques: multiplex PCR with HPV type-specific primers for amplification of viral DNA and array primer extension (APEX) for typing. This novel method has been validated with artificial mixtures of HPV DNAs and clinical samples that were already analyzed for the presence of mucosal HPV types by a different consensus PCR method, i.e., GP5+/GP6+. Our data showed a very good agreement between the results from the multiplex PCR/APEX assay and those from the GP5+/GP6+ PCR (overall rates of HPV positivity, 63.0 and 60.9%, respectively). Whereas the GP5+/GP6+ PCR was slightly more sensitive for the detection of HPV type 16 (HPV-16), multiplex PCR-APEX found a higher number of infections with HPV-33, HPV-53, and multiple HPV types. These favorable features and the high-throughput potential make our present novel assay ideal for large-scale clinical and epidemiological studies aimed at determining the spectrum of mucosal HR HPV types in cervical specimens.
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Affiliation(s)
- Tarik Gheit
- Infections and Cancer Biology Group, International Agency for Research on Cancer, 150, cours Albert-Thomas, 69372 Lyon, France
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33
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Albrecht V, Chevallier A, Magnone V, Barbry P, Vandenbos F, Bongain A, Lefebvre JC, Giordanengo V. Easy and fast detection and genotyping of high-risk human papillomavirus by dedicated DNA microarrays. J Virol Methods 2006; 137:236-44. [PMID: 16879879 DOI: 10.1016/j.jviromet.2006.06.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2006] [Revised: 06/13/2006] [Accepted: 06/15/2006] [Indexed: 11/25/2022]
Abstract
Persistent cervical high-risk human papillomavirus (HPV) infection is correlated with an increased risk of developing a high-grade cervical intraepithelial lesion. A two-step method was developed for detection and genotyping of high-risk HPV. DNA was firstly amplified by asymmetrical PCR in the presence of Cy3-labelled primers and dUTP. Labelled DNA was then genotyped using DNA microarray hybridization. The current study evaluated the technical efficacy of laboratory-designed HPV DNA microarrays for high-risk HPV genotyping on 57 malignant and non-malignant cervical smears. The approach was evaluated for a broad range of cytological samples: high-grade squamous intraepithelial lesions (HSIL), low-grade squamous intraepithelial lesions (LSIL) and atypical squamous cells of high-grade (ASC-H). High-risk HPV was also detected in six atypical squamous cells of undetermined significance (ASC-US) samples; among them only one cervical specimen was found uninfected, associated with no histological lesion. The HPV oligonucleotide DNA microarray genotyping detected 36 infections with a single high-risk HPV type and 5 multiple infections with several high-risk types. Taken together, these results demonstrate the sensitivity and specificity of the HPV DNA microarray approach. This approach could improve clinical management of patients with cervical cytological abnormalities.
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Affiliation(s)
- Valérie Albrecht
- Laboratoire de Virologie, Hôpital de l'Archet, BP 3079, 151 route de Saint-Antoine de Ginestière, 06200 Nice Cedex 3, France
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Coutlée F, Rouleau D, Petignat P, Ghattas G, Kornegay JR, Schlag P, Boyle S, Hankins C, Vézina S, Coté P, Macleod J, Voyer H, Forest P, Walmsley S, Franco E. Enhanced detection and typing of human papillomavirus (HPV) DNA in anogenital samples with PGMY primers and the Linear array HPV genotyping test. J Clin Microbiol 2006; 44:1998-2006. [PMID: 16757590 PMCID: PMC1489445 DOI: 10.1128/jcm.00104-06] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2006] [Revised: 03/07/2006] [Accepted: 03/17/2006] [Indexed: 11/20/2022] Open
Abstract
The Roche PGMY primer-based research prototype line blot assay (PGMY-LB) is a convenient tool in epidemiological studies for the detection and typing of human papillomavirus (HPV) DNA. This assay has been optimized and is being commercialized as the Linear Array HPV genotyping test (LA-HPV). We assessed the agreement between LA-HPV and PGMY-LB for detection and typing of 37 HPV genotypes in 528 anogenital samples (236 anal, 146 physician-collected cervical, and 146 self-collected cervicovaginal swabs) obtained from human immunodeficiency virus-seropositive individuals (236 men and 146 women). HPV DNA was detected in 433 (82.0%) and 458 (86.7%) samples with PGMY-LB and LA-HPV (P = 0.047), respectively, for an excellent agreement of 93.8% (kappa = 0.76). Of the 17,094 HPV typing results, 16,562 (1,743 positive and 14,819 negative results) were concordant between tests (agreement = 96.9%; kappa = 0.76). The mean agreement between tests for each type was 96.4% +/- 2.4% (95% confidence interval [CI], 95.6% to 97.2%; range, 86% to 100%), for an excellent mean kappa value of 0.85 +/- 0.10 (95% CI, 0.82 to 0.87). However, detection rates for most HPV types were greater with LA-HPV. The mean number of types per sample detected by LA-HPV (4.2 +/- 3.4; 95% CI, 3.9 to 4.5; median, 3.0) was greater than that for PGMY-LB (3.4 +/- 3.0; 95% CI, 3.1 to 3.6; median, 2.0) (P < 0.001). The number of types detected in excess by LA-HPV in anal samples correlated with the number of types per sample (r = 0.49 +/- 0.06; P = 0.001) but not with patient age (r = 0.03 +/- 0.06; P = 0.57), CD4 cell counts (r = 0.06 +/- 0.06; P = 0.13), or the grade of anal disease (r = -0.11 +/- 0.06; P = 0.07). LA-HPV compared favorably with PGMY-LB but yielded higher detection rates for newer and well-known HPV types.
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Affiliation(s)
- François Coutlée
- Laboratoire de Virologie Moléculaire du centre de Recherche, Département de Microbiologie et Infectiologie, Hôpital Notre-Dame du Centre Hospitalier de l'Université de Montréal, Montréal, Québec, Canada.
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Gillio-Tos A, De Marco L, Ghisetti V, Snijders PJF, Segnan N, Ronco G, Merletti F. Human papillomavirus typing with GP5+/6+ polymerase chain reaction reverse line blotting and with commercial type-specific PCR kits. J Clin Virol 2006; 36:126-32. [PMID: 16624614 DOI: 10.1016/j.jcv.2006.03.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2005] [Revised: 02/22/2006] [Accepted: 03/12/2006] [Indexed: 10/24/2022]
Abstract
BACKGROUND Infection with human papillomavirus (HPV) is a necessary step in the progression to cervical cancer. Many methods for HPV testing are currently available, most developed to detect pools of HPV types. OBJECTIVES To evaluate the HPV typing by molecular methods and to compare commercial kits with an established laboratory method. STUDY DESIGN Eighty-four cervical samples found to be positive for HPV DNA by GP5+/6+-polymerase chain reaction-enzyme immunoassay-reverse line blotting (PCR-EIA-RLB) were re-tested with two commercial methods, INNO-LiPA and Amplisense HPV typing, able to identify the HPV type predicted by PCR-EIA-RLB in 76 and 67 samples, respectively. RESULTS The INNO-LiPA assay revealed HPV DNA in 75/76 samples (98.7%; 95% CI, 0.93-0.99) that would contain HPV types identifiable by this assay. The Amplisense HPV assay revealed HPV DNA in 58/67 samples (86.6%; 95% CI, 0.76-0.93) containing HPV types detectable by this assay. For samples with a single infection, the unweighted kappa for concordance of HPV typing was 0.87 (95% CI, 0.78-0.97) for PCR-EIA-RLB versus INNO-LiPA, 0.94 (95% CI, 0.87-0.99) for INNO-LiPA versus Amplisense HPV, and 0.82 (95% CI, 0.70-0.94) for PCR-EIA-RLB versus Amplisense HPV typing. PCR-EIA-RLB revealed 12 multiple infections, INNO-LiPA revealed 14, and Amplisense HPV revealed 5. The agreement among tests for samples with multiple infections was lower, giving kappa values of 0.44 (95% CI, 0.18-0.70) for PCR-EIA-RLB versus INNO-LiPA, 0.52 (95% CI, 0.19-0.85) for PCR-EIA-RLB versus Amplisense HPV and 0.43 (95% CI, 0.12-0.74) for INNO-LiPA versus Amplisense HPV. CONCLUSIONS In HPV-positive samples, the agreement among tests for HPV typing was high for single infections but markedly lower for infections with multiple HPV types.
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Affiliation(s)
- Anna Gillio-Tos
- Unit of Cancer Epidemiology, C.E.R.M.S., University of Turin, via Santena 7, 10126 Turin, Italy.
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Perrons C, Brink N, Jalal H, Watts P, Jelley R. The impact of high risk human papillomavirus testing in an inner London colposcopy clinic. J Med Virol 2005; 76:576-82. [PMID: 15977240 DOI: 10.1002/jmv.20401] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
This is an audit of a new technique to improve the colposcopy service. Samples were tested for high risk HPV DNA using Digene Hybrid Capture II. Sixty-four percent of the sampled women under 30 had detectable high risk HPV DNA, decreasing to 44% in 30--39 year olds and to 27% in women over 40. High risk HPV prevalence increased with severity of cytology, although 22% with normal colposcopy had detectable high risk HPV. Of those women treated for cervical dysplasia, 83% had detectable high risk HPV prior to treatment, compared to only 32% afterwards. The audit has shown that high risk HPV testing has considerable discriminatory value. It has been integrated successfully into the service, particularly to manage low grade cervical abnormalities and to add valuable information following treatment for cervical dysplasia. Results need to be interpreted alongside colposcopy, cytology, and histology, and care must be taken in the interpretation of a single high risk HPV result.
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Affiliation(s)
- Chris Perrons
- Centre of Virology, Department of Infection, Division of Infection and Immunity, Royal Free and University College Medical School, London, United Kingdom.
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Rabelo-Santos SH, Levi JE, Derchain SFM, Sarian LOZ, Zeferino LC, Messias S, Moraes DLD, Campos EA, Syrjänen KJ. DNA recovery from Hybrid Capture II samples stored in specimen transport medium with denaturing reagent, for the detection of human papillomavirus by PCR. J Virol Methods 2005; 126:197-201. [PMID: 15847937 DOI: 10.1016/j.jviromet.2005.02.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2004] [Revised: 02/17/2005] [Accepted: 02/22/2005] [Indexed: 10/25/2022]
Abstract
The purpose of this study was to examine the quality of DNA recovered for human papillomavirus (HPV) detection using polymerase chain reaction (PCR) in samples that had been collected for Hybrid Capture II (HCII), testing and stored in specimen transport medium (STM) with denaturing reagent at -20 degrees C for 18 months. Endocervical tissue was collected from 92 women for HCII assay using the Digene STM, and a Papanicolaou smear was carried out in all cases. Seven women had normal colposcopy results. The remaining 85 patients underwent colposcopy-directed biopsy or cervical conization for histological investigation. Of the 92 samples tested, 84 were HCII-positive and 8 were negative. Quality control for amplification was carried out with beta-globin primers G73 and G74, and HPV was tested using PGMY09 and PGMY11. DNA was recovered from 83 of the 92 samples (90%). Among the 84 samples HCII-positive initially, HPV was detected by PCR in 56 (67%). PCR did not detect HPV DNA in the eight samples that were HCII-negative, although five of them were positive for beta-globin. This paper describes a novel DNA extraction technique that may permit exact HPV typing in stored samples collected originally for HCII testing, making it possible to carry out retrospective investigations to retrieve information on specific HPV types in large HCII series.
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Affiliation(s)
- Silvia H Rabelo-Santos
- Department of Obstetrics and Gynecology, Universidade Estadual de Campinas (UNICAMP), Caminas, SP, Brazil
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Cason J, Mant CA. High-risk mucosal human papillomavirus infections during infancy & childhood. J Clin Virol 2005; 32 Suppl 1:S52-8. [PMID: 15753012 DOI: 10.1016/j.jcv.2004.12.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2004] [Accepted: 12/07/2004] [Indexed: 12/20/2022]
Abstract
Human papillomaviruses (HPVs) are small DNA tumour viruses associated with a variety of proliferative diseases. More than 100 types have been identified and can broadly be grouped into cutaneous and mucosal types according to their site of infection, and can be further subdivided into low-risk (LR) and high-risk (HR) types depending upon their association with malignancy. The main route of transmission of HR mucosal HPVs is through sexual contact, although the acquisition of virus cannot be entirely explained by this mode alone. Evidence also exists for horizontal transmission by other routes and vertical transmission. HR HPVs, particularly HPV-16, have been detected in oral swabs from newborns, infants and children. Such alternative modes of transmission and acquisition may have an important impact in several areas, including vaccination strategies, epidemiological studies, and the clinical management of children with HPV-associated diseases. This article reviews the literature describing the detection of HPV infections during infancy and childhood and provides evidence for a role of vertical transmission in the spread of HPV infection.
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Affiliation(s)
- John Cason
- Programme in Infection and Immunity, Department of Infectious Diseases, 2nd Floor New Guy's House, Guy's Campus, Guy's, King's and St. Thomas' Schools of Medicine, King's College, London SE1 9RT, UK
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Gibbs MJ, Armstrong JS, Gibbs AJ. Individual sequences in large sets of gene sequences may be distinguished efficiently by combinations of shared sub-sequences. BMC Bioinformatics 2005; 6:90. [PMID: 15817134 PMCID: PMC1090557 DOI: 10.1186/1471-2105-6-90] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2004] [Accepted: 04/08/2005] [Indexed: 11/20/2022] Open
Abstract
Background Most current DNA diagnostic tests for identifying organisms use specific oligonucleotide probes that are complementary in sequence to, and hence only hybridise with the DNA of one target species. By contrast, in traditional taxonomy, specimens are usually identified by 'dichotomous keys' that use combinations of characters shared by different members of the target set. Using one specific character for each target is the least efficient strategy for identification. Using combinations of shared bisectionally-distributed characters is much more efficient, and this strategy is most efficient when they separate the targets in a progressively binary way. Results We have developed a practical method for finding minimal sets of sub-sequences that identify individual sequences, and could be targeted by combinations of probes, so that the efficient strategy of traditional taxonomic identification could be used in DNA diagnosis. The sizes of minimal sub-sequence sets depended mostly on sequence diversity and sub-sequence length and interactions between these parameters. We found that 201 distinct cytochrome oxidase subunit-1 (CO1) genes from moths (Lepidoptera) were distinguished using only 15 sub-sequences 20 nucleotides long, whereas only 8–10 sub-sequences 6–10 nucleotides long were required to distinguish the CO1 genes of 92 species from the 9 largest orders of insects. Conclusion The presence/absence of sub-sequences in a set of gene sequences can be used like the questions in a traditional dichotomous taxonomic key; hybridisation probes complementary to such sub-sequences should provide a very efficient means for identifying individual species, subtypes or genotypes. Sequence diversity and sub-sequence length are the major factors that determine the numbers of distinguishing sub-sequences in any set of sequences.
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Affiliation(s)
- Mark J Gibbs
- School of Botany and Zoology, Faculty of Science, Australian National University, ACT 0200, Australia
| | - John S Armstrong
- School of Botany and Zoology, Faculty of Science, Australian National University, ACT 0200, Australia
| | - Adrian J Gibbs
- School of Botany and Zoology, Faculty of Science, Australian National University, ACT 0200, Australia
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Nicol AF, Fernandes ATG, Bonecini-Almeida MDG. Immune response in cervical dysplasia induced by human papillomavirus: the influence of human immunodeficiency virus-1 co-infection - review. Mem Inst Oswaldo Cruz 2005; 100:1-12. [PMID: 15867955 DOI: 10.1590/s0074-02762005000100001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Human immunodeficiency virus (HIV-1) has become an important risk factor for human papillomavirus (HPV) infection and the development of HPV associated lesions in the female genital tract. HIV-1 may also increase the oncogenicity of high risk HPV types and the activation of low risk types. The Center for Disease Control and Prevention declared invasive cervical cancer an acquired immunodeficiency virus (AIDS) defining illness in HIV positive women. Furthermore, cervical cancer happens to be the second most common female cancer worldwide. The host's local immune response plays a critical factor in controlling these conditions, as well as in changes in the number of professional antigen-presenting cells, cytokine, and MHC molecules expression. Also, the production of cytokines may determine which arm of the immune response will be stimulated and may influence the magnitude of immune protection. Although there are many studies describing the inflammatory response in HPV infection, few data are available to demonstrate the influence of the HIV infection and several questions regarding the cervical immune response are still unknown. In this review we present a brief account of the current understanding of HIV/HPV co-infection, emphasizing cervical immune response.
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Affiliation(s)
- Alcina Frederica Nicol
- Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Pesquisa Clínica Evandro Chagas-Fiocruz, Av. Brasil 4365, 21040-900 Rio de Janeiro, RJ, Brazil
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Morris BJ. Cervical human papillomavirus screening by PCR: advantages of targeting the E6/E7 region. Clin Chem Lab Med 2005; 43:1171-7. [PMID: 16232081 DOI: 10.1515/cclm.2005.203] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractPCR is a promising method for detection of human papillomavirus (HPV), the high-risk forms of which are responsible for cervical cancer. PCR primers that target the L1 or E1 region can be unreliable and may miss more advanced disease, whereas those directed at the E6 or E7 regions, which encode oncogenic products, are preferable because 1) the LI/E1 regions, but never the E6/E7 regions, are lost during integration of viral DNA into host genomic DNA, a process that can represent an integral component of progression from infection to tumorigenesis; and 2) the E6/E7 nucleotide sequence exhibits less nucleotide variation. The choice of region used for PCR has implications for HPV screening strategies in the clinical diagnosis and management of cervical cancer.
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Affiliation(s)
- Brian J Morris
- Basic & Clinical Genomics Laboratory, School of Medical Sciences and Institute for Biomedical Research, The University of Sydney, Sydney, Australia.
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Beby-Defaux A, Bourgoin A, Ragot S, Battandier D, Lemasson JM, Renaud O, Bouguermouh S, Vienne Md MDL, Agius G. Human papillomavirus infection of the cervix uteri in women attending a Health Examination Center of the French social security. J Med Virol 2004; 73:262-8. [PMID: 15122802 DOI: 10.1002/jmv.20085] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Since human papillomavirus (HPV) is the central causal factor in cervical cancer, understanding the epidemiology of this infection constitutes an important step towards development of strategies for prevention. Six hundred and fifty seven cervical samples were tested for HPV using PCR with consensus primers (MY09/MY11), by genotyping (restriction and sequencing analyses) and by cervical cytology, from women who attended a Health Examination Center of the French social security. Women with no cervical smear as well as women with cytological abnormalities within the last 3 years were recruited. HPV DNA was detected in 7.3% of the women (5.3% for high-risk, 2.4% for low-risk, and 0.5% for unknown risk types) including 6 (0.9%) mixed infections. Fifteen different genotypes were detected, of which genotypes 16 (22.2%), 58 (13.0%), 18 (11.1%), 30 (9.2%), and 33 (9.2%) were the most prevalent. In age group 17-25 years, we found the highest frequencies for both any (22.1%) and high-risk (14.7%) HPV, and prevalences gradually decreased with age. 5.2% of low-grade squamous intraepithelial lesion, 0.3% of high-grade squamous intraepithelial lesion, and 1.2% of atypical squamous cells of undetermined significance were found. The frequencies of high risk and all HPV types were significantly higher in squamous intraepithelial lesions than in those with normal and reactive/reparative changes (P < 0.0001). The prevalence of high-risk HPV in the atypical squamous cells of undetermined significance/low-grade squamous intraepithelial lesion group (28.6%) was significantly higher than in the normal and reactive/reparative changes groups (3.4%) (P < 0.0001). HPV detection was associated with younger age, single marital and non-pregnant status (P < 0.0001), premenopausal status (P = 0.0004), and contraception (P = 0.0008). Marital status (OR 4.5; 95% CI = 2.3-9.0) and tobacco consumption (OR 3.0; 95% CI = 1.6-5.7) were predictive independent factors of HPV infection. The French system of Health Examination Centers might be of interest for following women regularly, especially those with a low socioeconomic status.
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Affiliation(s)
- A Beby-Defaux
- Laboratoire de Virologie, Centre Hospitalier Universitaire La Milétrie, Poitiers, France
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Bekkers RLM, Massuger LFAG, Bulten J, Melchers WJG. Epidemiological and clinical aspects of human papillomavirus detection in the prevention of cervical cancer. Rev Med Virol 2004; 14:95-105. [PMID: 15027002 DOI: 10.1002/rmv.416] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Cervical cancer is a major cause of death, and the second most frequent cancer in women worldwide. Many studies have indicated a causal relation between genital human papillomavirus (HPV) infections and cervical cancer. High-risk HPV genotypes have been detected in almost 100% of all cervical cancers, and the process of HPV mediated carcinogenesis has been partly clarified. The concept that HPV is a obligatory cause in cervical cancer development has lead to extensive research regarding the incorporation of HPV detection in (1) cervical cancer prevention programs, (2) triage of women with abnormal cervical scrapes in the screening program, and (3) follow-up of patients treated for cervical intraepithelial neoplasia (CIN). Epidemiological studies indicate that 50% of women becoming sexually active contract a genital HPV infection within 2 years. The lifetime risk of a genital HPV infection is estimated to be 80%, but very few of these women will develop cervical cancer. Several studies have shown that the persistence of genital HPV infections is especially related to the development of cervical cancer. As a result, HPV detection at a single moment was shown to be of limited clinical value in the triage of patients with abnormal cervical scrapes, or during follow-up after treatment for CIN. Furthermore, major variations in the sensitivity of different HPV detection methods, as well as differences in HPV detection related to the menstrual cycle, have shown that many facts regarding HPV transmission, replication, and detection need to be clarified, before HPV detection can be of clinical value.
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Affiliation(s)
- Ruud L M Bekkers
- Department of Obstetrics and Gynecology, University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands.
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Abstract
Testing for human papillomavirus (HPV) relies exclusively on techniques of molecular biology using nucleic acid probes. Tests for HPV using nucleic acid probes have been commercially available since the late 1980s, but early tests were cumbersome, involving the use of nucleic acid probes labeled with radioactive phosphorus (32P). These early HPV tests did not achieve widespread use because they did not detect all oncogenic HPV genotypes. The current commercial HPV detection kit, Digene's Hybrid Capture 2 kit, detects virtually all high-risk oncogenic HPV types, as well as most low-risk nononcogenic HPV genotypes. The Hybrid Capture 2 test format is a proprietary nucleic acid hybridization signal amplification system owned by Digene Corporation. Virtually all test formats for DNA sequence analysis are amenable to applications intended to detect and perhaps quantify the various HPV genotypes. These methods can involve direct hybridization with complementary DNA probes, such as Southern blotting or in situ hybridization, signal amplification, such as the Hybrid Capture 2 method or target nucleic acid amplification, most notably the polymerase chain reaction (PCR). Polymerase chain reaction has been used for HPV detection, genotyping, and viral load determination. General or consensus primer-mediated PCR assays have enabled screening for a broad spectrum of HPV types in clinical specimens using a single PCR reaction. Following amplification using consensus primers, individual HPV genotypes are identified using a variety of methods. Using consensus primers in a test format known as real-time quantitative PCR (RQ-PCR), it is possible to generate viral load (concentration) data from reaction curves generated by monitoring PCR reaction kinetics in real time.
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Affiliation(s)
- Roger A Hubbard
- Molecular Pathology Laboratory Network, Maryville, Tenn 37804, USA.
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Bekkers RLM, Melchers WJG, Bakkers JMJE, Hanselaar AGJM, Quint WGV, Boonstra H, Massuger LFAG. The role of genotype-specific human papillomavirus detection in diagnosing residual cervical intraepithelial neoplasia. Int J Cancer 2002; 102:148-51. [PMID: 12385010 DOI: 10.1002/ijc.10691] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We assessed prospectively whether residual cervical intraepithelial neoplasia (CIN) after treatment for high-grade CIN can be predicted by genotype-specific high-risk HPV (HR-HPV) detection in follow-up cervical scrapes. A broad spectrum, highly sensitive SPF(10)-LiPA-PCR HPV detection technique was used on cervical scrapes before large loop excision of the transformation zone (LLETZ), on the LLETZ biopsy and on follow-up scrapes of 90 patients treated for high-grade CIN. HR-HPV was detected in the biopsies of 93% (n = 84) of the patients and in the follow-up scrapes of 48% (n = 43) of the patients. In 12 patients, genotype-specific HR-HPV persistence was detected in both follow-up scrapes. In 10 patients, residual CIN was detected. In 5 of these patients (including all patients with residual CIN 3), the follow-up scrapes showed genotype-specific HR-HPV persistence. In 2 patients, a different HR-HPV was detected, and 3 patients had HR-HPV-negative follow-up scrapes. Conventional cytologic follow-up was abnormal in 13 patients including all 10 patients with residual CIN. The negative predictive value (NPV) of HR-HPV detection on follow-up scrapes was high (94%). Repeat detection of genotype-specific HR-HPV showed a lower sensitivity and NPV than repeat detection of any HR-HPV, but its specificity was higher. Repeat conventional cytologic follow-up showed the highest sensitivity and NPV. In conclusion, the presence of HR-HPV in cervical scrapes after LLETZ for high-grade CIN is a risk factor for the presence of residual CIN. HR-HPV genotype-specific persistence is specifically present in patients with residual CIN 3. However, HR-HPV detection cannot predict or exclude the presence of residual CIN in the individual patient and additional procedures remain necessary.
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Affiliation(s)
- Ruud L M Bekkers
- Department of Gynecology/Obstetrics, University Medical Center St. Radboud, PO Box 9101, 6500 HB Nijmegen, the Netherlands.
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