L1 Gene Methylation Research Articles

Detection of human papillomavirus type 16 L1 gene methylation in leftover DNA samples obtained from Cobas 4800 HPV test

Detection of human papillomavirus type 16 L1 gene methylation in leftover DNA samples obtained from Cobas 4800 HPV test

Human papillomavirus 16 L1 gene methylation as a potential biomarker for predicting anal intraepithelial neoplasia in men who have sex with men (MSM).

The human papillomavirus (HPV) 16 early promoter and L1 gene methylation were quantitatively measured using pyrosequencing assay in anal cells collected from men who have sex with men (MSM) to determine potential biomarkers for HPV-related anal cancer. The methylation patterns of HPV16 genes, including the early promoter (CpG 31, 37, 43, 52, and 58) and L1 genes (CpG 5600, 5606, 5609, 5615, 7136, and 7145), were analyzed in 178 anal samples. The samples were diagnosed as normal, anal intraepithelial neoplasia (AIN) 1, AIN2, and AIN3. Low methylation levels of the early promoter (< 10%) and L1 genes (< 20%) were found in all detected normal anal cells. In comparison, medium to high methylation (≥ 20–60%) in the early promoter was found in 1.5% (1/67) and 5% (2/40) of AIN1 and AIN2-3 samples, respectively. Interestingly, slightly increased L1 gene methylation levels (≥ 20–60%), especially at the HPV16 5’L1 regions CpGs 5600 and 5609, were demonstrated in AIN2-3 specimen. Moreover, a negative correlation between high HPV16 L1 gene methylation at CpGs 5600, 5609, 5615, and 7145 and a percentual CD4 count was found in AIN3 HIV positive cases. When comparing the methylation status of AIN2-3 to that of normal/AIN1 lesions, the results indicated the potential of using HPV16 L1 gene methylation as a biomarker for HPV-related cancer screening.

P–578 Human pappiloma virus 16,18 genome methylation patterns in subfertile women

Abstract Study question A comparison between L1 gene and LCR region methylation status of HPV16 and HPV18 viruses in subfertile women, investigating HPV methylation pattern in cervical cancer and asymptomatic HPV infection. Summary answer CpG methylation was more frequent in L1 gene compared to LCR in both HPV types. Methylation levels were associated with the grade of cervical dysplasia. What is known already HPV infection is a common sexually transmitted disease, related to genital warts and cancer. DNA methylation as a dynamic and strictly controlled process can be involved in numerous cellular processes, cell differentiation, gene expression regulation and genome reprogramming. Human pappiloma virus genome epigenetic alterations may play a key role in HPV life cycle as well as in the oncogenic process in general. However, whether the prevalence of high risk HPV is correlated with female infertility, has yet to be elucidated. Study design, size, duration From January 2015 to December 2019, about 2505 infertile couples were referred to the Human Reproduction Unit of Ioannina University Hospital. A total of 212 clinical and laboratory data from female partners were included in the study. Participants/materials, setting, methods Cervical smears were studied for HPV DNA methylation. CpG methylation was compared among L1 gene and LCR region in both HPV types. A bisulfite modification assay followed by DNA amplification and sequencing was performed to analyse HPV16 and HPV18 genome. Main results and the role of chance In HPV16 types, L1 gene and promoter region indicated high methylation levels in cervical cancer cases. LCR regions methylation levels ranged from 0,5% to 24,2% in asymptomatic HPV16 infection or cervical intraepithelial neoplasia and cervical cancer, respectively. As for L1 gene, the differences between asymptomatic HPV16 infection and cervical cancer cases were statistically significant (P = 0.003). In HPV18 types, L1 gene was methylated in cervical intraepithelial neoplasia and cervical cancer cases. Promoter region methylation levels were high in cervical cancer cases while LCR region methylation levels were low. Limitations, reasons for caution Main limitation is the relatively small size of the collected samples. Wider implications of the findings: HPV genome investigation, as for methylation status, may lead to better understanding and earlier diagnostics of cervical pathology in infertile population. These observations point out the importance of fertility preservation in women at high risk for cervical neoplasia. Trial registration number Not applicable

Methylation of the L1 gene and integration of human papillomavirus 16 and 18 in cervical carcinoma and premalignant lesions

High-risk human papillomavirus (HPV) is the primary cause of cervical carcinoma (CC). Viral integration into the host chromosomes is associated with neoplastic progression, and epigenetic changes may occur as a result. The objective of the present study was to analyze HPV L1 gene methylation and to compare the use of quantitative polymerase chain reaction (qPCR), in situ hybridization (ISH) and L1 methylation analysis as methods for detecting HPV integration. Cervical scrapes or biopsy samples positive for HPV 16 or 18, from 187 female patients with CC, squamous intraepithelial lesions (SILs) or no intraepithelial lesion (non-IL) were analyzed. Methylation of the L1 gene was determined using bisulfite modification followed by PCR, and HPV integration was subsequently analyzed. HPV 16 L1 gene methylation was revealed to increase with histological grade, with statistically significant differences observed as follows: Low-grade SIL vs. CC, P<0.0001 and non-IL vs. CC, P<0.0001. HPV 18 L1 gene methylation also increased according to histological grade, however, no statistically significant differences were observed. Methylation at CpG site 5608 of the HPV 16 L1 gene was associated with all grades of cervical lesions, whereas methylation at CpG site 5617 demonstrated the strongest association with CC (odds ratio, 42.5; 95% confidence interval, 4.7–1861; P<0.0001). The concordance rates between the various methods for the detection of the physical status of HPV 16 and HPV 18 were 96.1% for qPCR and ISH, 76.7% for qPCR and L1 gene methylation, and 84.8% for ISH and L1 gene methylation. In conclusion, methylation of the HPV 16 L1 gene increases significantly according to the grade of the cervical lesion, and methylation at CpG sites 5608 and 5617 of this gene may be used as prognostic biomarkers. ISH and L1 gene methylation have good concordance with qPCR with regards to the detection of HPV integration. Therefore, these are useful methods in determining the physical state of HPV.

Human Papilloma Virus L1 Gene Methylation as a Potential Biomarker for Precancerous Cervical Lesion: a Preliminary Report

Objective: To determine whether HPV L1 gene methylation can be used in triage of precancerous cervical lesions. The main objective is to determine the genotype of HPV in cervical precancerous lesions and to determine the percentage, the sensitivity, specificity, positive predictive value, negative predictive value, and likelihood ratio of DNA HPV L1 methylation in precancerous cervical lesions.&#x0D; Methods: A number of 57 samples of paraffin blocks (FFPE) from precancerous lesions and cervical cancer biopsies in the Department of Pathology Faculty of Medicine-Cipto Mangunkusumo General Hospital that had been re-evaluated by the pathologist, underwent extraction of HPV DNA. The genotypes of HPV DNA were examined using primers GP5 / 6 and specific HPV 16, HPV 18 and HPV 52 probes and analyzed by real time PCR. Sequencing was performed on samples with unknown HPV DNA type that were detected using the specific probes to determine the type of HPV. Bisulfite conversion procedure was then performed for the samples that met the inclusion criteria.&#x0D; Results: There were 30 samples (52.6%) with CIN 1, 12 samples (21.1%) CIN 2, 9 samples (15.8%) CIN 3 and 6 samples (10.5%) of cervical cancer. Most of the samples were 36-45 years (35.1%). Of the total 57 samples, 55 samples were successfully extracted and determined the DNA genotyping of HPV (96.5%). HPV 16 infections both in the form of single or multiple was found to be 76.36%. The samples were mostly dominated by co-infection of HPV16 and 18 (49.1%) followed by HPV 16 (24.6%) and HPV 18 (14.0%). Based on the sequencing results there were other types of high risk HPV infection found: HPV 33, HPV 35, HPV 58 and also undeterminate risk HPV 53 and low risk HPV 54. After several procedures of optimization for methylation examination of HPV DNA L1 there was thin band found in electrophoresis procedure in 8 of 42 samples (19%) of HPV 16 after bisulfite conversion but once it was purified there weren’t any band found so we can not proceed to the stage sequencing. Until now we are still in the stage of optimizing the methylation procedure.&#x0D; Conclusion: HPV 16 infection were most commonly found in the form of single or multiple. Co-infection of HPV 16 and 18 were found in the majority of the samples. There were no significant correlation between HPV type and the severity of cervical lesions. Until now, the examination of DNA methylation HPV L1 already obtained eight samples of HPV 16 with a thin band on electrophoresis but the result could not be concluded because it is still in&#x0D; the process of optimization.&#x0D; [Indones J Obstet Gynecol 2017; 5-2: 120-126]&#x0D; Keywords: HPV DNA genotype, L1 gene methylation, precancerous cervical lesions

Association between PD-L1 and HPV status and the prognostic value for HPV treatment in premalignant cervical lesion patients.

The difference of PD-L1 expression between only HPV-positive patients and premalignant cervical lesion patients did not be reported in present studies. And to test the PD-L1 expression in some cervical cell lesion studies using cervical exfoliated cells sample also was ignored. Meanwhile, the PD-L1 expression as a predictive biomarker still existed controversy. So in the study, first to compare the expression of PD-L1 between only HPV-positive patients and premalignant cervical lesion patients, then to research the association between PD-L1 and HPV status, lastly to explore the possible prognostic value for HPV treatment in premalignant cervical lesion patients.Cervical exfoliated cells samples of 54 premalignant cervical lesion patients with HPV16 infection were collected; meanwhile the cervical exfoliated cells samples from 20 healthy women without HPV infection and 20 patients with only HPV16 infection but cervical cytology normal were collected as 2 control groups. Flow-through hybridization and gene chip (FHGC) was used to detect the HPV type, the PD-L1 expression was tested by Flow cytometry analysis, the methylation-sensitive high-resolution melting (MS-HRM) was used to test the HPV16 L1 gene methylation. The 54 premalignant cervical lesion patients were followed up in 18 months to assess the prognostic value of PD-L1 for HPV treatment.The PD-L1 positive cell rate and mean fluorescence intensity of PD-L1 positive cell in premalignant cervical lesion patients with HPV16 infection were higher than 2 control groups. Mean fluorescence intensity of PD-L1 positive cell were increased in 54 cases when existing multiple HPV status and high HPV16-L1 gene methylation (L1 gene methylation more than 50%). High PD-L1 expression (PD-L1 positive cell rate more than 10%), high HPV16-L1 gene methylation, and multiple HPV infection status could prolong the time to clean HPV infection by Kaplan–Meier analysis. Multivariate Cox proportional hazards analysis also showed that all of high PD-L1 expression, high HPV-L1 methylation, and multiple HPV infection status should increase the risk of HPV unclearance in premalignant cervical lesion patients; the hazard ratio (HR) was 2.043 (CI: 1.050–3.973), 2.797 (CI: 1.277–6.122), and 3.050 (CI: 1.406–6.615).PD-L1 expression only was correction with HPV infection when the infection induced the cervical cells to create the lesion. PD-L1 was the risk factor of HPV unclearance in premalignant cervical lesion patients, so anti-PD-L1 therapy could be a potential effectiveness way of HPV infection in premalignant cervical lesion patients.

Targeted, Deep Sequencing Reveals Full Methylation Profiles of Multiple HPV Types and Potential Biomarkers for Cervical Cancer Progression.

Background: Invasive cervical cancer (ICC) and its premalignant phase (cervical intraepithelial neoplasia; CIN1-3) are distinguished by gynecologic and pathologic examination, yet no current methodologies can predict precancerous lesions that are destined to progress to ICC. Thus, development of reliable assays to assess patient prognosis is much needed.Methods: Human papillomavirus (HPV) DNA methylation is significantly altered in cervical disease. Using an HPV enrichment approach and next-generation DNA sequencing, methylation status was characterized in a case-case comparison of CIN (n = 2 CIN1; n = 2 CIN2; n = 20 CIN3) and ICC (n = 37) samples. Pyrosequencing validated methylation changes at CpGs of interest in a larger sample cohort (n = 61 CIN3; 50 ICC).Results: Global viral methylation, across HPV types, was significantly higher in ICC than CIN3. Average L1 gene methylation in 13 different HPV types best distinguished CIN3 from ICC. Methylation levels at individual CpG sites as a quantitative classifier achieved a sensitivity and specificity of >95% for detecting ICC in HPV 16 samples. Pyrosequencing confirmed significantly higher methylation of these CpGs in E1 of HPV 16 in ICC compared with CIN3.Conclusions: Global HPV methylation is significantly higher in ICC than CIN3, with L1 gene methylation levels performing best for distinguishing CIN3 from ICC. Methylation levels at CpGs in the E1 gene of HPV 16 (972, 978, 1870, and 1958) can distinguish between CIN3 and ICC.Impact: Higher methylation at specific E1 CpGs may associate with increased likelihood of progression to ICC in HPV 16-positive CIN3 lesions. Cancer Epidemiol Biomarkers Prev; 26(4); 642-50. ©2017 AACR.

Increased HPV L1 gene methylation and multiple infection status lead to the difference of cervical epithelial cell lesion in different ethnic women of Xinjiang, China.

Human papillomavirus (HPV) L1 gene methylation deeply involved in the progression and heterogeneity of cervical cell epithelial lesions. The DNA ploidy also represented the early lesions of cervical cell, and it was associated with different HPV infection status in different ethnic women. So, the research was to explore whether it was possible that HPV L1 gene methylation and HPV infection status as the risk factors to lead to the differences of cervical epithelial cells’ lesions in different ethnics women.The flow-through hybridization and gene chip for HPV genotypes test, general characteristics, and cervical exfoliated cell samples were collected from 94 Uygur and 79 Han women with HPV-16 infection. The cases were divided into the single HPV-16 (sHPV-16) infection group and multiple HPV-16 (mHPV-16) infection group in each ethnic women. The DNA ploidy was analyzed by flow cytometry, and the methylation-sensitive high resolution melting (MS-HRM) was used to test the HPV-16 L1 gene methylation, the results of methylation was segmented into mild methylation, moderate methylation, and severe methylation groups. Multifactor logistic analysis explored the relation between DNA heteroploid and HPV-16 infection status, HPV-16 L1 gene methylation in different ethnic women.The higher proportion of mHPV-16 infection in Uygur than Han women (61.7% vs 38.0%). L1 gene methylation had statistic difference between single and mHPV-16 infection under the same ethnic women. The proportion of DNA heteroploid had statistic difference between different HPV-16 infection status or different L1 gene methylation grades in Han or Uygur women. Both L1 gene methylation and HPV infection status were the risk factors of DNA heteroploid. Compared to the sHPV-16 infection, the odds ratio (OR) of mHPV-16 infection were 4.409 (CI: 1.398–13.910) and 3.279 (CI: 1.069–10.060) in Han and Uygur women. Compared the mild L1 gene methylation, the OR of moderate L1 gene methylation were 3.313 (CI: 1.002–10.952) and 5.075 (CI: 1.385–18.603) in Han and Uygur women, the OR of severe L1 gene methylation were 20.592 (CI: 3.691–114.880) and 63.634 (CI: 10.400–389.368) in Han and Uygur women.The study first reported that HPV L1 gene methylation and HPV infection status were the risk factors to the DNA heteroploid of cervical cell in different ethnics women, HPV L1 gene methylation and infection status should be recommended to the existing system of cervical lesion screening in order to provide better serves for the HPV infected women, especially for the ethnic women with high proportion of severe L1 gene methylation and multiple infection status.

Quantitative Measurement of L1 Human Papillomavirus Type 16 Methylation for the Prediction of Preinvasive and Invasive Cervical Disease.

Methylation of the human papillomavirus (HPV) DNA has been proposed as a novel biomarker. Here, we correlated the mean methylation level of 12 CpG sites within the L1 gene, to the histological grade of cervical precancer and cancer. We assessed whether HPV L1 gene methylation can predict the presence of high-grade disease at histology in women testing positive for HPV16 genotype. Pyrosequencing was used for DNA methylation quantification and 145 women were recruited. We found that the L1 HPV16 mean methylation (±SD) significantly increased with disease severity (cervical intraepithelial neoplasia [CIN] 3, 17.9% [±7.2] vs CIN2, 11.6% [±6.5], P < .001 or vs CIN1, 9.0% [±3.5], P < .001). Mean methylation was a good predictor of CIN3+ cases; the area under the curve was higher for sites 5611 in the prediction of CIN2+ and higher for position 7145 for CIN3+. The evaluation of different methylation thresholds for the prediction of CIN3+ showed that the optimal balance of sensitivity and specificity (75.7% and 77.5%, respectively) and positive and negative predictive values (74.7% and 78.5%, respectively) was achieved for a methylation of 14.0% with overall accuracy of 76.7%. Elevated methylation level is associated with increased disease severity and has good ability to discriminate HPV16-positive women that have high-grade disease or worse.

High-resolution melting analysis of HPV-16 L1 gene methylation: A promising method for prognosing cervical cancer

ObjectiveMethylation-sensitive high-resolution melting (MS-HRM) is a new technique for DNA methylation analysis, but it is rarely used for the detection of viral DNA methylation. In this study, we investigated the HPV-16L1 gene methylation that is detected by MS-HRM as a potential biomarker for prognosing cervical dysplasia and cancer. Design and methodsA total of 114 HPV-16 infected patients (normal (17), CIN1 (25), CIN2 (29), CIN3 (32), SCC (11)) who underwent liquid-based cytology test and biopsy were included in this study. 17 cases with HPV-16 infection and negative cytologic and histologic results served as the control group. The HPV-16L1 gene methylation statuses of these samples were investigated using a methylation-sensitive high-resolution melting (MS-HRM) assay after bisulfite modification. ResultsThe HPV-16L1 gene methylation statuses of all the 114 specimens were successfully detected by MS-HRM, and we observed increasing methylation levels in severe lesions, as determined using histologic assays. In addition, the methylation levels of CIN2+ (CIN2, CIN3 and SCC) were significantly higher than that of CIN2− (normal and CIN1, P<0.001). When taking CIN2+ as the reference, our HPV-16L1 DNA methylation assay achieved 91.7% sensitivity and 59.5% specificity, respectively. ConclusionsThe results of the present work demonstrated that HPV-16L1 gene methylation was closely associated with cervical precancerosis and cancer. Moreover, using MS-HRM to detect HPV-16L1 gene methylation may be a powerful assay for the triage of HPV-16-positive females, which could identify patients with high risk of invasive cancer.

L1 Gene Methylation in High-Risk Human Papillomaviruses for the Prognosis of Cervical Intraepithelial Neoplasia

The purpose of this study was to investigate the clinical significance of DNA methylation of the human papillomavirus (HPV) genome as a prognostic biomarker for cervical intraepithelial neoplasia (CIN). Clinical samples (paraffin-embedded tissues obtained by conization/hysterectomy or initial punch biopsy) were collected from patients at the Gynecologic Oncology of the Hyogo Cancer Center with informed consent. We evaluated the methylation status of the L1 gene of the HPV genome by bisulfite sequencing, calculating the methylation ratio (L1MR) as (number of methylated CpGs in the analyzed region of the L1 gene) / (number of all CpGs in the analyzed region of the L1 gene) × 100. The methylation analysis and in situ hybridization were performed with serial tissue-section slices. DNA methylation was observed in the L1 gene, but not in the long control region of HPV-16, -18, or the other high-risk HPV types including HPV-31, -52, and -58. L1MR was associated with the CIN grade; the median L1MR was 2.3%, 11.2%, 35.2%, and 50.0% for CIN1, CIN2, CIN3, and squamous cell carcinoma, respectively. L1MRs also seemed to indicate physical status (integrated or episomal form) of the HPV genome in the host cell. L1MR of the progression group was significantly higher than that of the regression group. L1MR was associated with the CIN grade and indicated the HPV genome status in the host cell: high L1MR indicated HPV genome integration linked to progression from early-stage CINs, whereas low L1MR indicated an episomal HPV genome location in host cells. L1MR may be a prognostic indicator of CIN.

PAPILLOPHAR: Impact of the human papillomavirus (HPV) status in the prognosis of oropharynx squamous cell carcinoma (OSCC).

TPS198 Background: According to retrospective series, HPV-positive OSCC would have a better overall and specific prognosis. Nevertheless, there is currently no evidence-based indication to modify treatment according to the HPV status. Methods: Papillophar is a multicentric (15 clinical, 5 biological centers) prospective study. The aim is to study the role of HPV characteristics in OSCC prognosis. With a clinical database (including follow-up), tumor and serum collections are constituted to analyse virological parameters of HPV positive tumors (HPV genotype, variants, load, DNA integration, E6-E7 transcript expression, L1 gene methylation, HPV serology), molecular tumor markers (EGFR, Kras, PTEN, PI3KCA, c-MET mutations), immunohistochemistry analysis (p16, p53, pRb, markers of EMT (vimentin, E-cadherine, beta-catenin) expression). Primary endpoint is Disease Free Survival (DFS) at 2 years according to HPV status. Secondary endpoints are: Overall Survival at 2 years; virological characteristics in HPV-positive tumors; molecular tumor characteristics in HPV positive vs negative tumors. We hypothesized that DFS in HPV-negative cancer is similar to DFS in OSCC (about 40%). To detect at least a 20% difference in DFS at 2 years, 324 patients are needed (25% HPV positive patients, 80% power, alpha equals 5%, two-sided). No interim analysis is planed. Prognosis value of HPV status on endpoints will be assessed using Cox regression hazard model independently from baseline characteristics. Patients are treated according to the usual multidisciplinary approach in each center and followed according to the recommendations of the French Otolaryngology head neck surgery Society. At least 2 years of follow-up after the completion of the treatment will be required. Major eligibility criteria are: invasive OSCC confirmed histologically in adult patients, all TNM stages and first head and neck cancer. SCC of other localization, non-invasive neoplasia and synchronous head and neck carcinomas are excluded. Enrollment has begun in May 2009. At this time (January 2011), 198 OSCC patients have been included and 34 % have reached 12 months of follow-up. Clinical trial registry number: NCT00918710.

Human papillomavirus-16 L1 gene methylation as a biomarker for progression of cervical intraepithelial lesions

Human papillomavirus-16 L1 gene methylation as a biomarker for progression of cervical intraepithelial lesions

Recombination of human papillomavirus‐16 and host DNA in exfoliated cervical cells: A pilot study of L1 gene methylation and chromosomal integration as biomarkers of carcinogenic progression

Human papillomavirus-16 DNA replicates in productive infections in circular form, but is found in most carcinomas integrated into the host cell DNA. Because this transition is essential for carcinogenesis, detailed research is desirable and may help to triage patients with abnormal Pap smears. Previous studies addressed the chromosomal integration of HPV-16 DNA in biopsies of tumors by an indirect biomarker, methylation of the viral L1 gene and by reverse ligation polymerase chain reaction (rliPCR). The pilot study reported here asked whether these techniques can be targeted successfully at DNA prepared from exfoliated cervical cells. Abnormal Pap smears of 21 patients that were positive for HPV-16 were analyzed for (i and ii) methylation of the L1 gene after bisulfite modification and PCR amplification by direct sequencing and indirectly in cloned DNA and (iii) recombination with chromosomal DNA by rliPCR. Four of these 21 patients contained highly methylated L1 DNA, which was integrated in three of the samples with sufficient DNA for rliPCR analysis. Seven patients contained sporadically methylated L1 DNA, which was integrated in two and episomal in three samples with sufficient DNA. Ten patients contained only unmethylated DNA, which was episomal in six but possibly integrated in two samples. It is concluded that HPV-16 is found integrated chromosomally in a fraction of precancerous infections, and with higher frequency in methylated than in low or unmethylated samples. Since L1 gene methylation indicates integration, it has the potential to be used as a clinical marker of cancer progression.

High-throughput detection of human papillomavirus-18 L1 gene methylation, a candidate biomarker for the progression of cervical neoplasia

The L1 gene of human papillomavirus-18 (HPV-18) is consistently hypermethylated in cervical carcinomas, but frequently hypo- or unmethylated in exfoliated cells from asymptomatic patients. In precancerous lesions, L1 is sporadically hypermethylated, correlating with the severity of the neoplasia. In order to explore the potential of using L1 methylation as a workable biomarker for carcinogenic progression of HPV-18 infections in routinely taken samples, our aim was to develop methylation–detection techniques that were sensitive and rapid without being overly complex technically. Therein, we developed a methylation-specific PCR (MSP) through the design of primer sets that specifically amplify either methylated or unmethylated HPV-18 L1 DNA within bisulfite-modified sample DNA. Amplification of unmethylated and in vitro methylated HPV-18 DNA by MSP resulted in 2500 copies of either of the two L1 DNA species being detected, a satisfactory sensitivity considering that bisulfite treatment leads to the fragmentation of about 99% of sample DNA. The primers proved specific and did not generate false positive results at concentrations exceeding the lowest limit of detection by a factor of 400. DNA from carcinomas yielded PCR signals only with the methylation-specific primers, and not with primers specific for unmethylated L1 genes. The inverse result was obtained with DNA from precursor lesions that contained only hypomethylated DNA. High-grade precursor lesions and carcinomas that contained hyper- as well as hypomethylated L1 DNA yielded PCR signals with both primers. By developing a fluorescence based real-time PCR, we quantitatively analyzed samples with in vitro methylated and unmethylated L1 DNA, and could distinguish clinical samples with hyper- and hypomethylated DNA or mixtures of both DNAs. The methylation-specific and real-time PCR techniques permitted efficient HPV-18 L1 methylation analyses and open the door for larger-scale clinical studies where the utility of methylation status to predict the progression of HPV-18 infection and HPV-18 associated lesions is assessed.