ArticleThe Journal of molecular diagnostics : JMD2006
Precision and performance characteristics of bisulfite conversion and real-time PCR (MethyLight) for quantitative DNA methylation analysis.
Article in The Journal of molecular diagnostics : JMD, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 244 papers, 2 of them syntheses that pooled it.
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Who cites it
244 citing papers in PubMed, 2 syntheses or guidelines pooled it, 407 citations in OpenAlex.
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- Identification of a common variant with potential pleiotropic effect on risk of inflammatory bowel disease and colorectal cancer.Carcinogenesis · 2015Pooled it
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- Randomized phase II study of axitinib versus physicians best alternative choice of therapy in patients with recurrent glioblastoma.Journal of neuro-oncology · 2016Trial
- CpG island methylator phenotype is associated with response to adjuvant irinotecan-based therapy for stage III colon cancer.Gastroenterology · 2014Trial
- DNA hypermethylation of tumors from non-small cell lung cancer (NSCLC) patients is associated with gender and histologic type.Lung cancer (Amsterdam, Netherlands) · 2010Trial
- The potential of methylation signal detection in eDNA toward functional ecological monitoring.Communications biology · 2026Review
- Bidirectional Interactions Between Immune Regulation and the Insulin-like Growth Factor Axis in Colorectal Cancer.International journal of molecular sciences · 2026Review
- Germline Predisposition to Oncogenic Alkylating Damage in Colorectal Cancer.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2026Article
- Genome-wide extraction of differentially methylated DNA regions using adapter-anchored proximity primers.Nucleic acids research · 2026Article
- Circulating methylated promoters of HK2 and EGFR as biomarkers in the early detection of cancer.Frontiers in oncology · 2026Article
- Cell-Free DNA Methylation-Based Liquid Biopsy Assay to Identify Lymph Node Metastasis in T1 Gastric Cancer.United European gastroenterology journal · 2025Article
- Comparative analysis of pyrosequencing and next-generation sequencing for assessing MGMT methylation in glioma patients.Journal of neuro-oncology · 2025Article
- Perinatal hypoxia-mediated neurodevelopment abnormalities in congenital heart disease mouse model.Molecular medicine (Cambridge, Mass.) · 2025Article
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- Frequency and Molecular Characteristics of Mismatch Repair-deficient Status among Multiple Synchronous Colorectal Cancers.Journal of the anus, rectum and colon · 2025Article
- FOXP3+/CD8+ ratio associated with aggressive behavior in RUNX3-methylated diffuse esophagogastric junction tumor.Cancer science · 2025Article
- Clinicopathological, molecular, and prognostic features of colorectal carcinomas with KRAS c.34G>T (p.G12C) mutation.Cancer science · 2024Article
- Review
184 more citing papers are in PubMed but not listed here.
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Authors and funding
11 authors at 4 institutions in 1 country.
Funding
Abstract
Assays to measure DNA methylation, which are important in epigenetic research and clinical diagnostics, typically rely on conversion of unmethylated cytosine to uracil by sodium bisulfite. However, no study has comprehensively evaluated the precision and performance characteristics of sodium bisulfite conversion and subsequent quantitative methylation assay. We developed quantitative real-time polymerase chain reaction (MethyLight) to measure percentage of methylated reference (PMR, ie, degree of methylation) for the MGMT, MLH1, and CDKN2A (p16) promoters. To measure the precision of bisulfite conversion, we bisulfite-treated seven different aliquots of DNA from each of four paraffin-embedded colon cancer samples. To assess run-to-run variation, we repeated MethyLight five times. Bisulfite-to-bisulfite coefficient of variation (CV) of PMR ranged from 0.10 to 0.38 (mean, 0.21), and run-to-run CV of PMR ranged from 0.046 to 0.60 (mean, 0.31). Interclass correlation coefficients were 0.74 to 0.84 for the three loci, indicating good reproducibility. DNA mixing study with methylated and unmethylated DNA showed good linearity of the assay. Of 272 colorectal cancers evaluated, most showed PMR either <1 or >10, and promoter methylation (PMR >4) was tightly associated with loss of respective protein expression (P < 10(-16)). In conclusion, sodium bisulfite conversion and quantitative MethyLight assays have good precision and linearity and can be effectively used for high-throughput DNA methylation analysis on paraffin-embedded tissue.
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