ArticleBMC genomics2014
Quantification of epigenetic biomarkers: an evaluation of established and emerging methods for DNA methylation analysis.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
24 citing papers in PubMed.
- Advancements in DNA methylation technologies and their application in cancer diagnosis.Epigenetics · 2025Review
- Plasmonic Molecular Entrapment for Label-Free Methylated DNA Detection and Machine-Learning Assisted Quantification.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Methylated Cell-Free Tumor DNA in Sputum as a Tool for Diagnosing Lung Cancer-A Systematic Review and Meta-Analysis.Cancers · 2024Review
- Methylated Circulating Tumor DNA in Blood as a Tool for Diagnosing Lung Cancer: A Systematic Review and Meta-Analysis.Cancers · 2023Review
- DNA Methylation in the Fields of Prenatal Diagnosis and Early Detection of Cancers.International journal of molecular sciences · 2023Review
- Early detection and prognosis prediction for colorectal cancer by circulating tumour DNA methylation haplotypes: A multicentre cohort study.EClinicalMedicine · 2023Article
- Article
- Methylation and Expression ofNutrients · 2021Article
- Evaluation of a panel of tumor-specific differentially-methylated DNA regions in IRF4, IKZF1 and BCAT1 for blood-based detection of colorectal cancer.Clinical epigenetics · 2021Article
- Comparison of Bisulfite Pyrosequencing and Methylation-Specific qPCR for Methylation Assessment.International journal of molecular sciences · 2020Article
- Quantification of DNA methylation independent of sodium bisulfite conversion using methylation-sensitive restriction enzymes and digital PCR.Human mutation · 2020Article
- Identification of Potential Biomarkers for CAD Using Integrated Expression and Methylation Data.Frontiers in genetics · 2020Article
- Novel Iodine-induced Cleavage Real-time PCR Assay for Accurate Quantification of Phosphorothioate Modified Sites in Bacterial DNA.Scientific reports · 2019Article
- Cell-free plasma hypermethylated CASZ1, CDH13 and ING2 are promising biomarkers of esophageal cancer.Journal of biomedical research · 2018Article
- Article
- Current, Emerging, and Future Applications of Digital PCR in Non-Invasive Prenatal Diagnosis.Molecular diagnosis & therapy · 2018Review
- gDNA extraction yield and methylation status of blood samples are affected by long-term storage conditions.PloS one · 2018Article
- Association between protocadherin 8 promoter hypermethylation and the pathological status of prostate cancer.Oncology letters · 2017Article
- Methylation analysis of plasma cell-free DNA for breast cancer early detection using bisulfite next-generation sequencing.Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine · 2016Article
- Experimental factors affecting the robustness of DNA methylation analysis.Scientific reports · 2016Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
backgroundDNA methylation is an important epigenetic mechanism in several human diseases, most notably cancer. The quantitative analysis of DNA methylation patterns has the potential to serve as diagnostic and prognostic biomarkers, however, there is currently a lack of consensus regarding the optimal methodologies to quantify methylation status. To address this issue we compared five analytical methods: (i) MethyLight qPCR, (ii) MethyLight digital PCR (dPCR), methylation-sensitive and -dependent restriction enzyme (MSRE/MDRE) digestion followed by (iii) qPCR or (iv) dPCR, and (v) bisulfite amplicon next generation sequencing (NGS). The techniques were evaluated for linearity, accuracy and precision.
resultsMethyLight qPCR displayed the best linearity across the range of tested samples. Observed methylation measured by MethyLight- and MSRE/MDRE-qPCR and -dPCR were not significantly different to expected values whilst bisulfite amplicon NGS analysis over-estimated methylation content. Bisulfite amplicon NGS showed good precision, whilst the lower precision of qPCR and dPCR analysis precluded discrimination of differences of < 25% in methylation status. A novel dPCR MethyLight assay is also described as a potential method for absolute quantification that simultaneously measures both sense and antisense DNA strands following bisulfite treatment.
conclusionsOur findings comprise a comprehensive benchmark for the quantitative accuracy of key methods for methylation analysis and demonstrate their applicability to the quantification of circulating tumour DNA biomarkers by using sample concentrations that are representative of typical clinical isolates.
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