ArticleProceedings of the National Academy of Sciences of the United States of America2005
Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 398 papers, 2 of them syntheses that pooled it.
What it found
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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.
The trial behind it
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
398 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Breastfeeding effects on DNA methylation in the offspring: A systematic literature review.PloS one · 2017Pooled it
- Different definitions of CpG island methylator phenotype and outcomes of colorectal cancer: a systematic review.Clinical epigenetics · 2016Pooled it
- Stability of the human sperm DNA methylome to folic acid fortification and short-term supplementation.Human reproduction (Oxford, England) · 2017Trial
- Prenatal maternal stress and wheeze in children: novel insights into epigenetic regulation.Scientific reports · 2016Trial
- Specific molecular signatures predict decitabine response in chronic myelomonocytic leukemia.The Journal of clinical investigation · 2015Trial
- Quantitative methylation level of the EPHX1 promoter in peripheral blood DNA is associated with polycystic ovary syndrome.PloS one · 2014Trial
- DNA methylation in interleukin-11 predicts clinical response to antidepressants in GENDEP.Translational psychiatry · 2013Trial
- The oxytocinergic system in functional neurological disorder: Preliminary testing of associations with interoception and childhood trauma.Comprehensive psychoneuroendocrinology · 2026Article
- Epigenetic activation of EBV BGLF4 determines antiviral-based regimen response in EBV+CNS lymphoproliferative disease.Blood neoplasia · 2026Article
- ACTB hypermethylation in blood is a potential biomarker as predictor to the risk of coronary heart disease.Scientific reports · 2026Article
- Epigenetic dysregulation of IRF9 drives excessive interferon signaling in COPD.EMBO molecular medicine · 2026Article
- DNA Methylation in Gastric Cancer and Preneoplastic Lesions: Emerging Insights and Future Directions.Cancers · 2026Review
- RRM1 inhibition sensitizes lung adenocarcinoma to decitabine treatment.Cell death & disease · 2026Article
- Oligonucleotide Selective Detection by Levitated Optomechanics.ACS nanoscience Au · 2026Article
- Single-Base Resolution DNA Methylation Analysis Through Targeted Locus-Specific Bisulfite Sequencing in Plants.Methods in molecular biology (Clifton, N.J.) · 2026Article
- The relationship between childhood trauma, rs1360780 genotypes,European journal of psychotraumatology · 2025Article
- DNA methylation and machine learning: challenges and perspective toward enhanced clinical diagnostics.Clinical epigenetics · 2025Review
- Personalized medicine for cardiovascular diseases: how next generation epigenetic technologies can contribute?Epigenomics · 2025Review
- CpG dinucleotide methylation of the SPDEF gene as a blood-based epigenetic biomarker for prostate cancer diagnosis.BMC urology · 2025Article
- Innovations in MALDI-TOF Mass Spectrometry: Bridging modern diagnostics and historical insights.Open life sciences · 2025Review
338 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Methylation is one of the major epigenetic processes pivotal to our understanding of carcinogenesis. It is now widely accepted that there is a relationship between DNA methylation, chromatin structure, and human malignancies. DNA methylation is potentially an important clinical marker in cancer molecular diagnostics. Understanding epigenetic modifications in their biological context involves several aspects of DNA methylation analysis. These aspects include the de novo discovery of differentially methylated genes, the analysis of methylation patterns, and the determination of differences in the degree of methylation. Here we present a previously uncharacterized method for high-throughput DNA methylation analysis that utilizes MALDI-TOF mass spectrometry (MS) analysis of base-specifically cleaved amplification products. We use the IGF2/H19 region to show that a single base-specific cleavage reaction is sufficient to discover methylation sites and to determine methylation ratios within a selected target region. A combination of cleavage reactions enables the complete evaluation of all relevant aspects of DNA methylation, with most CpGs represented in multiple reactions. We successfully applied this technology under high-throughput conditions to quantitatively assess methylation differences between normal and neoplastic lung cancer tissue samples from 48 patients in 47 genes and demonstrate that the quantitative methylation results allow accurate classification of samples according to their histopathology.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.