ArticleEpigenetics2024
Critical evaluation of the reliability of DNA methylation probes on the Illumina MethylationEPIC v1.0 BeadChip microarrays.
Article in Epigenetics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Comparison of nanopore sequencing, MethylationEPIC array, and EM-Seq for DNA methylation detection.Computational biology and chemistry · 2026Article
- DNA methylation changes following rapid maxillary expansion in children.Scientific reports · 2026Article
- Biological Versus Technical Reliability of Epigenetic Clocks and Implications for Disease Prognosis and Intervention Response.Aging cell · 2026Article
- Methylation signatures distinguish non-small cell lung cancer subtypes and are associated with survival in smokers with lung squamous cell carcinoma.Journal of the National Cancer Institute · 2026Article
- CpG Atlas: A centralized multi-layer database and AI interface for DNA methylation research.bioRxiv : the preprint server for biology · 2026Article
- Systematic investigation of interindividual variation of DNA methylation in human whole blood.Genome biology · 2026Article
- Epigenetic memory and allostatic integrity: a theoretical integration of the hierarchical-circular model using a longitudinal methylation signature of dementia.Frontiers in aging neuroscience · 2026Article
- Accounting for differences between Infinium MethylationEPIC v2 and v1 in DNA methylation-based tools.Life science alliance · 2025Article
- Weight-loss associated DNA methylation patterns: targetable biomarkers and pathway insights.BMC research notes · 2025Article
- Prognostic Significance of the Comprehensive Biomarker Analysis in Colorectal Cancer.Life (Basel, Switzerland) · 2025Review
- Quality control checkpoints for high throughput DNA methylation measurement using the human MethylationEPICv1 array: application to formalin-fixed paraffin embedded prostate tissue.BMC research notes · 2025Article
- Accounting for differences between Infinium MethylationEPIC v2 and v1 in DNA methylation-based tools.bioRxiv : the preprint server for biology · 2025Article
- Article
- Blood DNA methylation signature for incident dementia: Evidence from longitudinal cohorts.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2025Article
- Letter to the editor: critical evaluation of the reliability of DNA methylation probes on the illumina MethylationEPIC v1.0 BeadChip microarrays.Epigenetics · 2024Article
- Generations of epigenetic clocks and their links to socioeconomic status in the Health and Retirement Study.Epigenomics · 2024Article
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10 authors.
Funding
Abstract
DNA methylation (DNAm) plays a crucial role in a number of complex diseases. However, the reliability of DNAm levels measured using Illumina arrays varies across different probes. Previous research primarily assessed probe reliability by comparing duplicate samples between the 450k-450k or 450k-EPIC platforms, with limited investigations on Illumina EPIC v1.0 arrays. We conducted a comprehensive assessment of the EPIC v1.0 array probe reliability using 69 blood DNA samples, each measured twice, generated by the Alzheimer's Disease Neuroimaging Initiative study. We observed higher reliability in probes with average methylation beta values of 0.2 to 0.8, and lower reliability in type I probes or those within the promoter and CpG island regions. Importantly, we found that probe reliability has significant implications in the analyses of Epigenome-wide Association Studies (EWAS). Higher reliability is associated with more consistent effect sizes in different studies, the identification of differentially methylated regions (DMRs) and methylation quantitative trait locus (mQTLs), and significant correlations with downstream gene expression. Moreover, blood DNAm measurements obtained from probes with higher reliability are more likely to show concordance with brain DNAm measurements. Our findings, which provide crucial reliability information for probes on the EPIC v1.0 array, will serve as a valuable resource for future DNAm studies.
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