ArticleEpigenetics2021
Reliability of DNA methylation measures using Illumina methylation BeadChip.
Article in Epigenetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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
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Who cites it
25 citing papers in PubMed, 37 citations in OpenAlex.
- Systematic investigation of interindividual variation of DNA methylation in human whole blood.Genome biology · 2026Article
- Analysis Methods for Diagnosing Rare Neurodevelopmental Diseases with Episignatures: A Systematic Review of the Literature.Biomedicines · 2025Review
- Early-life nutrition supplementation and epigenetic age in middle-adulthood among Guatemalan adults.bioRxiv : the preprint server for biology · 2025Article
- Complete reference genome and pangenome improve genome-wide detection and interpretation of DNA methylation using sequencing and array data.Cell reports · 2025Article
- A novel framework to build saliva-based DNA methylation biomarkers: Quantifying systemic chronic inflammation as a case study.Aging cell · 2025Article
- Human genomic regions of systemic interindividual epigenetic variation are implicated in neurodevelopmental and metabolic disorders.medRxiv : the preprint server for health sciences · 2025Article
- Article
- easyEWAS: a flexible and user-friendly R package for epigenome-wide association study.Bioinformatics advances · 2025Article
- Epigenetic Clocks: Beyond Biological Age, Using the Past to Predict the Present and Future.Aging and disease · 2024Review
- Reliable detection of stochastic epigenetic mutations and associations with cardiovascular aging.GeroScience · 2024Article
- Critical evaluation of the reliability of DNA methylation probes on the Illumina MethylationEPIC v1.0 BeadChip microarrays.Epigenetics · 2024Article
- Technical variability across the 450K, EPICv1, and EPICv2 DNA methylation arrays: lessons learned for clinical and longitudinal studies.Clinical epigenetics · 2024Article
- Stability of Blood DNA Methylation Across Two Timepoints in Three Cohorts.Biomedicines · 2024Article
- Linking Prenatal Environmental Exposures to Lifetime Health with Epigenome-Wide Association Studies: State-of-the-Science Review and Future Recommendations.Environmental health perspectives · 2023Review
- Biological stability of DNA methylation measurements over varying intervals of time and in the presence of acute stress.Epigenetics · 2023Article
- Critical evaluation of the reliability of DNA methylation probes on the Illumina MethylationEPIC BeadChip microarrays.Research square · 2023Article
- Prenatal delta-9-tetrahydrocannabinol exposure is associated with changes in rhesus macaque DNA methylation enriched for autism genes.Clinical epigenetics · 2023Article
- A systematic evaluation of normalization methods and probe replicability using infinium EPIC methylation data.Clinical epigenetics · 2023Article
- Epigenetic-based age acceleration in a representative sample of older Americans: Associations with aging-related morbidity and mortality.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Beadchip technology to detect DNA methylation in mouse faithfully recapitulates whole-genome bisulfite sequencing.Epigenomics · 2023Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Illumina BeadChips are widely utilized in epigenome-wide association studies (EWAS). Several studies have reported that many probes on these arrays have poor reliability. Here, we compare different pre-processing methods to improve intra-class correlation coefficients (ICC). We describe the characteristics of ICC across the genome, within and between studies, and across different array platforms. Using technical duplicates from 128 subjects, we find that with raw data only 22.5% of the CpGs on 450 K array have 'acceptable' ICCs (>0.5). Data preprocessing steps, such as background correction and dye bias correction, can reduce technical noise and improve the percentage to 38.5%. Similar to previous studies, we found that ICC is associated with CpG methylation level such that 83% of CpGs with intermediate methylation (0.1< beta-value <0.9) have acceptable ICCs, whereas only 21% of CpGs with low or high methylation (beta-value <0.1 or >0.9) have acceptable ICCs. ICC is also correlated with CpG methylation variance; after mutual adjustment for beta-value and variance, only variance remains correlated. Many CpGs with poor ICCs (<0.5) are located in biologically important regulatory regions, including gene promoters and CpG islands. Poor ICC at these sites appears to be a consequence of low biologic variation among individuals rather than increased technical measurement variation. ICCs quality classifications are highly concordant across different array platforms and across different studies. We find that ICC can be reliably estimated with 30 pairs of duplicate samples. CpGs with acceptable ICC have higher study power and are more commonly reported in published epigenome-wide studies.
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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.