ArticleClinical epigenetics2024
Technical and biological sources of unreliability of Infinium probes on Illumina methylation microarrays.
Article in Clinical epigenetics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Non-parametric differential methylation analysis characterizes histotype-specific promoter regions in epithelial ovarian cancer.Epigenetics · 2026Article
- Biological Versus Technical Reliability of Epigenetic Clocks and Implications for Disease Prognosis and Intervention Response.Aging cell · 2026Article
- A comparison of differential DNA methylation analysis methods for continuous outcomes: implications for epigenetic studies.Epigenomics · 2026Article
- Examination of Genetic and Epigenetic Characteristics of Patients with Hyperhomocysteinemia Following High-Dose Folic Acid Consumption.Nutrients · 2025Article
- Article
- Cigarette Smoking and E-cigarette Use Induce Shared DNA Methylation Changes Linked to Carcinogenesis.Cancer research · 2024Article
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Authors and funding
14 authors.
Funding
Abstract
The Illumina Methylation array platform has facilitated countless epigenetic studies on DNA methylation (DNAme) in health and disease, yet relatively few studies have so studied its reliability, i.e., the consistency of repeated measures. Here we investigate the reliability of both type I and type II Infinium probes. We propose a method for excluding unreliable probes based on dynamic thresholds for mean intensity (MI) and 'unreliability', estimated by probe-level simulation of the influence of technical noise on methylation β values using the background intensities of negative control probes. We validate our method in several datasets, including newly generated Illumina MethylationEPIC BeadChip v1.0 data from paired whole blood samples taken six weeks apart and technical replicates spanning multiple sample types. Our analysis revealed that specifically probes with low MI exhibit higher β value variability between repeated samples. MI was associated with the number of C-bases in the respective probe sequence and correlated negatively with unreliability scores. The unreliability scores were substantiated through validation in a new EPIC v1.0 (blood and cervix) and a publicly available 450k (blood) dataset, as they effectively captured the variability observed in β values between technical replicates. Finally, despite promising higher robustness, the newer version v2.0 of the MethylationEPIC BeadChip retained a substantial number of probes with poor unreliability scores. To enhance current pre-processing pipelines, we developed an R package to calculate MI and unreliability scores and provide guidance on establishing optimal dynamic score thresholds for a given dataset.
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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.