ArticleClinical epigenetics2023
A systematic evaluation of normalization methods and probe replicability using infinium EPIC methylation data.
Article in Clinical epigenetics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers, 2 of them syntheses that pooled it.
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Who cites it
18 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Paediatric DNA methylation profile scores: a systematic review and open-source atlas.EBioMedicine · 2026Pooled it
- A meta-analysis of immune-cell fractions at high resolution reveals novel associations with common phenotypes and health outcomes.Genome medicine · 2023Pooled it
- DNA Methylation Profiling in IDH-Mutant Gliomas: Biological Evolution, Molecular Grading and Clinical Implementation.Neuropathology and applied neurobiology · 2026Review
- Genome-wide DNA methylation changes after 24 hours at high altitude.Environmental epigenetics · 2026Article
- DNA methylation signatures of frailty beyond age: a longitudinal study of female and male mice.bioRxiv : the preprint server for biology · 2025Article
- Analysis Methods for Diagnosing Rare Neurodevelopmental Diseases with Episignatures: A Systematic Review of the Literature.Biomedicines · 2025Review
- RAMEN: Dissecting individual, additive and interactive gene-environment contributions to DNA methylome variability in cord blood.Genome biology · 2025Article
- From population science to the clinic? Limits of epigenetic clocks as personal biomarkers.Epigenomics · 2025Article
- DNA methylation-wide association study of prevalent and incident dementia in the US Health and Retirement Study.medRxiv : the preprint server for health sciences · 2025Article
- Epigenomic Interactions Between Chronic Pain and Recurrent Pressure Injuries After Spinal Cord Injury.Epigenomes · 2025Article
- A Comprehensive Review of Deep Learning Applications with Multi-Omics Data in Cancer Research.Genes · 2025Review
- Epitranscriptomic analysis reveals clinical and molecular signatures in glioblastoma.Acta neuropathologica communications · 2025Article
- Age-related changes in DNA methylation in a sample of elderly Brazilians.Clinical epigenetics · 2025Article
- Using parenclitic networks on phaeochromocytoma and paraganglioma tumours provides novel insights on global DNA methylation.Scientific reports · 2024Article
- Critical evaluation of the reliability of DNA methylation probes on the Illumina MethylationEPIC v1.0 BeadChip microarrays.Epigenetics · 2024Article
- A validated restriction enzyme ddPCR cg05575921 (AHRR) assay to accurately assess smoking exposure.Clinical epigenetics · 2024Article
- Critical evaluation of the reliability of DNA methylation probes on the Illumina MethylationEPIC BeadChip microarrays.Research square · 2023Article
- Fresh and frozen cardiac tissue are comparable in DNA methylation array β-values, but formalin-fixed, paraffin-embedded tissue may overestimate DNA methylation levels.Scientific reports · 2023Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe Infinium EPIC array measures the methylation status of > 850,000 CpG sites. The EPIC BeadChip uses a two-array design: Infinium Type I and Type II probes. These probe types exhibit different technical characteristics which may confound analyses. Numerous normalization and pre-processing methods have been developed to reduce probe type bias as well as other issues such as background and dye bias.
methodsThis study evaluates the performance of various normalization methods using 16 replicated samples and three metrics: absolute beta-value difference, overlap of non-replicated CpGs between replicate pairs, and effect on beta-value distributions. Additionally, we carried out Pearson's correlation and intraclass correlation coefficient (ICC) analyses using both raw and SeSAMe 2 normalized data.
resultsThe method we define as SeSAMe 2, which consists of the application of the regular SeSAMe pipeline with an additional round of QC, pOOBAH masking, was found to be the best performing normalization method, while quantile-based methods were found to be the worst performing methods. Whole-array Pearson's correlations were found to be high. However, in agreement with previous studies, a substantial proportion of the probes on the EPIC array showed poor reproducibility (ICC < 0.50). The majority of poor performing probes have beta values close to either 0 or 1, and relatively low standard deviations. These results suggest that probe reliability is largely the result of limited biological variation rather than technical measurement variation. Importantly, normalizing the data with SeSAMe 2 dramatically improved ICC estimates, with the proportion of probes with ICC values > 0.50 increasing from 45.18% (raw data) to 61.35% (SeSAMe 2).
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