ArticleGenome biology2016
Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling.
Article in Genome biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT03923335 (The Predictive Value of Guangzhou Panel for Recurrence in Early-stage Colorectal Cancer), which is not on this map. Cited by 906 papers, 5 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.
The Predictive Value of Guangzhou Panel for Recurrence in Early-stage Colorectal Cancer
Who cites it
906 citing papers in PubMed, 5 syntheses or guidelines pooled it.
- Prenatal Smoking Exposures and Epigenome-Wide Methylation in Newborn Blood.Environmental health perspectives · 2026Pooled it
- DNA methylation signatures of bilateral hippocampal volume, asymmetry and atrophy: a cross-omics analysis in the general population.EBioMedicine · 2026Pooled it
- The aging epigenome: integrative analyses reveal intersection with Alzheimer's disease.GeroScience · 2026Pooled it
- Paediatric DNA methylation profile scores: a systematic review and open-source atlas.EBioMedicine · 2026Pooled it
- Meta-analysis examining fetal sex-specific placental DNA methylation intensities and estimated cell composition post IVF.Molecular human reproduction · 2025Pooled it
- A predictive endocrine resistance index accurately stratifies luminal breast cancer treatment responders and nonresponders.The Journal of clinical investigation · 2025Trial
- Heat-stress-induced DNA methylation remodeling in cattle: a systematic evidence synthesis and meta-analytic feasibility assessment.Veterinary and animal science · 2026Review
- Article
- Whole-genome DNA methylation analysis reveals distinct subtype characteristics in epithelial ovarian cancer.Cancer gene therapy · 2026Article
- Multi-omics identifies promoter methylation and gene expression changes associated with human skeletal muscle atrophy.Experimental physiology · 2026Article
- Comparison of nanopore sequencing, MethylationEPIC array, and EM-Seq for DNA methylation detection.Computational biology and chemistry · 2026Article
- A Guide to Enzymatic Targeted Methylation Sequencing Bioinformatics Workflow: Best Practices.Current protocols · 2026Article
- Article
- Gliomas with pleomorphic and pseudopapillary features (GPAP) are circumscribed tumors with targetable mutations, prolonged survival, and frequent tumor predisposition.Brain pathology (Zurich, Switzerland) · 2026Article
- Buccal DNA Methylation-Derived EpiScores are Associated with Neonatal Morbidity Burden in Infants born Very Preterm.medRxiv : the preprint server for health sciences · 2026Article
- Recurrent mechanisms of biallelic epigenetic inactivation reveal new putative tumour suppressor genes in prostate cancer.Nature communications · 2026Article
- Effects of a randomized controlled trial of unconditional cash transfers on epigenetic measures of ageing and cognition in children and mothers.Nature human behaviour · 2026Article
- The length of the embryo culture in assisted reproductive technology does not have a major impact on newborn DNA methylation.Bioscience reports · 2026Article
- DNA methylation changes following rapid maxillary expansion in children.Scientific reports · 2026Article
- Integrative Epigenomics: Bioinformatics Strategies for Multi-Omics Data Analysis in Health and Disease.Epigenomes · 2026Review
846 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
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIn recent years the Illumina HumanMethylation450 (HM450) BeadChip has provided a user-friendly platform to profile DNA methylation in human samples. However, HM450 lacked coverage of distal regulatory elements. Illumina have now released the MethylationEPIC (EPIC) BeadChip, with new content specifically designed to target these regions. We have used HM450 and whole-genome bisulphite sequencing (WGBS) to perform a critical evaluation of the new EPIC array platform.
resultsEPIC covers over 850,000 CpG sites, including >90 % of the CpGs from the HM450 and an additional 413,743 CpGs. Even though the additional probes improve the coverage of regulatory elements, including 58 % of FANTOM5 enhancers, only 7 % distal and 27 % proximal ENCODE regulatory elements are represented. Detailed comparisons of regulatory elements from EPIC and WGBS show that a single EPIC probe is not always informative for those distal regulatory elements showing variable methylation across the region. However, overall data from the EPIC array at single loci are highly reproducible across technical and biological replicates and demonstrate high correlation with HM450 and WGBS data. We show that the HM450 and EPIC arrays distinguish differentially methylated probes, but the absolute agreement depends on the threshold set for each platform. Finally, we provide an annotated list of probes whose signal could be affected by cross-hybridisation or underlying genetic variation.
conclusionThe EPIC array is a significant improvement over the HM450 array, with increased genome coverage of regulatory regions and high reproducibility and reliability, providing a valuable tool for high-throughput human methylome analyses from diverse clinical samples.
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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.