ArticleBMC genomics2024
Characterisation and reproducibility of the HumanMethylationEPIC v2.0 BeadChip for DNA methylation profiling.
Article in BMC genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- miR2Meth: An R package for dissecting DNA methylation heterogeneity at microRNA promoters.Quantitative biology (Beijing, China) · 2026Article
- Machine learning-assisted analysis of saliva-containing mixtures using a saliva-specific multi-CpG-microhaplotype marker system.International journal of legal medicine · 2026Article
- Epigenome-wide profiling identifies distinct DNA methylation architecture underlying ME/CFS and fibromyalgia symptom burden.Journal of translational medicine · 2026Article
- Sellar region neurocytomas exhibit a CIMP and neuroendocrine-like epigenetic signature distinct from other intra-axial neurocytomas.Acta neuropathologica · 2026Article
- Longitudinal Changes in Inflammation-Related Methylation Risk Score for C-Reactive Protein Among People with HIV.Epigenomes · 2026Article
- Placental Methylation Profile in Women Exposed to Fluoride and Its Association with Kidney Volume at Birth.Clinical journal of the American Society of Nephrology : CJASN · 2026Article
- The role of epigenetic age acceleration and social disadvantage in cardiometabolic health in southeast Louisiana women.Clinical epigenetics · 2026Article
- DeepMethylation: A deep learning framework for tissue-specific DNA methylation prediction and functional variant annotation.PLoS computational biology · 2026Article
- TiSMeD: A tissue-specific methylation and expression database for biomarker and translational applications.Molecular therapy. Nucleic acids · 2026Article
- DNA methylation signatures associated with bipolar disorder in peripheral blood improve prediction models.EBioMedicine · 2026Article
- Circulating cell-free methylated DNA immunoprecipitation sequencing (cfMeDIP-seq) in oncology: from technological advances to clinical applications.NPJ precision oncology · 2026Review
- Clinical utility of sarcoma methylation classifiers in soft tissue sarcoma diagnosis.Journal of cancer research and clinical oncology · 2026Article
- From Spatial Epigenomes to Clinical Diagnostics: Integrative Methylomics Across Scales and Modalities.International journal of molecular sciences · 2026Review
- Beyond Small Molecules: Orchestrating Cell Fate with Engineered Water-Soluble Membrane Proteins.Biomolecules · 2026Article
- Cell-specific DNA methylation in human alpha and beta cells regulates gene expression in type 2 diabetes.Nature metabolism · 2026Article
- Epigenetic age and cardiometabolic disease in Guatemalan adults: a cross-sectional analysis.Journal of health, population, and nutrition · 2026Article
- Non-invasive epidermis sampling for DNA methylation-based prediction of skin cancer phenotypes.NPJ precision oncology · 2026Article
- Associations of arsenic exposure and folate in maternal leukocyte DNA methylation: a case-control study of mothers with spina-bifida affected children.Environmental health : a global access science source · 2026Article
- Integrative Analyses of Individual Patient Genomic-Data to Discover Novel Biomarkers: Application to Cervical Pre-Cancer DNA-Methylation Datasets.Cancer informatics · 2026Article
- Low-grade glial neoplasms of germ cell origin may represent maturation of embryonic-type neuroectodermal elements.Histopathology · 2026Article
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Authors and funding
14 authors.
Funding
Abstract
backgroundThe Illumina family of Infinium Methylation BeadChip microarrays has been widely used over the last 15 years for genome-wide DNA methylation profiling, including large-scale and population-based studies, due to their ease of use and cost effectiveness. Succeeding the popular HumanMethylationEPIC BeadChip (EPICv1), the recently released Infinium MethylationEPIC v2.0 BeadChip (EPICv2) claims to extend genomic coverage to more than 935,000 CpG sites. Here, we comprehensively characterise the reproducibility, reliability and annotation of the EPICv2 array, based on bioinformatic analysis of both manifest data and new EPICv2 data from diverse biological samples.
resultsWe find a high degree of reproducibility with EPICv1, evidenced by comparable sensitivity and precision from empirical cross-platform comparison incorporating whole genome bisulphite sequencing (WGBS), and high correlation between technical sample replicates, including between samples with DNA input levels below the manufacturer's recommendation. We provide a full assessment of probe content, evaluating genomic distribution and changes from previous array versions. We characterise EPICv2's new feature of replicated probes and provide recommendations as to the superior probes. In silico analysis of probe sequences demonstrates that probe cross-hybridisation remains a significant problem in EPICv2. By mapping the off-target sites at single nucleotide resolution and comparing with WGBS we show empirical evidence for preferential off-target binding.
conclusionsOverall, we find EPICv2 a worthy successor to the previous Infinium methylation microarrays, however some technical issues remain. To support optimal EPICv2 data analysis we provide an expanded version of the EPICv2 manifest to aid researchers in understanding probe design, data processing, choosing appropriate probes for analysis and for integration with methylation datasets from previous versions of the Infinium Methylation BeadChip.
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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.