ArticleClinical epigenetics2017
Validation of the MethylationEPIC BeadChip for fresh-frozen and formalin-fixed paraffin-embedded tumours.
Article in Clinical epigenetics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers, 1 of them a synthesis that pooled it.
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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.
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Who cites it
45 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Entorhinal cortex epigenome-wide association study highlights four novel loci showing differential methylation in Alzheimer's disease.Alzheimer's research & therapy · 2023Pooled it
- Genome-wide DNA Methylation Differences in Nonfunctioning Pituitary Adenomas With and Without Postsurgical Progression.The Journal of clinical endocrinology and metabolism · 2022Trial
- Impact of Tissue Sampling Strategy on the Diagnostic Accuracy of DNA Methylation Profiling in Central Nervous System Tumors.Pathology international · 2026Article
- Discovery and validation of PARP4 methylation in distinguishing thyroid cancer from benign nodule.Journal of endocrinological investigation · 2026Article
- High MGMT expression identifies aggressive colorectal cancer with distinct genomic features and immune evasion properties.Journal for immunotherapy of cancer · 2025Article
- Extensive epigenomic dysregulation is a hallmark of homologous recombination deficiency in triple-negative breast cancer.International journal of cancer · 2025Article
- Transcriptomics and epigenomics datasets of primary brain cancers in formalin-fixed paraffin embedded format.Scientific data · 2025Article
- Prediction of brain metastasis development with DNA methylation signatures.Nature medicine · 2025Article
- The Impact of Inherited Genetic Variation on DNA Methylation in Prostate Cancer and Benign Tissues of African American and European American Men.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2024Article
- Aberrant PRDM2 methylation as an early event in serrated lesions destined to evolve into microsatellite-instable colorectal cancers.The journal of pathology. Clinical research · 2024Article
- Long-read sequencing for brain tumors.Frontiers in oncology · 2024Review
- Article
- 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
- Epigenome-wide methylation analysis of colorectal carcinoma, adenoma and normal tissue reveals novel biomarkers addressing unmet clinical needs.Clinical epigenetics · 2023Article
- Reproducibility of the Infinium methylationEPIC BeadChip assay using low DNA amounts.Epigenetics · 2022Article
- Review
- DNA methylation profiling improves routine diagnosis of paediatric central nervous system tumours: A prospective population-based study.Neuropathology and applied neurobiology · 2022Article
- Review
- DNA methylation alterations across time and space in paediatric brain tumours.Acta neuropathologica communications · 2022Article
- Epigenome-Wide Association Study Reveals Differential Methylation Sites and Association of Gene Expression Regulation with Ischemic Moyamoya Disease in Adults.Oxidative medicine and cellular longevity · 2022Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA methylation is the most studied epigenetic modification due to its role in regulating gene expression, and its involvement in the pathogenesis of cancer and several diseases upon aberrations in methylation. The method of choice to evaluate genome-wide methylation has been the Illumina HumanMethylation450 BeadChip (450K), but it was recently replaced with the MethylationEPIC BeadChip (EPIC). We therefore sought to validate the EPIC array in comparison to the 450K array for both fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) tumours. We also performed analysis on the EPIC array with paired FF and FFPE samples to adapt to a clinical setting where FFPE is routinely used. Further, we compared two restoration methods, REPLI-g and Infinium, for FFPE-derived DNA on the EPIC array. The Pearson correlation of β values for common probes on the 450K and EPIC array was high for both FF (mean: 0.992) and FFPE (mean: 0.984) samples. The β values generated from the EPIC array for FFPE samples correlated well with the paired FF tumours, but varied between 0.901 and 0.987. We did note that sample pairs with lower correlation had less bimodal density distributions of β values and displayed higher noise in the copy number alteration plots (generated from the methylation array data) in the FFPE sample. Both REPLI-g and the Infinium restoration for FFPE samples performed well on the EPIC array and generated equivalent correlation scores to the paired FF sample.
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