In 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. EPIC 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, b...Continue Reading
Prostate cancer risk and IRS1, IRS2, IGF1, and INS polymorphisms: strong association of IRS1 G972R variant and cancer risk
Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity
Effect of DHA supplementation during pregnancy on maternal depression and neurodevelopment of young children: a randomized controlled trial
Complete pipeline for Infinium(®) Human Methylation 450K BeadChip data processing using subset quantile normalization for accurate DNA methylation estimation
Genetic variants in CASP3, BMP5, and IRS2 genes may influence survival in prostate cancer patients receiving androgen-deprivation therapy
Cross-reactive DNA microarray probes lead to false discovery of autosomal sex-associated DNA methylation
A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data
Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray
Cytosine methylation changes in enhancer regions of core pro-fibrotic genes characterize kidney fibrosis development
Reducing the risk of false discovery enabling identification of biologically significant genome-wide methylation status using the HumanMethylation450 array
Genome-wide DNA methylation analysis of human pancreatic islets from type 2 diabetic and non-diabetic donors identifies candidate genes that influence insulin secretion
Validation of the MethylationEPIC BeadChip for fresh-frozen and formalin-fixed paraffin-embedded tumours
Annual Research Review: DNA methylation as a mediator in the association between risk exposure and child and adolescent psychopathology
Profiling DNA methylation differences between inbred mouse strains on the Illumina Human Infinium MethylationEPIC microarray
The role of pregnancy, perinatal factors and hormones in maternal cancer risk: a review of the evidence
Epigenome-wide analysis reveals specific DNA hypermethylation of T cells during human hematopoietic differentiation
The correlation of methylation levels measured using Illumina 450K and EPIC BeadChips in blood samples
Evolving paradigms for the biological response to low dose ionizing radiation; the role of epigenetics
Characterization of parent-of-origin methylation using the Illumina Infinium MethylationEPIC array platform
Identification of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome-associated DNA methylation patterns
Characterizing genetic and environmental influences on variable DNA methylation using monozygotic and dizygotic twins
Comparison of DNA methylation measured by Illumina 450K and EPIC BeadChips in blood of newborns and 14-year-old children
Evaluation of cross-platform and interlaboratory concordance via consensus modelling of genomic measurements
Variation in DNA methylation of human blood over a 1-year period using the Illumina MethylationEPIC array
Exposure to polybrominated biphenyl (PBB) associates with genome-wide DNA methylation differences in peripheral blood
Genome-wide epigenetic signatures of childhood adversity in early life: Opportunities and challenges
Intratumor DNA methylation heterogeneity in glioblastoma: implications for DNA methylation-based classification
DNA methylation changes associated with Parkinson's disease progression: outcomes from the first longitudinal genome-wide methylation analysis in blood
DNA methylation signatures in mendelian developmental disorders as a diagnostic bridge between genotype and phenotype
Pilot study of DNA methylation, molecular aging markers and measures of health and well-being in aging
EPIC-TABSAT: analysis tool for targeted bisulfite sequencing experiments and array-based methylation studies
DNA methylation signal has a major role in the response of human breast cancer cells to the microenvironment
Exposure to polybrominated biphenyl and stochastic epigenetic mutations: application of a novel epigenetic approach to environmental exposure in the Michigan polybrominated biphenyl registry
Whole-blood DNA Methylation Markers for Risk Stratification in Colorectal Cancer Screening: A Systematic Review
Human placental methylome in the interplay of adverse placental health, environmental exposure, and pregnancy outcome
Age-related changes in DNA methylation levels at CpG sites in bull spermatozoa and in vitro fertilization-derived blastocyst-stage embryos revealed by combined bisulfite restriction analysis
Assisted reproductive technologies are associated with limited epigenetic variation at birth that largely resolves by adulthood
Mediation by Placental DNA Methylation of the Association of Prenatal Maternal Smoking and Birth Weight
Retinoic acid and arsenic trioxide induce lasting differentiation and demethylation of target genes in APL cells
Integrating DNA methylation measures to improve clinical risk assessment: are we there yet? The case of BRCA1 methylation marks to improve clinical risk assessment of breast cancer.
Acute alcohol withdrawal and recovery in men lead to profound changes in DNA methylation profiles: a longitudinal clinical study
Race-specific alterations in DNA methylation among middle-aged African Americans and Whites with metabolic syndrome
Differential methylation of imprinting genes and MHC locus in 22q11.2 deletion syndrome-related schizophrenia spectrum disorders
pwrEWAS: a user-friendly tool for comprehensive power estimation for epigenome wide association studies (EWAS)
Dietary folate levels alter the kinetics and molecular mechanism of prostate cancer recurrence in the CWR22 model
DNA methylation associated with postpartum depressive symptoms overlaps findings from a genome-wide association meta-analysis of depression
Locus-Specific Differential DNA Methylation and Urinary Arsenic: An Epigenome-Wide Association Study in Blood among Adults with Low-to-Moderate Arsenic Exposure
Epigenome-wide cross-tissue correlation of human bone and blood DNA methylation - can blood be used as a surrogate for bone?
Genome-wide DNA methylation differences and polychlorinated biphenyl (PCB) exposure in a US population.
Age prediction of children and adolescents aged 6-17 years: an epigenome-wide analysis of DNA methylation
Environmental exposure to polybrominated biphenyl (PBB) associates with an increased rate of biological aging
Hypermethylation-associated downregulation of microRNA-4456 in hypersexual disorder with putative influence on oxytocin signalling: A DNA methylation analysis of miRNA genes
Epigenetic signatures associated with maternal body mass index or gestational weight gain: a systematic review
Epigenome-wide association study of DNA methylation and adult asthma in the Agricultural Lung Health Study.
Epigenetic Modifications as Biomarkers of Tumor Development, Therapy Response, and Recurrence across the Cancer Care Continuum
A Low Glycaemic Index Diet in Pregnancy Induces DNA Methylation Variation in Blood of Newborns: Results from the ROLO Randomised Controlled Trial
Epigenetic changes in preterm birth placenta suggest a role for ADAMTS genes in spontaneous preterm birth
Longitudinal genome-wide DNA methylation analysis uncovers persistent early-life DNA methylation changes
Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease
Epigenome-Wide Comparative Study Reveals Key Differences Between Mixed Connective Tissue Disease and Related Systemic Autoimmune Diseases
Comparison of methylation patterns generated from genomic and cell-line derived DNA using the Illumina Infinium MethylationEPIC BeadChip array
Altered Genome-Wide DNA Methylation in Peripheral Blood of South African Women with Gestational Diabetes Mellitus
Replication and expansion of epigenome-wide association literature in a black South African population
Methylomic profiling in trisomy 21 identifies cognition- and Alzheimer's disease-related dysregulation
Placental Epigenome-Wide Association Study Identified Loci Associated with Childhood Adiposity at 3 Years of Age
The end of the beginning: epigenetic variation in utero as a mediator of later human health and disease
SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions
Dose Response and Prediction Characteristics of a Methylation Sensitive Digital PCR Assay for Cigarette Consumption in Adults
Validation of differentially methylated microRNAs identified from an epigenome-wide association study; Sanger and next generation sequencing approaches
Exploring the effect of antenatal depression treatment on children's epigenetic profiles: findings from a pilot randomized controlled trial
Epigenome-wide Analysis Identifies Genes and Pathways Linked to Neurobehavioral Variation in Preterm Infants
Replication timing and epigenome remodelling are associated with the nature of chromosomal rearrangements in cancer
Association of Arsenic Exposure with Whole Blood DNA Methylation: An Epigenome-Wide Study of Bangladeshi Adults
Impact of Acute Aerobic Exercise on Genome-Wide DNA-Methylation in Natural Killer Cells-A Pilot Study
Methylation of drug resistance-related genes in chemotherapy-sensitive Epstein-Barr virus-associated gastric cancer
Alterations in the methylome of the stromal tumour microenvironment signal the presence and severity of prostate cancer
Epigenome-Wide Association Study for All-Cause Mortality in a Cardiovascular Cohort Identifies Differential Methylation in Castor Zinc Finger 1 (CASZ1 )
Genome-wide DNA methylation signatures to predict pathologic complete response from combined neoadjuvant chemotherapy with bevacizumab in breast cancer
SurvivalMeth: a web server to investigate the effect of DNA methylation-related functional elements on prognosis
Phenotypic profiling with a living biobank of primary rhabdomyosarcoma unravels disease heterogeneity and AKT sensitivity
"Epigenome-wide methylation profile of chronic kidney disease-derived arterial DNA uncovers novel pathways in disease-associated cardiovascular pathology."
Identification of Potential Biomarkers of Chronic Kidney Disease in Individuals with Diabetes: Protocol for a Cross-sectional Observational Study
A new approach to epigenome-wide discovery of non-invasive methylation biomarkers for colorectal cancer screening in circulating cell-free DNA using pooled samples
BoostMe accurately predicts DNA methylation values in whole-genome bisulfite sequencing of multiple human tissues
Candidate genes linking maternal nutrient exposure to offspring health via DNA methylation: a review of existing evidence in humans with specific focus on one-carbon metabolism
Methylome of human skeletal muscle after acute & chronic resistance exercise training, detraining & retraining
DNA methylation profiling of acute chorioamnionitis-associated placentas and fetal membranes: insights into epigenetic variation in spontaneous preterm births
A combined epigenome- and transcriptome-wide association study of the oral masticatory mucosa assigns CYP1B1 a central role for epithelial health in smokers
Epigenome-Wide Association Analysis of Differentially Methylated Signals in Blood Samples of Patients with Non-Small-Cell Lung Cancer
Genome-wide methylation profiling identified novel differentially hypermethylated biomarker MPPED2 in colorectal cancer
The DNA methylome of inflammatory bowel disease (IBD) reflects intrinsic and extrinsic factors in intestinal mucosal cells.
An overview about DNA methylation in childhood obesity: Characteristics of the studies and main findings.
Gene-methylation interactions: discovering region-wise DNA methylation levels that modify SNP-associated disease risk
DNA Methylome Distinguishes Head and Neck Cancer from Potentially Malignant Oral Lesions and Healthy Oral Mucosa
Epigenetic regulation of the lineage specificity of primary human dermal lymphatic and blood vascular endothelial cells
Guidelines for whole genome bisulphite sequencing of intact and FFPET DNA on the Illumina HiSeq X Ten
Comparison of DNA methylation profiles associated with spontaneous preterm birth in placenta and cord blood
No genome-wide DNA methylation changes found associated with medium-term reduced graphene oxide exposure in human lung epithelial cells
Systematic evaluation of library preparation methods and sequencing platforms for high-throughput whole genome bisulfite sequencing
Integrative analysis of gene expression, DNA methylation, physiological traits, and genetic variation in human skeletal muscle
Placental NEGR1 DNA methylation is associated with BMI and neurodevelopment in preschool-age children
Epigenome-wide association study of narcolepsy-affected lateral hypothalamic brains, and overlapping DNA methylation profiles between narcolepsy and multiple sclerosis
DNA methylation across the genome in aged human skeletal muscle tissue and muscle-derived cells: the role of HOX genes and physical activity
Association Between Stress and Coping with DNA Methylation of Blood Pressure-Related Genes Among African American Women
Effect of maternal preconceptional and pregnancy micronutrient interventions on children's DNA methylation: Findings from the EMPHASIS study.
Mediation Analysis Supports a Causal Relationship between Maternal Hyperglycemia and Placental DNA Methylation Variations at the Leptin Gene Locus and Cord Blood Leptin Levels
Discovery of Molecular DNA Methylation-Based Biomarkers through Genome-Wide Analysis of Response Patterns to BCG for Bladder Cancer
Differentiation of Induced Pluripotent Stem Cells towards Mesenchymal Stromal Cells is Hampered by Culture in 3D Hydrogels
Comprehensive evaluation of targeted multiplex bisulphite PCR sequencing for validation of DNA methylation biomarker panels
Genome-wide DNA methylation analysis of heavy cannabis exposure in a New Zealand longitudinal cohort.
Rheumatoid arthritis-relevant DNA methylation changes identified in ACPA-positive asymptomatic individuals using methylome capture sequencing
Epigenome-wide analysis identifies genes and pathways linked to acoustic cry variation in preterm infants
The DNA methylome of human sperm is distinct from blood with little evidence for tissue-consistent obesity associations
Genome-wide DNA methylation profiling in human breast tissue by illumina TruSeq methyl capture EPIC sequencing and infinium methylationEPIC beadchip microarray
CUE: CpG impUtation ensemble for DNA methylation levels across the human methylation450 (HM450) and EPIC (HM850) BeadChip platforms.
Serious neonatal morbidities are associated with differences in DNA methylation among very preterm infants
Accelerated Epigenetic Aging and Methylation Disruptions Occur in Human Immunodeficiency Virus Infection Prior to Antiretroviral Therapy
DNA methylation profiling identifies epigenetic differences between early versus late stages of diabetic chronic kidney disease
Maternal dysglycaemia, changes in the infant's epigenome modified with a diet and physical activity intervention in pregnancy: Secondary analysis of a randomised control trial
A longitudinal and transancestral analysis of DNA methylation patterns and disease activity in lupus patients
Rare genetic variation at transcription factor binding sites modulates local DNA methylation profiles
Deconvolution of cellular subsets in human tissue based on targeted DNA methylation analysis at individual CpG sites
Comparison of methylation capture sequencing and Infinium MethylationEPIC array in peripheral blood mononuclear cells.
Methylomic Analysis of Ovarian Cancers Identifies Tumor-Specific Alterations Readily Detectable in Early Precursor Lesions
The Altered Transcriptome and DNA Methylation Profiles of Docetaxel Resistance in Breast Cancer PDX Models
Epigenome-wide association study of maternal hemoglobin A1c in pregnancy and cord blood DNA methylation.
Dioxin-like compound exposures and DNA methylation in the Anniston Community Health Survey Phase II.
Genome-wide DNA methylation profiling of peripheral blood reveals an epigenetic signature associated with severe COVID-19.
Twin study designs as a tool to identify new candidate genes for depression: A systematic review of DNA methylation studies
Aggresomes predict poor outcomes and implicate proteostasis in the pathogenesis of pediatric choroid plexus tumors.
Colorectal cancer screening and diagnosis: omics-based technologies for development of a non-invasive blood-based method.
Genome-wide DNA methylation profiling is able to identify prefibrotic PMF cases at risk for progression to myelofibrosis.
Longitudinal analysis of healthy colon establishes aspirin as a suppressor of cancer-related epigenetic aging
DNA methylation signature in blood mirrors successful weight-loss during lifestyle interventions: the CENTRAL trial
Associations of combined genetic and epigenetic scores with muscle size and muscle strength: a pilot study in older women
Systems Biology Methods Applied to Blood and Tissue for a Comprehensive Analysis of Immune Response to Hepatitis B Vaccine in Adults
Comprehensive Analysis of DNA Methylation and Prediction of Response to NeoadjuvantTherapy in Locally Advanced Rectal Cancer
Blood-based epigenetic estimators of chronological age in human adults using DNA methylation data from the Illumina MethylationEPIC array
Altered transcriptional and chromatin responses to rhinovirus in bronchial epithelial cells from adults with asthma
Single cell sequencing reveals endothelial plasticity with transient mesenchymal activation after myocardial infarction.
Cross-reactive probes on Illumina DNA methylation arrays: a large study on ALS shows that a cautionary approach is warranted in interpreting epigenome-wide association studies.
The relationship between DNA methylation in neurotrophic genes and age as evidenced from three independent cohorts: differences by delirium status
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