We propose a novel approach to background correction for Infinium HumanMethylation data to account for technical variation in background fluorescence signal. Our approach capitalizes on a new use for the Infinium I design bead types to measure non-specific fluorescence in the colour channel opposite of their design (Cy3/Cy5). This provides tens of thousands of features for measuring background instead of the much smaller number of negative control probes on the platforms (n = 32 for HumanMethylation27 and n = 614 for HumanMethylation450, respectively). We compare the performance of our methods with existing approaches, using technical replicates of both mixture samples and biological samples, and demonstrate that within- and between-platform artefacts can be substantially reduced, with concomitant improvement in sensitivity, by the proposed methods.
Epigenetic profiling of somatic tissues from human autopsy specimens identifies tissue- and individual-specific DNA methylation patterns
Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis
SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips
Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia
A pilot genome-scale profiling of DNA methylation in sporadic pituitary macroadenomas: association with tumor invasion and histopathological subtype
Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays
Functional normalization of 450k methylation array data improves replication in large cancer studies
A donor-specific epigenetic classifier for acute graft-versus-host disease severity in hematopoietic stem cell transplantation
Sensitivity Analysis of the MGMT-STP27 Model and Impact of Genetic and Epigenetic Context to Predict the MGMT Methylation Status in Gliomas and Other Tumors
CpG island methylation profile in non-invasive oral rinse samples is predictive of oral and pharyngeal carcinoma
The effect of 5-fluorouracil/leucovorin chemotherapy on CpG methylation, or the confounding role of leukocyte heterogeneity: An illustration
DNA methylation levels and long-term trihalomethane exposure in drinking water: an epigenome-wide association study
Many obesity-associated SNPs strongly associate with DNA methylation changes at proximal promoters and enhancers
DNA Methylation and Somatic Mutations Converge on the Cell Cycle and Define Similar Evolutionary Histories in Brain Tumors
Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data
Gene chip analysis of Arabidopsis thaliana genomic DNA methylation and gene expression in response to carbendazim
Long-range epigenetic regulation is conferred by genetic variation located at thousands of independent loci
Comparison of pre-processing methodologies for Illumina 450k methylation array data in familial analyses
Methylation quantitative trait loci within the TOMM20 gene are associated with metabolic syndrome-related lipid alterations in severely obese subjects
GSTP1, APC and RASSF1 gene methylation in prostate cancer samples: comparative analysis of MS-HRM method and Infinium HumanMethylation450 BeadChip beadchiparray diagnostic value
Validation of the MethylationEPIC BeadChip for fresh-frozen and formalin-fixed paraffin-embedded tumours
Alpha-oxoglutarate inhibits the proliferation of immortalized normal bladder epithelial cells via an epigenetic switch involving ARID1A
Peripheral DNA methylation, cognitive decline and brain aging: pilot findings from the Whitehall II imaging study
Smoking is associated with hypermethylation of the APC 1A promoter in colorectal cancer: the ColoCare Study
Cumulative lifetime maternal stress and epigenome-wide placental DNA methylation in the PRISM cohort
Exposure to Low Levels of Lead in Utero and Umbilical Cord Blood DNA Methylation in Project Viva: An Epigenome-Wide Association Study
Residential Proximity to Major Roadways at Birth, DNA Methylation at Birth and Midchildhood, and Childhood Cognitive Test Scores: Project Viva(Massachusetts, USA)
The Role of DNA Methylation in Cardiovascular Risk and Disease: Methodological Aspects, Study Design, and Data Analysis for Epidemiological Studies
Cell type-specific DNA methylation in neonatal cord tissue and cord blood: a 850K-reference panel and comparison of cell types
Brain metastasis DNA methylomes, a novel resource for the identification of biological and clinical features
Metastable DNA methylation sites associated with longitudinal lung function decline and aging in humans: an epigenome-wide study in the NAS and KORA cohorts
DNA methylation in blood as a mediator of the association of mid-childhood body mass index with cardio-metabolic risk score in early adolescence
Gain-of-function DNMT3A mutations cause microcephalic dwarfism and hypermethylation of Polycomb-regulated regions
Longitudinal analysis of epigenome-wide DNA methylation reveals novel smoking-related loci in African Americans
The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions
Genome-wide DNA methylation detection by MethylCap-seq and Infinium HumanMethylation450 BeadChips: an independent large-scale comparison
Prenatal maternal depressive symptoms and infant DNA methylation: a longitudinal epigenome-wide study
Assessment of DNA Methylation Patterns in the Bone and Cartilage of a Nonhuman Primate Model of Osteoarthritis
Novel age-associated DNA methylation changes and epigenetic age acceleration in middle-aged African Americans and whites
The relation between DNA methylation patterns and serum cytokine levels in community-dwelling adults: a preliminary study
Long-term prenatal exposure to paracetamol is associated with DNA methylation differences in children diagnosed with ADHD
Socioeconomic status and DNA methylation from birth through mid-childhood: a prospective study in Project Viva
Machine learning analysis of DNA methylation profiles distinguishes primary lung squamous cell carcinomas from head and neck metastases.
Differential gene expression and limited epigenetic dysregulation at the materno-fetal interface in preeclampsia
Evaluation of pre-processing on the meta-analysis of DNA methylation data from the Illumina HumanMethylation450 BeadChip platform
Race-specific alterations in DNA methylation among middle-aged African Americans and Whites with metabolic syndrome
Differential methylation of enhancer at IGF2 is associated with abnormal dopamine synthesis in major psychosis
Early detection of gastric cancer using global, genome-wide and IRF4, ELMO1, CLIP4 and MSC DNA methylation in endoscopic biopsies
DNA methylation landscape of hepatoblastomas reveals arrest at early stages of liver differentiation and cancer-related alterations
Monozygotic twins and triplets discordant for amyotrophic lateral sclerosis display differential methylation and gene expression
Varying levels of serum estradiol do not alter the timing of the early endometrial secretory transformation.
Integrated analysis of the gene expression profile and DNA methylation profile of obese patients with type 2 diabetes
Epigenome-wide cross-tissue correlation of human bone and blood DNA methylation - can blood be used as a surrogate for bone?
Epigenetic clock analysis of human fibroblasts in vitro : effects of hypoxia, donor age, and expression of hTERT and SV40 largeT
Rapamycin retards epigenetic ageing of keratinocytes independently of its effects on replicative senescence, proliferation and differentiation
Paradoxical epigenetic regulation of XAF1 mediates plasticity towards adaptive resistance evolution in MGMT-methylated glioblastoma
Quantitative methodology is critical for assessing DNA methylation and impacts on correlation with patient outcome
Comprehensive characterization, annotation and innovative use of Infinium DNA methylation BeadChip probes
Persistent DNA methylation changes associated with prenatal mercury exposure and cognitive performance during childhood
Ultra-high dimensional variable selection with application to normative aging study: DNA methylation and metabolic syndrome
Preconception urinary phthalate concentrations and sperm DNA methylation profiles among men undergoing IVF treatment: a cross-sectional study
SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions
Longitudinal genome-wide DNA methylation analysis uncovers persistent early-life DNA methylation changes
Analysis of repeated leukocyte DNA methylation assessments reveals persistent epigenetic alterations after an incident myocardial infarction
Genome-wide DNA methylation comparison between live human brain and peripheral tissues within individuals
DNA methylation signature of smoking in lung cancer is enriched for exposure signatures in newborn and adult blood
Epigenome-wide DNA methylation in placentas from preterm infants: association with maternal socioeconomic status
Screening for genes that accelerate the epigenetic aging clock in humans reveals a role for the H3K36 methyltransferase NSD1
Genome-wide DNA methylation analysis of heavy cannabis exposure in a New Zealand longitudinal cohort.
Epigenetic prediction of complex traits and mortality in a cohort of individuals with oropharyngeal cancer.
Genome-Wide DNA Methylation in Peripheral Blood and Long-Term Exposure to Source-Specific Transportation Noise and Air Pollution: The SAPALDIA Study
Methylation changes in the TFAP2E promoter region are associated with BRAF mutation and poorer overall & disease free survival in colorectal cancer
Cross-tissue integration of genetic and epigenetic data offers insight into autism spectrum disorder
Somatic mutations and promotor methylation of the ryanodine receptor 2 is a common event in the pathogenesis of head and neck cancer
Subgroup-specific outcomes of children with malignant childhood brain tumors treated with an irradiation-sparing protocol
Blood DNA Methylation and Aging: A Cross-Sectional Analysis and Longitudinal Validation in the InCHIANTI Study.
Pediatric bithalamic gliomas have a distinct epigenetic signature and frequent EGFR exon 20 insertions resulting in potential sensitivity to targeted kinase inhibition.
DNA methylation study of Huntington's disease and motor progression in patients and in animal models
Comprehensive analysis of diverse low-grade neuroepithelial tumors with FGFR1 alterations reveals a distinct molecular signature of rosette-forming glioneuronal tumor
Mutant IDH1 gliomas downregulate phosphocholine and phosphoethanolamine synthesis in a 2-hydroxyglutarate-dependent manner
Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease
Systematic evaluation of DNA methylation age estimation with common preprocessing methods and the Infinium MethylationEPIC BeadChip array
Improved filtering of DNA methylation microarray data by detection p values and its impact on downstream analyses
Small extracellular vesicles deliver miR-21 and miR-217 as pro-senescence effectors to endothelial cells
Steroid hormones regulate genome-wide epigenetic programming and gene transcription in human endometrial cells with marked aberrancies in endometriosis.
Altered mechanisms of genital development identified through integration of DNA methylation and genomic measures in hypospadias
Germline-driven replication repair-deficient high-grade gliomas exhibit unique hypomethylation patterns
Spatial intratumoral heterogeneity and temporal clonal evolution in esophageal squamous cell carcinoma
Epigenome-wide cross-tissue predictive modeling and comparison of cord blood and placental methylation in a birth cohort
Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types
Prenatal maternal antidepressants, anxiety, and depression and offspring DNA methylation: epigenome-wide associations at birth and persistence into early childhood
Placental CpG Methylation of Inflammation, Angiogenic, and Neurotrophic Genes and Retinopathy of Prematurity
No genome-wide DNA methylation changes found associated with medium-term reduced graphene oxide exposure in human lung epithelial cells
A DNA methylation clock associated with age-related illnesses and mortality is accelerated in men with combat PTSD
Accelerated epigenetic aging in adolescents from low-income households is associated with altered development of brain structures
DNA Methylation in Inflammatory Pathways Modifies the Association between BMI and Adult-Onset Non-Atopic Asthma
Maternal Intake of n-3 Polyunsaturated Fatty Acids During Pregnancy Is Associated With Differential Methylation Profiles in Cord Blood White Cells
DNA methylation and adiposity phenotypes: an epigenome-wide association study among adults in the Strong Heart Study
Epigenome-wide association study of total serum immunoglobulin E in children: a life course approach
Serum dioxin and DNA methylation in the sperm of operation ranch hand veterans exposed to Agent Orange
Interaction Among Sex, Aging, and Epigenetic Processes Concerning Visceral Fat, Insulin Resistance, and Dyslipidaemia
Use of the Illumina EPIC methylation array for epigenomic research in the crab-eating macaque (Macaca fascicularis).
Accelerated Epigenetic Aging and Methylation Disruptions Occur in Human Immunodeficiency Virus Infection Prior to Antiretroviral Therapy
Genome-wide DNA methylation analysis of peripheral blood cells derived from patients with first-episode schizophrenia in the Chinese Han population
Evidence for the placenta-brain axis: multi-omic kernel aggregation predicts intellectual and social impairment in children born extremely preterm.
Association between epigenetic age acceleration and depressive symptoms in a prospective cohort study of urban-dwelling adults
Integrated Epigenome, Exome, and Transcriptome Analyses Reveal Molecular Subtypes and Homeotic Transformation in Uterine Fibroids
Accelerated epigenetic aging in adolescents living with HIV is associated with altered development of brain structures.
Sperm DNA methylation mediates the association of male age on reproductive outcomes among couples undergoing infertility treatment.
De novo DNA methyltransferase activity in colorectal cancer is directed towards H3K36me3 marked CpG islands.
Blood-based epigenetic estimators of chronological age in human adults using DNA methylation data from the Illumina MethylationEPIC array
Integrated digital pathology and transcriptome analysis identifies molecular mediators of T-cell exclusion in ovarian cancer
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.
Phase I trial of TRC102 (methoxyamine HCl) in combination with temozolomide in patients with relapsed solid tumors and lymphomas
Prenatal Multivitamin Use and MTHFR Genotype Are Associated with Newborn Cord Blood DNA Methylation.
Identification of epigenetic memory candidates associated with gestational age at birth through analysis of methylome and transcriptional data.
Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.
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