The proper identification of differentially methylated CpGs is central in most epigenetic studies. The Illumina HumanMethylation450 BeadChip is widely used to quantify DNA methylation; nevertheless, the design of an appropriate analysis pipeline faces severe challenges due to the convolution of biological and technical variability and the presence of a signal bias between Infinium I and II probe design types. Despite recent attempts to investigate how to analyze DNA methylation data with such an array design, it has not been possible to perform a comprehensive comparison between different bioinformatics pipelines due to the lack of appropriate data sets having both large sample size and sufficient number of technical replicates. Here we perform such a comparative analysis, targeting the problems of reducing the technical variability, eliminating the probe design bias and reducing the batch effect by exploiting two unpublished data sets, which included technical replicates and were profiled for DNA methylation either on peripheral blood, monocytes or muscle biopsies. We evaluated the performance of different analysis pipelines and demonstrated that: (1) it is critical to correct for the probe design type, since the amplitude of ...Continue Reading
The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores
Lineage-specific DNA methylation in T cells correlates with histone methylation and enhancer activity
Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts
MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis
Differential variability improves the identification of cancer risk markers in DNA methylation studies profiling precursor cancer lesions
Complete pipeline for Infinium(®) Human Methylation 450K BeadChip data processing using subset quantile normalization for accurate DNA methylation estimation
SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips
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Trans effects of chromosome aneuploidies on DNA methylation patterns in human Down syndrome and mouse models
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Power and sample size estimation for epigenome-wide association scans to detect differential DNA methylation
Cesarean delivery and hematopoietic stem cell epigenetics in the newborn infant: implications for future health?
Removing unwanted variation in a differential methylation analysis of Illumina HumanMethylation450 array data
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An epigenetic map of age-associated autosomal loci in northern European families at high risk for the metabolic syndrome
Monozygotic twins discordant for common variable immunodeficiency reveal impaired DNA demethylation during naïve-to-memory B-cell transition
Epigenetic modifications of the glucocorticoid receptor gene are associated with the vulnerability to psychopathology in childhood maltreatment
Identification of functionally methylated regions based on discriminant analysis through integrating methylation and gene expression data
Independent genomewide screens identify the tumor suppressor VTRNA2-1 as a human epiallele responsive to periconceptional environment
Pan-cancer stratification of solid human epithelial tumors and cancer cell lines reveals commonalities and tissue-specific features of the CpG island methylator phenotype
Considerations for normalization of DNA methylation data by Illumina 450K BeadChip assay in population studies
Report on the 2nd Annual Infinium Humanmethylation450 Array Workshop: 15 April 2013 QMUL, London, UK
Immortalization of T-cells is accompanied by gradual changes in CpG methylation resulting in a profile resembling a subset of T-cell leukemias
DNA methylation modifies urine biomarker levels in 1,6-hexamethylene diisocyanate exposed workers: a pilot study
Methylome-wide Analysis of Chronic HIV Infection Reveals Five-Year Increase in Biological Age and Epigenetic Targeting of HLA
Mitochondrial DNA Polymerase POLG1 Disease Mutations and Germline Variants Promote Tumorigenic Properties
seqlm: an MDL based method for identifying differentially methylated regions in high density methylation array data
Genome wide DNA methylation profiles provide clues to the origin and pathogenesis of germ cell tumors
Intra-Monozygotic Twin Pair Discordance and Longitudinal Variation of Whole-Genome Scale DNA Methylation in Adults
Comparison of pre-processing methodologies for Illumina 450k methylation array data in familial analyses
Methylation of SOCS3 is inversely associated with metabolic syndrome in an epigenome-wide association study of obesity
Global methylation profiling to identify epigenetic signature of gallbladder cancer and gallstone disease
Maternal Smoking during Pregnancy and DNA-Methylation in Children at Age 5.5 Years: Epigenome-Wide-Analysis in the European Childhood Obesity Project (CHOP)-Study
Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays
A novel cell-type deconvolution algorithm reveals substantial contamination by immune cells in saliva, buccal and cervix
Genetic, epigenetic and transcriptional variations at NFATC2IP locus with weight loss in response to diet interventions: The POUNDS Lost Trial.
The Role of DNA Methylation in Cardiovascular Risk and Disease: Methodological Aspects, Study Design, and Data Analysis for Epidemiological Studies
Genome-Wide Analysis of DNA Methylation and Fine Particulate Matter Air Pollution in Three Study Populations: KORA F3, KORA F4, and the Normative Aging Study
Defiant: (DMRs: easy, fast, identification and ANnoTation) identifies differentially Methylated regions from iron-deficient rat hippocampus
SIPA1L3 methylation modifies the benefit of smoking cessation on lung adenocarcinoma survival: an epigenomic-smoking interaction analysis
Associations among child abuse, mental health, and epigenetic modifications in the proopiomelanocortin gene (POMC): A study with children in Tanzania
Comparing genome-scale DNA methylation and CNV marks between adult human cultured ITGA6+ testicular cells and seminomas to assess in vitro genomic stability
The tissue-specific aspect of genome-wide DNA methylation in newborn and placental tissues: implications for epigenetic epidemiologic studies
Comprehensive mapping of the effects of azacitidine on DNA methylation, repressive/permissive histone marks and gene expression in primary cells from patients with MDS and MDS-related disease
Bioenergetics of acquired cisplatin resistant H1299 non-small cell lung cancer and P31 mesothelioma cells
Altered DNA methylation in neonates born large-for-gestational-age is associated with cardiometabolic risk in children
Ewastools: Infinium Human Methylation BeadChip pipeline for population epigenetics integrated into Galaxy.
Modular bioinformatics analysis demonstrates that a Toll‑like receptor signaling pathway is involved in the regulation of macrophage polarization
Epigenome-wide gene-age interaction analysis reveals reversed effects of PRODH DNA methylation on survival between young and elderly early-stage NSCLC patients
Loss of DIP2C in RKO cells stimulates changes in DNA methylation and epithelial-mesenchymal transition
Therapeutic efficacy of dimethyl fumarate in relapsing-remitting multiple sclerosis associates with ROS pathway in monocytes
Machine Learning-Based DNA Methylation Score for Fetal Exposure to Maternal Smoking: Development and Validation in Samples Collected from Adolescents and Adults
Immunosenescence-Related Transcriptomic and Immunologic Changes in Older Individuals Following Influenza Vaccination
DNA Methylation Profiles of Blood Cells Are Distinct between Early-Onset Obese and Control Individuals
Unraveling the Genomic-Epigenomic Interaction Landscape in Triple Negative and Non-Triple Negative Breast Cancer
Methylation Data Processing Protocol and Comparison of Blood and Cerebral Spinal Fluid Following Aneurysmal Subarachnoid Hemorrhage
Evaluation of commonly used analysis strategies for epigenome- and transcriptome-wide association studies through replication of large-scale population studies
KCNMA1 cooperating with PTK2 is a novel tumor suppressor in gastric cancer and is associated with disease outcome
Characterisation of DNA methylation changes in EBF3 and TBC1D16 associated with tumour progression and metastasis in multiple cancer types
Discrimination between human populations using a small number of differentially methylated CpG sites: a preliminary study using lymphoblastoid cell lines and peripheral blood samples of European and Chinese origin
Epigenetic methylation in Eosinophilic Esophagitis: Molecular aging and novel biomarkers for treatment response
Epigenetic-smoking interaction reveals histologically heterogeneous effects of TRIM27 DNA methylation on overall survival among early-stage NSCLC patients
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