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Characterization of the Illumina EPIC array for optimal applications in epigenetic research targeting diverse human populations
The Illumina EPIC array is widely used for high-throughput profiling of DNA cytosine modifications in human samples, covering more than 850,000...
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Characterising sex differences of autosomal DNA methylation in whole blood using the Illumina EPIC array
BackgroundSex differences are known to play a role in disease aetiology, progression and outcome. Previous studies have revealed autosomal epigenetic...
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A systematic evaluation of normalization methods and probe replicability using infinium EPIC methylation data
BackgroundThe Infinium EPIC array measures the methylation status of > 850,000 CpG sites. The EPIC BeadChip uses a two-array design: Infinium Type I...
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Low reliability of DNA methylation across Illumina Infinium platforms in cord blood: implications for replication studies and meta-analyses of prenatal exposures
BackgroundThere is an increasing interest in the role of epigenetics in epidemiology, but the emerging research field faces several critical...
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The ENmix DNA methylation analysis pipeline for Illumina BeadChip and comparisons with seven other preprocessing pipelines
BackgroundIllumina DNA methylation arrays are high-throughput platforms for cost-effective genome-wide profiling of individual CpGs. Experimental and...
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An EPIC predictor of gestational age and its application to newborns conceived by assisted reproductive technologies
BackgroundGestational age is a useful proxy for assessing developmental maturity, but correct estimation of gestational age is difficult using...
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Batch-effect detection, correction and characterisation in Illumina HumanMethylation450 and MethylationEPIC BeadChip array data
BackgroundGenomic technologies can be subject to significant batch-effects which are known to reduce experimental power and to potentially create...
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An effective processing pipeline for harmonizing DNA methylation data from Illumina’s 450K and EPIC platforms for epidemiological studies
ObjectiveIllumina BeadChip arrays are commonly used to generate DNA methylation data for large epidemiological studies. Updates in technology over...
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Repeatability of methylation measures using a QIAseq targeted methyl panel and comparison with the Illumina HumanMethylation450 assay
ObjectiveIn previous studies using Illumina Infinium methylation arrays, we have identified DNA methylation marks associated with cancer...
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Incorporation of DNA methylation quantitative trait loci (mQTLs) in epigenome-wide association analysis: application to birthweight effects in neonatal whole blood
BackgroundEpigenome-wide association studies (EWAS) have helped to define the associations between DNA methylation and many clinicopathologic and...
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Epigenome-wide methylation analysis of colorectal carcinoma, adenoma and normal tissue reveals novel biomarkers addressing unmet clinical needs
BackgroundBiomarker discovery in colorectal cancer has mostly focused on methylation patterns in normal and colorectal tumor tissue, but adenomas...
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Differential methylation EPIC analysis discloses cisplatin-resistance related hypermethylation and tumor-specific heterogeneity within matched primary and metastatic testicular germ cell tumor patient tissue samples
Testicular germ cell tumors (TGCTs) are among the most common solid malignancies in young-adult men, and currently most mortality is due to...
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A validated restriction enzyme ddPCR cg05575921 (AHRR) assay to accurately assess smoking exposure
Background & MethodsIn this study, a novel restriction enzyme (RE) digestion-based droplet digital polymerase chain reaction (ddPCR) assay was...
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DNA methylation profile of inflammatory breast cancer and its impact on prognosis and outcome
BackgroundInflammatory breast cancer (IBC) is a rare disease characterized by rapid progression, early metastasis, and a high mortality rate.
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Evaluating Reliability of DNA Methylation Measurement
DNA methylation is a widely studied epigenetic phenomenon. Alterations in methylation patterns influence human phenotypes and risk of disease. The...
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DNA methylation sites in early adulthood characterised by pubertal timing and development: a twin study
BackgroundPuberty is a highly heritable and variable trait, with environmental factors having a role in its eventual timing and development. Early...
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Creation and validation of the first infinium DNA methylation array for the human imprintome
BackgroundDifferentially methylated imprint control regions (ICRs) regulate the monoallelic expression of imprinted genes. Their epigenetic...
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Investigating the effects of maltreatment and acute stress on the concordance of blood and DNA methylation methods of estimating immune cell proportions
BackgroundImmune cell proportions can be used to detect pathophysiological states and are also critical covariates in genomic analyses. The complete...
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Analysis of cancer-associated fibroblasts related genes identifies COL11A1 associated with lung adenocarcinoma prognosis
BackgroundThe treatment of lung adenocarcinoma is difficult due to the limited therapeutic options. Cancer-associated fibroblasts play an important...
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The X-factor in ART: does the use of assisted reproductive technologies influence DNA methylation on the X chromosome?
BackgroundAssisted reproductive technologies (ART) may perturb DNA methylation (DNAm) in early embryonic development. Although a handful of...
