GEO DataSets

(Submitter supplied) We developed a comprehensive analysis pipeline to conduct Epigenome-wide Association Studies (EWAS) using the Illumina Infinium HumanMethylation450 BeadChip, based on data from 2,664 individuals, and 36 samples measured in duplicate. We propose new approaches to quality control, data normalisation and batch correction through control-probe adjustment, and demonstrate that these improve data-quality. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

2711 Samples

Download data: TXT

(Submitter supplied) This study performed a genome-wide methylation analysis of positively isolated CD19+ B cells in rheumatoid arthritis (RA) and healthy controls. The Ilumina HumanMethylation450 BeadChip was uset to obtain the methylation levels at >400,000 CpG sites. Samples include 49 RA patients and 73 healthy controls.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

122 Samples

Download data: IDAT

(Submitter supplied) The pathophysiology of intervertebral disc (IVD) degeneration is not entirely understood; however, environmental and endogenous factors under genetic predisposition are considered to initiate the degenerative changes of human IVDs. Aberrant epigenetic alterations play a pivotal role in several diseases, including osteoarthritis. However, epigenetic alternations, including DNA methylation, in IVD degeneration have not been evaluated. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

16 Samples

Download data: IDAT, TXT

(Submitter supplied) In this study, we examined the association of DNA methylation with metabolic traits in humans using adipose tissue samples from the Metabolic Syndrome in Men (METSIM) cohort. The METSIM cohort has been thoroughly characterized for longitudinal clinical data of metabolic traits including a 3-point oral glucose tolerance test, cardiovascular disorders, diabetes complications, drug and diet questionnaire, as well as high density genotyping, and genome-wide expression in adipose. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

205 Samples

Download data: TXT

(Submitter supplied) (1) In clinical practice and biomedical research populations are often divided categorically into distinct racial and ethnic groups. In reality, these categories comprise diverse groups with highly heterogeneous histories, cultures, traditions, religions, as well as social and environmental exposures. While the factors captured by these categories contribute to clinical practice and biomedical research, the use of race/ethnicity is widely debated. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL16304

573 Samples

Download data: TSV

(Submitter supplied) Illumina Infinium Human Methylation (HM) BeadChips are a widely used platform for measuring genome-scale DNA methylation, particularly in relation to epigenetic GWAS (EWAS) studies. The methylation profile of human samples can be assessed accurately and reproducibly using the HM27 BeadChip (27,578 CpG sites) or its successor, the HM450 BeadChip (485,577 CpG sites). To date no mouse equivalent has been developed greatly hindering the application of this methodology to the wide range of valuable murine models of disease and development in existence. more...

Organism:

Mus musculus; Homo sapiens

Type:

Methylation profiling by genome tiling array

Platforms:

GPL8490 GPL13534

15 Samples

Download data: TXT

(Submitter supplied) Genome wide DNA methylation profiling in infant's blood from a mother/child cohort in The Gambia. The main variables of the analyses were the intra-uterine exposure to aflatoxin B1 (AFB1) and the season of conception. The Illumina Infinium HumanMethylation 450k Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in whole peripheral blood obtained at 3-6 months of age. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

124 Samples

Download data: CSV, TXT

(Submitter supplied) We performed a comparative study of European and Asian populations using Illumina HM450K. We found that the majority of Infinium probes, which differentiated two examined groups, had SNPs in their target sequence. We investigated the impact of those SNPs on methylation readouts by Illumina HM450K Array. Our study clearly demonstrates that SNP variation existing in the genome, if not accounted for, may lead to false interpretation of the methylation signal differences suggested by some of the Illumina Infinium probes.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

36 Samples

Download data: IDAT, TXT

(Submitter supplied) Abstract Background: Schizophrenia is a severe, highly heritable, neuropsychiatric disorder characterized by episodic psychosis and altered cognitive function. Despite success in identifying genetic variants associated with schizophrenia, there remains uncertainty about the causal genes involved in disease pathogenesis and how their function is regulated. Insights into the functional complexity of the genome have focussed attention on the role of non-sequence-based genomic variation in health and disease. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

847 Samples

Download data: CSV

(Submitter supplied) Background: Schizophrenia is a severe, highly heritable, neuropsychiatric disorder characterized by episodic psychosis and altered cognitive function. Despite success in identifying genetic variants associated with schizophrenia, there remains uncertainty about the causal genes involved in disease pathogenesis and how their function is regulated. Insights into the functional complexity of the genome have focussed attention on the role of non-sequence-based genomic variation in health and disease. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

675 Samples

Download data: CSV

(Submitter supplied) Smoking-associated DNA hypomethylation has been observed in blood cells and linked to lung cancer risk. However, its cause and mechanistic relationship to lung cancer remain unclear. We studied the association between tobacco smoking and epigenome-wide methylation in non-tumor lung (NTL) tissue from 237 lung cancer cases in the Environment And Genetics in Lung cancer Etiology study, using the Infinium HumanMethylation450 BeadChip. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: BED, BW

(Submitter supplied) Smoking-associated DNA hypomethylation has been observed in blood cells and linked to lung cancer risk. However, its cause and mechanistic relationship to lung cancer remain unclear. We studied the association between tobacco smoking and epigenome-wide methylation in non-tumor lung (NTL) tissue from 237 lung cancer cases in the Environment And Genetics in Lung cancer Etiology study, using the Infinium HumanMethylation450 BeadChip. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

11 Samples

Download data: TXT

(Submitter supplied) Genome wide DNA methylation from peripheral white blood cells (PWBCs) from individuals from different cohorts included in the MENA project. Samples included 474 individuals (DiOGenes-UNAV n=52, OBEPALIP n=29, Food4Me-UNAV n=39, GEDYMET n=57, ICTUS n=7, NUGENOB-UNAV n=22, PREDIMED-UNAV n=116, RESMENA n=44, OBEKIT n=96, and NormoP n=12). The Illumina Infinium 450k Human DNA methylation Beadchip or Infinium MethylationEPIC Beadchip (for OBEKIT) was used to obtain DNA methylation profiles across approximately 450,000 CpGs in these samples.

Organism:

Homo sapiens

Type:

Methylation profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL16304 GPL21145

474 Samples

Download data: IDAT, TXT

(Submitter supplied) Monozygotic (MZ) twin pair discordance for childhood-onset Type 1 Diabetes (T1D) is ~50%, implicating roles for genetic and non-genetic factors in the aetiology of this complex autoimmune disease. Although significant progress has been made in elucidating the genetics of T1D in recent years, the non-genetic component has remained poorly defined. We hypothesized that epigenetic variation could underlie some of the non-genetic component of T1D aetiology and, thus, performed an epigenome-wide association study (EWAS) for this disease. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

100 Samples

Download data: TXT

(Submitter supplied) DNA methylation analysis of 68 glioblastoma specimen of patients treated within clinical trials, 5 samples of normal brain tissue (non-tumor brain) and 4 tumor-derived glioma sphere lines. The data was used to identify changes in DNA methylation which contribute to the aberrant of expression of HOX transcription factors. Our group had previously demonstrated that expression of HOX genes was associated with increased resistance to chemo-radiotherapy and worse outcome in GBM patients Keywords: Disease state comparison

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

77 Samples

Download data: IDAT

(Submitter supplied) Genetic and environmental risk factors contribute to periodontal disease, but the underlying susceptibility pathways are not fully understood. Epigenetic mechanisms are malleable regulators of gene function that can change in response to genetic and environmental stimuli, thereby providing a potential mechanism mediating risk effects in periodontitis. The aim of this study is to identify epigenetic changes across tissues that are associated with periodontal disease.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

480 Samples

Download data: IDAT, TXT

(Submitter supplied) The pooled sample method is used in epigenomic research and expression analysis and is a cost-effective screening approach for small amounts of DNA. Evaluation of the pooled sample method in epigenomic studies is performed using the Illumina Infinium Methylation 450K BeadChip array; however, subsequent reports on the updated 850K array are lacking. A previous study demonstrated that the methylation levels obtained from individual samples were accurately replicated using pooled samples but did not address epigenome-wide association study (EWAS) statistics. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL23976

4 Samples

Download data: CSV, IDAT

(Submitter supplied) There is increasing evidence that interindividual epigenetic variation is an etiological factor in common human diseases. Such epigenetic variation could be genetic or non-genetic in origin, and epigenome-wide association studies (EWASs) are underway for a wide variety of diseases/phenotypes. However, performing an EWAS is associated with a range of issues not typically encountered in genome-wide association studies (GWASs), such as the tissue to be analyzed. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

22 Samples

Download data: TXT

(Submitter supplied) There is increasing evidence that interindividual epigenetic variation is an etiological factor in common human diseases. Such epigenetic variation could be genetic or non-genetic in origin, and epigenome-wide association studies (EWASs) are underway for a wide variety of diseases/phenotypes. However, performing an EWAS is associated with a range of issues not typically encountered in genome-wide association studies (GWASs), such as the tissue to be analyzed. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

28 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array; Methylation profiling by high throughput sequencing

Platform:

GPL13534

22 Samples

Download data