Methylation arrays
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00010002321 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:DNA methylation arrays (850K, Illumina)
| EGAD00010002608 | EGA
Project description:Functional Validation of Common Idiopathic Pulmonary Fibrosis Genetic Risk Variants [850k methylation arrays]
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Project description:The integration of genomic and epigenomic data is becoming increasingly popular as we try to gain better understanding of the complex mechanisms driving the development and progression of cancer. However, this results in increased cost and sample depletion, the latter being particularly important when considering intra-tumour heterogeneity. We therefore sought to investigate the possible utility of high-density DNA methylation arrays to assess both aberrant methylation as well as changes in gene copy number. Comparing CN (Copy Number) data derived from the Infinium Human Methylation 450K arrays with that generated on SNP arrays, we demonstrate the utility of the Infinium arrays to detect single copy alterations as well as homozygous deletions and high level amplification with the reliability of current gold standard platforms. Furthermore, we show that the gene centric design of the Infinium methylation arrays allows identification of small single gene alterations, which would not be detected using standard SNP array analysis. These results show that Infinium 450K methylation arrays provide a robust and economic platform for detecting copy number and methylation changes in a single experiment. The ability to integrate such data from the same sample is critical for cancer research and will improve our understanding of how complex genomic and epigenomic interactions are driving the development and progression of a malignant phenotype.
2016-05-31 | GSE48941 | GEO
Project description:Genome wide DNA methylation in blood, subcutaneous and omental visceral adipose tissue from two-step surgical approach (N=9) was analysed in patients with severe obesity using Illumina 850K EPIC technology before and after metabolic surgery (Leipzig Obesity BioBank (LOBB) cohort). Additionally, a validation blood cohort of patients with obesity undergoing metabolic surgery was analyzed for results validation.
2024-03-31 | E-MTAB-13564 | biostudies-arrayexpress
Project description:Illumina Infinium Epic Human DNA Methylation Beadchip V1.2.8 The Illumina Infinium Epic Human DNA Methylation Beadchip V1.2.8 is used to obtain DNA methylation profiles of about 850k CpG in osteoarthritis and normal cells to find differences, approximately 850k CpGs in osteoarthritis and normal cell
2021-05-18 | GSE174525 | GEO
Project description:Epic methylation arrays of DNMT1 inhibitor treated AML cell lines
| PRJNA557724 | ENA
Project description:Illumina Infinium DNA Methylation (5mC) profiling arrays are a popular technology to measure genome-scale distribution of 5mC at low cost and high throughput, especially in cancer and other complex diseases. Following the success of the HumanMethylation450 array (450k), Illumina released the MethylationEPIC array (850k) featuring increased coverage of enhancers in addition to regulatory regions primarily covered by the 450k (i.e. promoters, gene bodies). Despite its widespread use, the analysis of 850k data remains suboptimal as it mostly still relies on Illumina’s default annotation, which underestimates enhancers and long noncoding RNAs (lncRNAs). We thus developed an approach, based on ENCODE and LNCipedia databases, that greatly improves Illumina’s default annotation of enhancers and long noncoding transcripts. Comparisons between the re-annotated 850k and its precursor, the 450k, or RRBS, another high-throughput 5mC profiling technology, revealed that the 850k covers at least three times more enhancers and lncRNAs than the other two technologies. We further investigated the reproducibility of the three technologies and applied various normalisation methods to 850k data, showing that most of them reduce variability to a level below that of RRBS. When analyzed with our new annotation and normalization pipeline, profiling for 5mC changes in breast cancer biopsies with the 850k highlighted aberrant enhancers methylation as the predominant feature, confirming previous reports. In conclusion, our study provides an updated analysis pipeline for 850k data based on a refined probe annotation and normalization that allows for the improved analysis of methylation at enhancers and long noncoding transcripts.
2022-11-11 | GSE198627 | GEO
Project description:Illumina Infinium DNA Methylation (5mC) profiling arrays are a popular technology to measure genome-scale distribution of 5mC at low cost and high throughput, especially in cancer and other complex diseases. Following the success of the HumanMethylation450 array (450k), Illumina released the MethylationEPIC array (850k) featuring increased coverage of enhancers in addition to regulatory regions primarily covered by the 450k (i.e. promoters, gene bodies). Despite its widespread use, the analysis of 850k data remains suboptimal as it mostly still relies on Illumina’s default annotation, which underestimates enhancers and long noncoding RNAs (lncRNAs). We thus developed an approach, based on ENCODE and LNCipedia databases, that greatly improves Illumina’s default annotation of enhancers and long noncoding transcripts. Comparisons between the re-annotated 850k and its precursor, the 450k, or RRBS, another high-throughput 5mC profiling technology, revealed that the 850k covers at least three times more enhancers and lncRNAs than the other two technologies. We further investigated the reproducibility of the three technologies and applied various normalisation methods to 850k data, showing that most of them reduce variability to a level below that of RRBS. When analyzed with our new annotation and normalization pipeline, profiling for 5mC changes in breast cancer biopsies with the 850k highlighted aberrant enhancers methylation as the predominant feature, confirming previous reports. In conclusion, our study provides an updated analysis pipeline for 850k data based on a refined probe annotation and normalization that allows for the improved analysis of methylation at enhancers and long noncoding transcripts.
2022-11-11 | GSE198626 | GEO
Project description:Preeclampsia (PE) is a complex, heterogeneous disorder of pregnancy, demonstrating considerable variability in observed maternal symptoms and fetal outcomes. We recently identified five clusters of placentas within a large gene expression microarray dataset (N=330, GSE75010), of which four contained a substantial number of PE samples. However, while transcriptional analysis of placentas can subtype patients, we hypothesized that the addition of epigenetic information should reveal gene regulatory mechanisms behind the distinct PE pathologies. We, therefore, subjected 48 of our samples to Infinium Human Methylation 450K arrays and investigated relationships between the gene expression and DNA methylation data.
2018-03-07 | GSE98224 | GEO
Project description:DNA methylation profiling for 850k reannotation and normalization evaluation [850k]
| PRJNA816179 | ENA