Project description:Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling [MethylationEPIC]
Project description:We performed a genome-wide methylation study in whole-blood DNA from 404 ischemic stroke patient cohort, distributed across 3 ischemic stroke subtypes: Large-artery atherosclerosis (n=132), Small-artery disease (n=141) and Cardio embolic (n=127) . Illumina HumanMethylation450 BeadChip array was used to measure DNA methylation in CpG sites. We performed a genome-wide methylation study in whole-blood DNA from 185 ischemic stroke patient cohort. Illumina HumanMethylation450 BeadChip array was used to measure DNA methylation in CpG sites.
Project description:An Infinium microarray (Illumina HumanMethylation450 BeadChip) was used to generate DNA methylation data from human tissue samples.
Project description:Genome wide DNA methylation profiling of normal whole blood samples. The data consist of 100 samples with Illumina HumanMethylation450 BeadChip data.
Project description:Genome wide DNA methylation profiling of normal whole blood samples. The data consist of 43 samples with Illumina HumanMethylation450 BeadChip data.
Project description:Genome-wide DNA methylation level was studied to identify the clustering of correlated DNA methylation at CpGs in whole blood. We used Illumina HumanMethylation450 BeadChip array to identify the clustering of correlated DNA methylation in whole blood from normal individuals from Baltimore Longitudinal Study of Aging (BLSA).
Project description:Genome wide DNA methylation profiling of ATRTs and extracranial malignant rhabdoid tumors (eMRTs) samples harboring mutations in SMARCA4 and of small cell carcinoma of the ovary hypercalcemic type (SCCOHT) was performed . The Illumina Infinium HumanMethylation450 BeadChip and the Illumina Infinium MethylationEPIC arrays were used to obtain DNA methylation profiles across approximately 450,000 CpGs and 850,000 CpGs, respectively, in FFPE derived tumor samples. In total n=14 ATRT, n=6 eMRTs and n=28 SCCOHT samples were analyzed.
Project description:DNA methylation is the most well-known epigenetic mark and CpG methylation is critical for many cellular processes and human disorders. Cancer has highlighted the relevance of an aberrant DNA methylation landscape, including promoter CpG island hypermethylation-associated silencing of tumor suppressor genes and the presence of DNA hypomethylation blocks, but an altered DNA methylome is also now evident in other pathologies. However, progresses in delivering complete DNA methylation maps are compromised by the high price and labor and interpretation-consuming aspects of the single nucleotide methods nowadays used for whole genome bisulfite sequencing analyses. Following the success of the industry-leading HumanMethylation450 BeadChip (Infinium) methylation microarray that assess close to 450,000 CpG sites (450K), we have biologically and technically validated the newly developed MethylationEPIC BeadChip (Infinium) microarray that covers over 850,000 CpG methylation sites (850K). The 850K microarray contains >90% of the original 450K methylation sites, but add new 350,000 CpGs located in enhancers regions identified by the ENCODE and FANTOM5 projects. Herein, we show that the 850K DNA methylation array demonstrates high reproducibility for the previously analyzed CpG sites included in the 450K microarray; it is consistent among technical replicates; it is reliable in the matched study of fresh frozen vs formalin-fixed paraffin-embeded samples; and it is useful for both 5-methylcytosine and 5-hydroxymethylcytosine determination. The provided validation milestones highlights the value of the MethylationEPIC BeadChip as an informative and useful tool for the analyses of the DNA methylation profile of the human genome.
