The CGI offers the Illumina Methylation EPIC v2 Bead Chip for genome-wide methylation analyses in human samples. The EPIC v2 Bead Chip targets ~930K unique methylation sites across the genome, including:

• CpG islands
• Non-CpG (CHH) methylated sites identified in human stem cells sites
• ENCODE open chromatin and enhancers
• FANTOM5 enhancers
• DNase hypersensitivity sites
• miRNA promoter regions
• differentially methylated sites identified in tumor versus normal samples for multiple cancers
• enhancers and super-enhancers identified by ChIP-Seqin cancer and cell line samples
• differentially accessible chromatin regions identified in primary human cancers using ATAC-Seq. 

Data from the EPIC v2 Bead Chip can be used to assess differential methylation across samples, detecting loss of imprinting or CpG island methylation, deriving DNAge or linking methylation changes to gene transcription (LINK OUT) and/or SNPs and structural variants (LINK OUT). 

Starting with at least 500ng of DNA (including FFPE using Infinium FFPE QC and DNA Restoration Kits), we process samples using the Zymo EZ DNA Methylation Kit for bisulfite conversion. Each array supports up to 8 samples and arrays are scanned either on the Illumina NextSeq 550 or Illumina iScan system. Data is processed through GenomeStudio for QC prior to sharing the data.

Third party Bioconductor packages offer the most functionality for downstream analysis, with many packages available in R for normalization and differential analysis of methylation data. If you would like full data analysis for your EPIC v2 data, contact the Computational Biology Core for a quote.