Illumina’s MethylationEPIC array interrogates the methylation status of over 850,000 cytosines in the human genome. Since Because the MethylationEPIC array is closely related to the Infinium HumanMethylation450 BeadChip, the steps presented in this document can be applied to either platform. The analysis laid out in the tutorial is based on detection of differentially methylated CpG sites and their subsequent filtering and annotation.

• Importing and normalizing methylation data
• Annotating the samples
• Performing exploratory data analysis
• Detecting differentially methylated loci
• Visualizing the methylation at each locus
• Obtaining methylation signatures
• Biological interpretation
• Detecting differentially methylated CpG islands regions

This tutorial illustrates how to:

The data set accompanying this document consists of sixteen human samples processed by Illumina MethylationEPIC arrays. The data set is taken from a study of DNA methylation in human B cells and  B cells infected with Epstein-Barr virus (EBV). 

Infecting B cells with EBV in vitro transforms them, making them capable of indefinite growth in vitro. These immortalized cell lines are referred to as lymphoblastoid cell lines (LCLs). LCLs behave similarly to activated B cells, making them useful for expanding T cells in vitro. Because EBV is a carcinogen and immortalized cell growth is a hallmark of cancer, examining the effects of EBV transformation on B cell DNA methylation might shed light on the roles of DNA methylation in tumor development.  

The data files can be downloaded from Gene Expression Omnibus using accession number GSE93373 or by selecting this link - Differential Methylation Analysis data set. To follow this tutorial, download the 32 .idat files (note that two .idat files are generated for each array) and unzip them on your local computer using 7-zip, WinRAR, or a similar program.