The Illumina Methylation Assay uses 'BeadChip' technology to generate a comprehensive genome-wide profiling of human DNA methylation. It quantifies methylation levels at various loci within the genome.

The pipeline can automatically call differentially methylated probes from methylation arrays (450K or EPIC). This pipeline consists of five analysis steps. Loading data is always the first step. After data read-in, probes can be filtered based on detection P-values, chromosomal location, presence of single nucleotide polymorphisms in the probe sequence and cross-hybridization. After obtaining beta-values, beta-values are further normalized to adjust the data for bias introduced by the Infinium type 2 probe design. If batch effects are present, ComBat is used to correct for these effects. Finally, Differentially Methylated Probes (DMPs) are identified. The above process is performed using the R package ChAMP.

The schematic diagram of Methylation BeadChip pipeline is as follows:

Software and references:

• ChAMP: ChAMP: updated methylation analysis pipeline for Illumina BeadChips