Regulome

Illumina Infinium MethylationEPIC

DNA methylation profiling using microarrays relies on sodium bisulfite genome conversion, which converts unmethylated cytosines into uracils, followed by specific hybridization onto functionalized beads (Infinium I and II) and fluorescent single-base extension at single-nucleotide resolution.

Evolution from Version v1.0 to Version v2.0 (Zhuang et al., 2025).

The Infinium MethylationEPIC v1.0 covered approximately 850,000 CpG sites, mainly targeting CpG islands, promoters, and coding gene regions.The EPIC v2.0 array (930K+) introduces major enhancements:

• Expanded Genomic Coverage:Addition of over 180,000 probes targeting regulatory elements, including enhancers, open chromatin regions, and CTCF-binding sites.
• Optimized Probe Design: Removal of over 140,000 underperforming probes or those susceptible to non-specific hybridization biases caused by single-nucleotide polymorphisms (SNPs).
• Genome Realignment and Quality Control: Comprehensive re-annotation against the GRCh38/hg38 reference genome build and inclusion of internal probe replicates to assess intra-array reproducibility.

Application to FFPE Samples

Analyzing formalin-fixed paraffin-embedded (FFPE) tissues presents technical challenges due to cross-linking and severe DNA fragmentation. To overcome this limitation, the protocol incorporates a dedicated FFPE DNA restoration process (Infinium HD FFPE). Following bisulfite conversion, degraded DNA undergoes an enzymatic repair reaction prior to whole-genome isothermal amplification. This step rescues damaged templates, providing high-quality probe call rates equivalent to those achieved with fresh-frozen DNA samples.

Mise à jour : Août 2026