What are the ch probes in the MethylationEPIC Array manifest?

The non-cg labelled probes in the MethylationEPIC Array manifest are non-CpG methylation sites in the genome. These probes are carried over from the Infinium HumanMethylation450K Array.

• The probe name gives the chromosome and genomic coordinate and indicates in which strand, Forward (F) or Reverse (R), the cytosine is located.

• The probe names with the ch- prefix denote a methylated C followed by an A, T, or C (CA, CT, or CC) rather than the traditional CG, which is considered ambiguous.

• The DNA Nucleotide Code H, based on the IUPAC codes, is equivalent to either base A, T, or C. Instead of CpG, ch probes are C followed by A, T, or C, as denoted by the IUPAC codes in which the H = A, T or C, hence the probe name ch.

Examples: ch.5.44854267F ch.16.2085963R ch.11.1111744F

For further information, search for Knowledge Base article Infinium MethylationEPIC Manifest Column Headings.

Additional Resources

• Technical Note: CpG Loci Identification

• Product Files:

  • Infinium MethylationEPIC BeadChip Product Files

  • Infinium HumanMethylation450K BeadChip Product Files

For any feedback or questions regarding this article (Illumina Knowledge Article #5501), contact Illumina Technical Support [e-mail].