# 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](https://www.illumina.com/content/dam/illumina/gcs/assembled-assets/marketing-literature/cpg-loci-identification-tech-note-m-gl-00921/cpg-loci-identification-tech-note-m-gl-00921.pdf)
* Product Files:
  * [Infinium MethylationEPIC BeadChip Product Files](https://support.illumina.com/array/array_kits/infinium-methylationepic-beadchip-kit/downloads.html)
  * [Infinium HumanMethylation450K BeadChip Product Files](https://support.illumina.com/array/array_kits/infinium_humanmethylation450_beadchip_kit/downloads.html)

\
\
\ <br>

|                                                                                                                                                                                                                                                                                                                                                                   |
| :---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
| *For any feedback or questions regarding this article (Illumina Knowledge Article #5501), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000005501%20-%20Microarray%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |