I am not sure why some Illumina probe ids start with ch, e.g ch.8.128185533F in the Illumina Epic methylation array. Most of the CpGs start with cg, e.g cg25251478. What are the ids starting with ch? and are these CpGs?
These are probes targeting non-CpG sites. They measure methylation in Cs which do not belong to CpG sites. You will also see "rs." probes. These do not measure methylation, they target known SNPs.
Thank you for the response. May I know, what is the purpose of targeting these non-CpG sites?
Well, although (in mammals) DNA methylation occurs mostly at CpG sites, it is known to occur at other genomic cytosines albeit at lower levels, in tissues such as brain or ESCs (see this reference, for example), indicating that it could have functional roles. Thus, it may be of interest to researchers to screen levels of non-CpG methylation.
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