Why Different naming for this 450k CpG in IlluminaHumanMethylation450kanno.ilmn12.hg19

Question

[christophersugai]

Hello all, I have a question regarding the annotation of cpgs in the lluminaHumanMethylation450kanno.ilmn12.hg19 library. During my analysis, a cpg with the 'Name' ch.1.xxxxxxxF (where x's are numbers) rather than the normal cgxxxxxxxx. I also happen to get another probe ch.21.xxxxxxR. What do these mean? Why are they named differently? I am having a hard time finding anything online, and any info on what to research would be greatly appreciated!

Answer 1

[Charles Warden]

The probe name indicates the methylation context, which can be either CpG or CpH (or a SNP probe with an rsID).

For example, ch.9.7776528F has hg19 coordinate chr9:7786528. The probe is for a CpH on the forward strand, so that position is a "C" and the next nucleotide is an "A" (H=A, C, or T).

In contrast, cg00000029 is a methylated C in the CpG context with hg19 poistion chr16:53468112, where that nucleotide is a "C" and the next nucleotide is a "G".