Question about Illumina Infinium 450K

Question

[99syzygy]

Hi Bioinformaticians,

Could you possibly help me understand in simple terms what is a "probe" (ex: cg06928838 (GSTP1 gene)) in an Infinium HumanMethylation450K BeadChip and how is a probe "made"? I mean to get methylation values.

Am I correct in saying that probes target specific loci of genes, not the whole gene to get a methylation value?

I would appreciate all responses. Thanks!

Answer 1

[Charles Warden]

You are correct: the 450k array provides methylation for CpG sites (or genotypes for some sites, and some methylation for individual sites that aren't in the CpG context).

You'll need to use some sort of method to define regions from your site signal (or at least have site annotations and your own way of looking for consistent signal among nearby sites).