Positive Control for Methylation Studies

Recently, methylation arrays have been introduced as an easy tool to scan the genome for methylation differences.

Without a positive control, how do you know your protocol is working?

Bock C, et al (PMID 16520826 ) reported one gene PDE9, to be highly methylated in lymphocytic DNA. It might be used as a positive control gene. Like so called house-keeping genes, the methylation of this gene, however, might be regulated under some special circumstances.

A second method calls for spike-in. One can artificially spiking his samples with SssI methylase methylated DNA. SssI methylates all CpG resides with high efficiency.