Measuring global methylation using real time PCR - (Apr/20/2010 )
does anyone have experience measuring global methylation levels using real-time PCR? How sensitive is this method (for LINE-1, ALU etc.)? Who has designed the best assay?
The primers designed by Issa's group seem to work really well for pyrosequencing and I have seen them being used in a number of papers.
However, I am not sure to what extent SNP's for the repeat family members could mask the methylation results you are getting, it is certainly something you should keep in the back of you mind when performing such experiments.
I agree that SNP's can cause problems. While I was reading some articles about pyrosequencing, I noticed that people more frequently use pyrosequencing, when analyzing methylation status of repetitive elements, than qMSP. I dont fully understand reasons for this.