Epigenetics and handling the results

[peacounter]

hi everybody,
I have a problem with the interpretation of my methylation-screening-results, and I hope anybody can help me answer some fundamental questions.

I performed successful the screening and could observe methylation of the CpGs in the promoter-region of my gene between 0 and 100% (I analyzed 83CpGs in total). The problem is, that one chromosome is “silenced” by methylation (chromosomal imprinting) and I can not distinguish between the “imprinted” and “unimprinted” chromosome.

Also, the rate of methylation at the imprinted chromosome can vary between 0 (unmethylated) and 100% (full-methylated) and is unknown to me. (for example: if the imprinted gene would ALWAYS be 100% (but for sure in fact it is not!), then I could (in theory ) substract 50% of the total methylation-rate that I had measured and get the methylation-rate of my gene on the un-imprinted chromosome.)

Well, for sure I searched in literature for a solution, how to handle my data. In every literature I read, no one ever mentioned the fact, that they have also detected the methylation of the imprinted chromosome. And no one every discussed this fact (as far as I know…).

Only two situations are easy to interpret: really weak methylation (0-10%) or very strong methylation (90-100%). In these cases we can say, that both genes on both chromosomes show either weak or strong methylation.

But, how to handle for example 50% methylation?
….Maybe both alleles on both chromosomes are 25% methylated?
….Or one of them is 100%, while the other is completely unmethylated?
….Or something in between?

Also, I would be interested in how to set the limit for a weak, moderate and strong methylation? I often found: weak (0-33%), moderate (34-66%) and strong (67-100%). Is this a wide-range accepted classification?

I performed the study by pyrosequencing, I already asked the company to help me with the interpretation-problem. but they just said, "that they have only a technical service and no scientific service, and that it is my problem how to interpret the results". really kind company!

anyway, I really hope someone can help me by interpreting my results.

Best regards
Stefan

[JackBean]

But, how to handle for example 50% methylation?
….Maybe both alleles on both chromosomes are 25% methylated?

If each had 25%, that would mean 25% in total If you get 50% methylated, one allele is methylated while other is not. How is this hard to understand?

[SecondAmendment]

where did you get the tests done?