Epigenetics and handling the results

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    • #15961
      peacounter
      Participant

      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

    • #109149
      JackBean
      Participant

      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?

    • #109646
      SecondAmendment
      Participant

      where did you get the tests done?

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