Hello,
I am wondering what technology I should use best for the detection of methylated DNA. More specifically, I am investigating the MLH1 gene and was thinking of using either MS-HRM, pyrosequencing, qMSP, MSRE analysis. What would you recommend in term of convenience, efficiency and price?
Many thanks :)
This article could help you a little bit.
Article DNA Methylation Analysis: Choosing the Right Method
Regards
Saurabh
Dear Frédérique,
You might have some restrictions on some methods based on the genetic motive you're analyzing. Very dense CpGs would make it hard to find CpG free primers binding sites which is needed for Pyrosequencing, and HRM. I worked a lot on the MLH1 promoter and used HRM and Pyrosequencing. If you want, you can check if the regions I've successfully analyzed are also of interest to you.
HRM: Two very good assays for the MLH1 promoter in my PhD thesis
https://publications.ub.uni-mainz.de/theses/volltexte/2017/100001696/pdf/100001696.pdf
PSQ: Three PSQ assays Article Vitamin and antioxidant rich diet increases MLH1 promoter DN...
good luck,
Best, Olivier
Hello, I recommend to you nested methylation PCR for detection methylation of MLH1 promotor region and methylation specific MLPA. I used it my PhD thesis
good luck
Different technologies have different pros and cons, and I think your choice depends on your research objectives and accuracy requirements. Pyrosequencing can rapidly quantify one or more methylation sites in one test, which is the most ideal verification method at present. Therefore, this technique has gradually become the gold standard of data analysis in epigenetics research, but it is relatively expensive in the case of multiple samples.
I may offer to try our GLAD-PCR-assay - new method of DNA methylation analysis without bisulfite.
We used it recently for the development of epigenetic diagnostic tests.
http://epigene.bio/en/medica2019/
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