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differential methylation hybridisation (DMH)
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Differential methylation hybridisation (DMH) is a microarray-based technique used to analyse DNA methylation on a global scale. This method was first described by Huang et al. (Hum Mol Genet, 1999, 8:459-470). It allows for the identification of changes in DNA methylation patterns that is commonly observed in cancer and other disease states.

DMH experiments can be performed using the Agilent platforms.

Agilent offers human and mouse (CpG island and promoter) arrays for DMH experiments, as well as custom designed arrays for any species. With the Agilent platform, two methods can be used to examine DMH: MeDIP, an immunocapturing approach to enrich methylated DNA, and a method that involves methylation sensitive restriction enzymes and PCR amplification.

The UHNMAC CpG island (CGI) arrays can also be used to perform DMH experiments. CGIs are genomic regions rich in the CpG dinucleotide pattern. It is estimated that about 60% of human genes and 47% of mouse genes are associated with CGIs, usually in 5`end, and that the vast majority of CGIs are within -500 to +1500 bp of the transcription start site.

For the DMH experiment service, we ask that researchers prepare the genomic DNA and perform methylation-sensitive restrictions and PCR amplification, or perform MeDIP (for Agilent platform).

Quick questions:
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What kind of samples should be submitted and how much is required?

We require a minimum of 6 μg of each PCR amplified genomic DNA sample per array. As well, we ask that you submit an additional 1μg of each PCR amplified genomic DNA sample for analysis on an agarose gel and, if necessary, for OD purposes.

We ask that users of the DMH service complete up to, and including, step 2.2.4 of the Yan et al. protocol. If you choose another protocol, we still ask that you send PCR amplified genomic DNA that has been column purified. Users of the service should also complete the appropriate checklist and submit the information with the samples. Please contact us for more information.

Why use the DMH technique with CpG island microarrays?

Methylation of CpG islands located in promoter regions regulates the transcription of downstream genes. It has been shown that DMH using CpG island arrays is useful in classifying tumors according to their methylation profiles.

What is used as a control for a DMH experiment?

Typically, a sample that has been treated with a methylation sensitive enzyme is co-hybridised with a sample that has not been treated with a methylation sensitive enzyme or a methylation insensitive enzyme.