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What defines a DMR - the impact of profiling methods.

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What defines a DMR - the impact of profiling methods.

Postby CIMPhenotype » Fri Sep 28, 2012 11:26 am

Hi there,

I've been looking at ways to map probe level data from methods that profile CpGs at single base pair resolution to define region level data. With MeDIP-Seq/MeDIP-Chip, the low resolution of analysis basically yields results in terms of DMRs, but with bisulfite sequencing or Illumina CpG array data there is a clear distinction between methylation variable positions and differentially methylated regions. Would you happen to know of any approaches that have sought to define the relationship?

Cheers!

CIMPhenotype
 
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Re: What defines a DMR - the impact of profiling methods.

Postby Feehery » Sun Sep 30, 2012 5:31 am

Hi-
The only real way to accurately define a region of interest with regard to CpG methylation is to do old school bisulfite sequencing of the area of interest. This may include a two-step PCR of the bisulfite DNA, followed by cloning of the fragment and sanger sequencing, or direct labeling followed by Ion Torrent PGM or MiSeq Illumina. The stuff coming off MeDip may be just too heterogeneous to make heads or tails from the data.

Rick

Feehery
 
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