High throughput methylation mapping - Infinium or other? - (May/30/2011 )

I would like to asses DNA methylation on a genome wide scale.
Please if you can advise me with your experience which method is currently best?

I am thinking about Infinium (450 BeadChip or Infinium HumanMethylation27). The plan is to send a set of samples, so the provider would do whole genome analysis, which I would afterwards validate through qPCR and immunohistochemistry on a greater sample number.


What are your experiences with whole genome scale methylation studies?


Thank you in advance,

lmg

Hi Img,

I'm also working with Human methylation 450 K (Illumina). As i see your post in related to 30 may 2011 and I'm wondering whether you have any result from your expriment after analysis till now because I'm very interested to learn about these analysis method. I have my raw data generated in GenomeStudio but don't know how I have to look at the data and so on. I appreciate any suggestion if you did analysis.

Thanks,
Noushin

Dear lmg and Noushin

The infinium array is indeed a widely used technology to study genome-wide methylation. However this technology has its disadvantages... this technology is biased since it uses pre-defined probes and it only focuses on a limited set of methylation sites.

We have set up a company that offers genome-wide methylation sequencing services (based on next-generation sequencing technology). We have done a head-to-head comparison with the infinium 450K array and we see that this array picks up only 5% of what we tend to pick up with our technology!! Secondly our technology is unbiased and will pick up methylation anywhere in the genome. By using this technology we have been able to show that methylation appears to have an effect on alternative splicing and thereby affecting protein function. This is mainly a result of methylation located in exon 1 or exon 2 regions. The infinium mainly focuses on promotor regions and therefore completely ignores this (and miRNA, lncRNA, etc effects) which is not the case for our technology.

We offer a full-scope service including sample shipment, methylation capture, next-gen sequencing, data cleaning and mapping (including access to your mapped data in a visualisation software).

I just wanted to inform you that there are other options besides the infinium array. Feel free to visit our website or to contact us directly.

http://www.nxt-dx.com

Maarten

If you have infinium data already, I would look up minfi also consider peak-based correction for type I and type II chemistry.