For genome-wide DNA methylation analysis, outside of cost what is the advantage/disadvantage of the 450k array versus WGBS? When performing genome-wide DNA methylation studies what features are the most important to you and are there any other assays you prefer?
In my opinion choosing a method always depends on the structure of your analysis. 450K chips are only applicable for humans so if you have a mouse model this won't be the best choice. Of course there is also the cost factor and in what resolution you want your data. If you are interested in common genes and regions to analyze 450k chips should suffice. More robust and specific results can be obtained with a single base resolution obtained by WGBS. And as Anna said RRBS is a compromise between those two methods.
So I would say it always depends on your project setup (organism, which regions are you interested, etc.) and the results you expect.
Hope this helps :)
In addition to the excellent points raised previously, while WGBS and RRBS do provide single-base resolution DNA methylation information, the analyses of these data are more bioinformatically intensive. The HM450 data, while only representing less than 1% of all CpGs in the human genome, are more easily digestible and the data can be handled in excel or another spreadsheet. HM450 is also much more cost effective, and if one is interested in understanding the DNA methylation changes in human cancers, the same platform was used for TCGA DNA methylation data production, and serves as an excellent validation set for over 30 cancer types.
DNA Methylation Data Analysis Workshop
How to use bisulfite-treated sequencing to study DNA methylation
When?
12-15 November 2019
Where?
Berlin, Germany
Link?
https://www.ecseq.com/workshops/workshop_2019-07-NGS-DNA-Methylation-Data-Analysis
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