The Kobor lab, where I’m currently working, does a lot of epigenetics and have been working with the Illumina 450K Human methylation array. In some ways, it’s a stepping stone towards a next-gen platform, and in other ways, it’s still a perfectly valid platform all on it’s own. I’m not really an array person (yet?), but I can see the advantages when it comes to bisulfite sequencing – mapping with bisulfite treated DNA is a bit of a dark art. (I know it can be done, but it’s not ideal.)
Anyhow, they’ve undertaken an interesting project, with a few collaborators, to re-annotate the 450k methylation array, identifying probes that are give erroneous results due to the presence of snps or cross hybridization. They show it in action with a couple of data sets as well, so it’s not just a theory paper. Anyhow, it’s a quick, but interesting must-read for those interested in using the 450k human methylation array.
You can find it at http://www.epigeneticsandchromatin.com/content/6/1/4/abstract