I work in a clinical research studying global methylation in normal and cancer tissue using the Illumina 450k array. 

My question is pretty straightforward: I am looking for resources (ie. documentation, articles, etc.) that detail how the probe annotations have been derived for the manifests/anotation files available. I am interested in specific experiments and procedures used to come up with these annotations.

Specifically, I would like to know how Enhancer status was defined (what assay(s) were used? How was it determined these regions were associated with the listed gene?). 

In case it is helpful, I have been using the manifest implemented in the Bioconductor package minfi.

cheers,

Sean

Clinical Research Division

Fred Hutch

smaden@fredhutch.org

UPDATE 7/7/15: An Illumina rep pointed me to a handy bulletin on the Illumina website with details on the annotation. It says Enhancer status is determined informatically by Encode, however it is still not clear which track(s) correspond to what was used. Also it would be great to find a reference to the specific algorithm(s) in question. S

Hi Kasper,

Thanks for your quick response. I checked with Illumina, and you are correct; they cite ENCODE as the source for enhancer status in their official annotation. However, there wasn't too much specification as to what work at ENCODE was cited to make their manifest, at least for enhancer status. In their microarray bulletin, details on manifest headings had this to say: 

Enhancer: Predicted enhancer elements (determined by the ENCODE Consortium using informatics) are marked “True”.

The bulletin is from Oct 2014, so I take it this information can't be more recent than last year. UCSC has several relevant tracks for gene regulation, some of which seem more concordant with the probe enhancer annotation than others. So it's still not apparent exactly where the information is from. I'll have to dig a bit more and reach out to ENCODE.

Thanks again, Sean