checking whether SNP is covered by certain microArray?

Question

[Mathias]

Hi all

I'm assisting in retrieving some data, someone in our center is interested in ~90 specific human variants. We've got the option to retrieve an older set of genotyping data, originating from GWAS using different Illumina microArrays (e.g. humanhap300, humanhap550...).

I want to check whether those ~90 positions are captured by the microArrays used or not - we haven't got the actual data yet.

I'm a bit lost currently, seeing I haven't worked with microArray data or their analysis tools. Can someone point me in the right direction? Are there tools containing multiple array mappings, or will I need to look for packages per array - and if so, can anyone tell me if I'll even find mappings of those older arrays? If not, it's probably easier to simply download the actual GWAS data and see if the variants are in there?

Answer 1

[LChart]

You can grab the GPL files for the associated arrays - humanhap300 is here for instance: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL5677 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6980

you can query the rsid or position in that file -- though be careful as the positions are likely with respect to hg18

[Mathias]

Hi, thanks! I was looking at the support files from Illumina already, but couldn't easily find all the info I needed. Accessing that info through GEO is a good idea, awesome!