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Genotyping hundreds of samples using SNP microarrays. How to design the assay? - (Jul/07/2011 )

Hi all! I'm a microarray beginner and I'd appreciate your help...

My purpose is to design an association study involving 200 family trios (~600 samples) and investigate a possible association between SNPs/tagSNPs (located in 6 different genes) and Attention Deficit Hiperactivity disorder.

I could use microarrays for genotyping...I don't know which platform I'll use yet but my questions are related with the study design:

- Which methods can I use to label the target DNA, namely each SNP?
- Can I genotype all the 600 samples and analyze all the SNPs simultaneously in a single microarray assay? Each "spot" of the array would correspond to a different sample and withing each spot there are immobilized probes complementar to all the SNPs?
- Please can someone highlight me about how to run a SNP microarray assay in this situation?

Very nooby questions but I'm really confused :(

-Andreia Marques-


I´m new in the forum and only see your post today...... but do you already start?