illumina - (Aug/18/2005 )

for illumina paltform, after we selected the candidate genes, how to select the SNPs on each genes?

Big question!
You have decided to use a candidate gene approach.
What I did was to look up all the candidate genes in the SNPper database (snpper.chip.org). I decided if I would like to include all the SNPs (introns, 5'UTR, exon and so forth), and send a list of the final rs# to Illumina where they told me which ones could actually be designed on their platform. Thereafter I had 10 selection rounds where I decreased the numbers of SNPs to fit the assay.
So depending on which SNPs you find most interesting and how many SNPs you can put in your assay differnet approaches can be made