What issues should be considered in selecting SNPs?
NCBI-designated “double-hit” or “submitter-validated” SNPs are more likely to succeed. It is advisable to use “Illumina-validated” SNPs from dbSNP and to avoid SNPs that are not validated (dbSNP category 0) or are missing heterozygosity values. If you want to use “tag” SNPs, you must keep in mind that a definitive list of such markers is not available at this time. Also, tags will differ depending on population, etc. There are several Web sites that can help with tag SNP selection. As each site has pluses and minuses, you will want to familiarize yourself with these before deciding on a particular site. Additional issues to consider when picking SNPs are whether the SNP is polymorphic in your population, whether it is in a repeated and polymorphic region of the genome, whether there are other known SNPs near the target SNP, etc. A poster describing the genotyping center’s experience with Illumina Golden Gate chemistry SNP selection is available here.
