ABSTRACT
Before discussing in detail the chemistries and platforms used to score SNPs, it is useful to consider the important characteristics of large-scale SNP analysis for drug discovery applications because the requirements in this setting are very different from those of a smaller scale research setting. As discussed above, though estimates vary for applications related to gene discovery, on the order of 100,000 SNP markers will have to be screened in thousands to tens of thousands of individuals. Thus, any single application will likely require the scoring of millions of SNPs. This scale of analysis involves particular consideration of issues of throughput and cost that will influence the choice of assay chemistry and analysis platform. Two issues that are especially important in this regard are the amenability of methods to automation and the multiplexed analysis of many SNPs in each sample.
