When genotyping SNPs in a candidate gene, the number of SNPs to be genotyped is unlikely to exceed the hundreds. Such quantities are usually easily genotyped using low throughput, PCR-based methods 13. However, when genotyping a candidate region, the number of SNPs is likely be in the thousands. With increasingly large numbers of SNPs, it will be more cost efficient to conduct genotyping using high throughput array-based products, similar to those used in Genomewide association (GWA) studies. Such custom-made arrays are normally designed as multiplexes with a fixed number of markers that can be genotyped per chip (for example, Illumina's custom arrays are currently designed in panels of up to 1536 SNPs or >7800 SNPs and Affymetrix at present offers solutions for customized genotyping in configurations of 3K, 5K, 10K and 20K markers). The manufacturers of these panels also publish scores indicating the likelihood of genotype failure of individual SNPs on the relevant panel, thus helping the investigator choose a set of SNPs that will suffer minimal failure.
