each follow-up platform. For the purpose of our calculations, we assumed the Illumina Human660W-Quad platform would be used for genotyping 500,000 viable SNPs in stage 1 and Illumina’s GoldenGate 96, 384 and 1,536 SNP panels and Illumina’s Custom iSelect Infinium 7,600 and 16,720 SNP panels would be used as the follow-up platforms for stage 2. Given that genotyping costs are constantly changing, rather than using dollar amounts, we report the relative total cost of genotyping all study subjects based on current prices. Using the cost of genotyping 500,000 SNPs for an individual sample on a genome-wide panel as a baseline, the relative total cost of genotyping 16,000, 7,500, 1,500, and 100 SNPs for that sample were assumed to be 1/2, 1/3, 1/5, 1/10 and 1/12 of the cost, respectively, based on the most recent genotype prices at the CIDR genotyping facility (www.cidr.jhmi.edu/pricing.pdf).
