Genotyping was carried out using one of two different methods: an oligonucleotide ligation, PCR assay for simultaneous genotyping of 48 single nucleotide polymorphisms (SNPs) in a multiplexed, 384-well plate method, SNPlex (Applied Biosystems), and a single-step homogeneous SNP genotyping using a 5′-nuclease assay, TaqMan (Applied Biosystems). The SNPlex assay, pooling 48 different SNPs into a single genotyping assay, was applied to DNA samples processed in 384-well plate format through an automated protocol which included: SNP-specific oligonucleotide ligation, PCR amplification, immobilization, hybridization, elution, and separation and fluorescent detection on an ABI 3730xl capillary instrument. For all SNPs genotyped by SNPlex, the call rate on the 932 individuals in the UT and WI cohort was 99.26% after 35 individuals were excluded for low genotyping rates (>10% missing genotypes). TaqMan genotyping was processed in 384-well plate format on the five SNPs in the combined UT-WI-LHS cohorts, and the call rate on 2,006 individuals was 99.42% after 29 individuals were excluded for missing genotypes. For the five SNPs genotyped by TaqMan and SNPlex methods in 236 individuals, there were three discordant calls, all in
