population (http://www.ncbi.nlm.nih.gov/SNP/) or had a minor allele frequency of > 0.01 in the CADD sample in our previous work (Ehringer et al. 2007)) were included. Genomic DNA was extracted from buccal or blood cells and amplified with primer extension preamplification (Anchordoquy et al. 2003) or using the REPLI-g kit according to the manufacturers protocol (Qiagen, Valencia, California). TaqMan assays were used for SNP genotyping according to the manufacturer’s instructions (Applied Biosystems, Foster City, California). Polymerase Chain Reaction (PCR) reactions were set up with a Biomek® 3000 Laboratory Automation Workstation (Beckman Coulter Inc, Brea, California) and cycled in an ABI GeneAmp® 9700 PCR thermocycler (Applied Biosystems, Foster City, California) or ABI PRISM® 7900 (Applied Biosystems, Foster City, California). The ABI PRISM® 7900 was used to analyze PCR products. Initially, the genotype clusters were auto-called by the Applied Biosystems TaqMan® Genotyper software (Applied Biosystems, Foster City, California), then visually examined by two independent lab personnel. DNA samples with overall call rates <90% were excluded. All SNPs were genotyped in a subset of samples in replicate reactions to determine the genotyping error rate. Five SNPs (rs1127313, rs7543174, rs2072660, rs3787140 and rs3787138) had an error rate above 1% and thus were excluded from further
