DNA was extracted from the buffy coat fraction of centrifuged blood using the QIAmp Blood Kit (Qiagen, Chatsworth, CA). The primary genotyping technique was Taqman SNP allelic discrimination by means of an ABI 7900HT (Applied Biosystems, Foster City, CA) and the primers and probes used were designed by Applied Biosystems: 1919A>T (rs1417938), 2667G>C (rs1800947), 3014G>A (rs1130864), 3872C>T (rs1205), 4362A>T (rs3093080), 4741G>C (rs3093068), 5237A>G (rs2808630), and 5606G>T (rs3093071). Replicate quality control samples were included and genotyped with 100% concordance. Cases were not perfectly matched to controls because a few subjects could not be genotyped with this platform, but genotype call rates did not differ between cases and controls. We initially genotyped the NHS, and then conducted a replication study in the HPFS. Among NHS, the minor allele frequencies for 4362A>T (0.6% cases, 1.1% controls) and 5606G>T (1% cases, 0.5% controls) were very low; thus, we did not further genotype them in the HPFS. The remaining 6 SNPs were selected for final analyses.
