Details of data cleaning have been reported previously.27 In brief, SNPs were excluded owing to genotyping failure (23 SNPs), call rate less than 95% (9 SNPs), minor allele frequency less than 2% (47 SNPs), and Hardy-Weinberg equilibrium deviations (27 SNPs); 1430 SNPs were retained for analyses (Supplemental Table 2 shows the complete list). The mean call rate for 1294 non-opioid receptor SNPs remaining after data cleaning exceeded 99.9%. Samples of DNA from 1506 cases, 538 neighborhood controls, and 1500 ATR controls were genotyped. Data from samples were excluded owing to genotyping failure (1 ATR control), phenotypic-genotypic gender mismatch (1 case; 2 neighborhood controls), duplication due to participation in the project multiple times (29 cases; 3 neighborhood controls – phenotypic data from the most recent, non-pilot study interview were retained), and cryptic relatedness with identity by descent greater than 0.5 (17 cases, 4 neighborhood controls, and 4 ATR controls – individuals with the higher project identifier were excluded). The sample used for analyses consisted of 1459 cases, 531 neighborhood controls, and 1495 ATR controls.
