marker but associated with sex at p < 1e-7; 8) had a significant batch effect at p < 1e-7; or 8) there were more than 2 heterozygous X chromosome calls for males or mitochondrial calls for anyone. In total, 32,153 (5.7%) of the 559,982 SNP markers were eliminated by these screens, with the majority (3.6%) being eliminated because of low MAF. Samples were eliminated if: 1) they had > 5000 no-calls; 2) had a low GenCall score; 3) had extreme heterozygosity or homozygosity; or 4) represented a sample mix-up or we could not confirm known genetic relationships. In total, 160 (2.2%) of the total genotyped sample of 7438 failed one or more of these criteria, with the majority (1.7%) failing because of low call rate. Of the 3672 twins initially enrolled in the study, 3365 provided usable genotypes, of which 3231 were Caucasian and used for the present analysis. Only those individuals with genotypes were used in the present study analyses. Those twins with genotypes versus those without did not differ significantly on measures of nicotine use (CPD, days smoked per month, or DSM-IIIR nicotine dependence symptomatology) or alcohol use, with the exception that individuals with genotypes drank slightly more
