To account for linkage disequilibrium (LD; the correlation between SNPs) in our heterogeneous sample, our second method for estimating false positives was to calculate the number of statistically significant associations observed when genotypes were randomly assigned to individuals (i.e., a permutation analysis). By randomly assigning intact genotypes to individuals (and keeping each individual’s sensation seeking and covariate scores the same as in the real association tests), we were able to observe the number of false-positive results obtained when keeping allelic distributions and LD patterns in our sample intact.
