We tested 1,252,387 SNPs for association with four personality scales; Harm Avoidance, Novelty Seeking, Reward Dependence and Persistence. The Quantile-Quantile (QQ) plots for each scale, illustrating the observed p-values for the autosomal associations in relation to the expected p-values (based on the number of tests, under the null hypothesis of no association), are presented in Figure 2. Lambda (a measure for quantifying population stratification effects) for all variables is close to 1, indicating the residual population stratification effects are minimal. For three of the four scales we found fewer extremely low (at the very low end of the distribution) p-values than expected by chance. We checked whether this was due to the fact we use family data by running a GWAS with only independent individuals in Merlin as well as in PLINK (Purcell, et al., 2007). We also checked whether it was due to high LD between SNPs by testing only independent SNPs in Plink. The QQ-plots from these analyses did not differ markedly from the original analyses.
