As expected under polygenicity23, we observe inflation of the median test statistic in each GWAS (λGC,DEP = 1.36, λGC,NEUR = 1.24, λGC,SWB = 1.28; Supplementary Figure 4, Supplementary Table 6). The intercept estimates from LD score regression are all below 1.02, however, suggesting that nearly all of the observed inflation is due to polygenic signal14 (Supplementary Figure 5). When we report GWAS results, as in the SSGAC study11 we account for the potential bias due to this small amount of stratification by inflating the standard errors of our GWAS estimates by the square root of the LD score regression intercept.
