Nevertheless, there was a noticeable loss of genetic signal as measured by mean χ2 and the genomic inflation factor. The greatest decrease was observed for the down-sampled GWAS on SMOK (Δ mean χ2 = 2.06–3.15 = – 1.09; – 34.6%), while the decrease for CANN was less pronounced (– 1.3%). Similar decreases were observed for the genomic inflation factor: – 25.9% and – 1.0% for SMOK and CANN, respectively. The overall stability we observed for the heritability estimates and attenuation ratios suggest that the factor loadings in the down-sampled Genomic SEM factor analysis will resemble those of the original paper (Step 2). The decrease in genetic signal in SMOK and CANN should translate into larger standard errors in the factor analysis and loss of statistical power to detect SNP effects in the multivariate GWAS of EXT-minus-23andMe (Step 3).
