As with the computation of model χ2 outlined above, QSNP is calculated using a two-step procedure. In Step 1, a common pathway model is fit in which both factor loadings, the SNP effect on the common factor(s), and the residual variances of the common and unique factors are freely estimated (with one factor loading fixed to unity for factor identification and scaling). No paths representing direct effects of the SNP on the genetic components of the individual phenotypes are estimated. In Step 2, a common plus independent pathways model is specified, in which the factor loadings and the SNP effect on the common factor are fixed to the values estimated in Step 1, and direct effects of the SNP on individual indicators and the residual variances of each indicator are freely estimated. Supplementary Figure 30 depicts this model, as applied to a single common factor model, with parameters that are fixed in Step 2 depicted in red and those that are freely estimated in Step 2 depicted in black.
