In Saccone et al. (4), we conducted a sensitivity analysis of how changes in the user’s prioritization scores effect the rankings, and we performed simulations to assess the difference between selecting SNPs after a GWAS using just P-value rankings and using the GIN method. Neither of these analyses was designed to use a ‘training set’ to establish predictive properties. We found the rankings are not very sensitive to changes in the scores and that in general with default scoring parameters there is about a one order of magnitude difference between SNPs selected by P-value and those selected by the GIN method.
