high to ensure that all of the SNPs that would have been detected at the overall level of significance with the Cox model are contained within this subset, for example, 1 × 10−4 if the overall significance threshold is 5 × 10−8. Prentice-weighted Cox models could then be fitted to this subset of SNPs, avoiding the vast computational time required to complete an entire GWAS using the Prentice-weighted Cox model, while obtaining accurate estimates of effect and inference (including P-values) for the SNPs of particular interest. This two-step procedure could also be applied in the cohort setting to reduce computational time.
