Figure 1

Power comparisons of Pathway-PDT with the PLINK set-based test and ALIGATOR. Disease models for the power analyses included two additive models, Model 1 and Model 2, with 10 causal variants at minor allele frequencies near 0.2 and odds ratios of 1.2 and 1.3, respectively. A pathway with 24 genes, which contain 285 variants, for a total of 500 replicates of 500 nuclear families (two parents and three siblings, where at least one sibling is affected) was used to evaluate power. For scenario 1, we assumed all 500 families had parents. For scenario 2, we assumed 50% of the families had missing parents. Gene weights were set to be 1 as used by GSEA and Wang et al. study [17, 18]. Default parameters in PLINK and ALIGATOR were used for the simulations.