Figure 3. Power loss from the inclusion of non-causal SNPs with complex LD structure using an LD approach to include inter-genic SNPs.

Figure 3 illustrates behavior observed for different methods when using an LD aware approach to assigning inter-genic SNPs to genes. In particular, an LD-aware approach limits the number of inter-genic SNPs assigned to the set, which reduces the number of non-causal SNPs assigned to the set if no causal SNPs are located outside of the gene. While GATES, LR and LR-PC showed improved power from the LD-aware approach, VEGAS-sum illustrated a loss in power from the addition of non-causal SNPs in LD with causal intra-genic SNPs.