Following Price et al. [15], the confounding effect of PS can be corrected by adjusting for a defined set of PCs. The typical method adjusts for L top-ranked PCs, with L being either pre-determined (e.g., 10), or the number of significant PCs (e.g., those with P-value <0.05 based on the Tracy-Widom test). To evaluate this strategy, we estimated over-dispersion factors for association tests (1 d.f. Wald test) based on results on the set of 241,238 genomic control SNPs with adjustment for varying numbers (from 1 to 10) of top ranked PCs (Table 5). We observe that the over-dispersion factor does not necessarily decrease as the number of adjusted PCs increases. Table 5 also suggests that adjusting non-significant PCs does not appear to have a major impact on the inflation reduction
