Similar to the Guam data analysis, a Q – Q plot of p-values in the Kosrae data analysis reveals that the χ2 test results in a high false positive rate, but these false associations diminished in two corrected χ2 tests (Figure 6F). Since, in the Kosrae study, the pedigree information of the case group was available, the corrected χ2 tests were performed with ϕped. However, since the known genealogy does not include complete information of relatedness among individuals, the corrected χ2 tests work better with ϕest than with ϕped. The 1% and 5% quantiles of the χ2 test are 0.0014 and 0.0095, and the 1% and 5 % quantiles of the corrected χ2 test with ϕest are 0.0095 and 0.036, much closer to their nominal levels. We had 50 significant markers at significance level 0.05 with the χ2 test, but 22 of these markers were not significant after correcting relatedness by using ϕest.
