For the IFIH1 gene in Table 5, we applied the effective sample size method both globally or pedigree-type-specifically. Using Eqs.(2,5,6,7), and by a conservative use of relatives in assuming all relatives to be sibships, we have the averaged effective number of allele counts: 2(67+512·2/(1+0.5)+64·3/(1+2×0.5)+8·4/(1+3×0.5)+5/(1+4×0.5)+8/(1+7×0.5) ≈ 1724, or, the average sample reduction of α = 861.9111/1328 ≈ 0.649. The ESS-based method leads to a p-value of 0.0023 in chi-square test, improved upon the p-value of 0.0179 when only one case per family is used (second line in Table 5). At the significance level of 0.01, adding correlated samples in this dataset makes an insignificant result significant.
