To properly reduce spurious positive evidence of association, it is important to get accurate estimates of relationships. Our results indicate that estimated kinship coefficients can be more accurate than are pedigree-based or posterior kinship coefficients. The reasons for this improved accuracy are that pedigree-based kinship coefficients allow no variability within a class of relative pair, and posterior kinship coefficients do not allow for sources of relationship other than the pedigree. The one exception to this is the case of unrelated pairs, for which MLEs can be biased because only non-negative values are allowed for estimated kinship coefficients, thereby resulting in overcorrection of the test statistic. An ad hoc method might be considered to avoid overcorrecting for such related pairs, such as setting kinship coefficients to 0 for pairs with estimated kinship coefficients smaller than a specific threshold. This might improve the over correction of inflated false positive rates. Another concern in estimating relatedness is potential violation of the HWE assumption which might affect the resulting MLEs if there is Hardy-Weinberg Disequilibrium (HWD) in the sample. We have not formally evaluated
