As above, the experimental validation shows that the accuracy of the inference program can heavily impact the results of the dTDT and MH tests. The disagreement of results from these two tests on the real data could be attributed to several sources. First, the sample size of informative data is small. In total, we have 3,567 individuals from 453 EA families included for inference calculation. Within all these individuals, only 471 individuals were selected for SNP validation genotyping. This requires genotypes of more than 85% of individuals to be estimated. In addition, compared to the total number of SNPs, the number of microsatellite markers is also trivial (722 vs. 1 million).
