To evaluate the performance of kinship estimation, we carried out a simulation study based on Scenario I. Multiallelic marker simulation was done without reference to the fixed disease status, thus representing genotypes generated under H0. The relationships in this sample are 150 parent-offspring (PO), 50 avuncular (AV), 100 grand parent-grand child (GG) and 50 first cousin (CO) pairs. Also, 124,400 unrelated pairs (UN) were included in the sample. For each individual, we simulated 400 microsatellite markers as described above and among these simulated markers, subsets of 50, 100, 200 and 400 markers were used to calculate MLEs of kinship coefficients using the EM algorithm. Allele frequencies were assumed unknown and sample allele frequencies were used for such estimation.
