To investigate the performance of kinship estimation, we estimated kinship coefficients based on both simulated data and CEPH family data. The simulated data was used to evaluate performance for use with multiallelic marker and with varying available relationship information, and the CEPH data was used to evaluate performance for use with denser SNP markers. We also performed a simulation study to explore the null distribution of p-values and to compare the power of the corrected χ2 tests using different types of kinship coefficients with the classical χ2 test. Four kinship coefficients were considered: actual (ϕact), pedigree-based (ϕped), estimated (ϕest), and posterior (ϕpost) kinship coefficients. The actual kinship coefficient, ϕact, is computed based on the underlying truth in the simulation and the pedigree-based kinship coefficient, ϕped, is assigned from a known pedigree structure. The estimated kinship coefficient, ϕest, is the maximum-likelihood estimate computed based on genome data only, without pedigree information. The posterior kinship coefficient, ϕpost, is also an estimated coefficient, but based on both genome data and pedigree information. In all cases, we used the average of posterior kinship coefficients
