We also investigated the performance of kinship estimation based on diallelic markers by estimating kinship coefficients of CEPH families based on the real data, single-nucleotide polymorphism (SNP) markers from the version 10 CEPH data at ftp://ftp.cephb.fr/ceph_genotype_db/. We selected 91 individuals of 12 pedigrees with more than 80% genotyped markers. To investigate the effect of use of different numbers of markers, three marker panels were used: 500 SNP markers, 5,000 SNP markers, and all of the 16,977 SNP markers of the whole genome. In the first two panels, the markers were randomly chosen from the 16,977 SNP markers. Kinship coefficients were estimated for all possible pairs of 91 individuals based on these two marker panels. The entire pedigree information was known and estimated kinship coefficients were compared with pedigree-based kinship coefficients.
