Finally, we note that LOKI assumes the markers are in linkage equilibrium (LD). However, substantial pair-wise LD exists between the SNPs, especially in the Affymetrix map. Considering all pairs of Affymetrix SNPs on chromosome 7, 59 pairs have a correlation greater than 0.9. For Illumina, 13 pairs have a correlation greater than 0.9. Recent work [10] suggests that when parental genotypes are unavailable, this linkage disequilibrium between SNPs can artificially inflate IBD estimates and may also inflate estimates of information content because the inflated IBD estimate has an artificially high precision. Although many of the COGA pedigrees have parental genotypes, we conjectured that a less dense SNP map might still contain most of the information. The Illumina map began with lower LD so we chose to reduce it (rather than the Affymetrix map) because fewer deletions would be required. We constructed a subset of 166 markers from the Illumina dataset on chromosome 7. Markers were deleted from the dataset if they had a D' value greater than 0.1 with nearby markers. When possible, we retained markers with the highest possible minor allele frequency. The results are presented in Figure 3.
