Direct comparisons between SNP-based and microsatellite-based results in this analysis were hindered by several factors. First, we used the genetic maps as provided to us, which were not aligned among the three marker sets. Further, the presence of linkage disequilibrium among SNPs can lead to inflated LOD scores [5]. However, we did not test the hypothesis of both linkage and association, since the average marker spacing was 600 kb and 210 kb for the SNP1 and SNP2 maps, respectively. Another limitation is that we calculated multipoint IBDs using an approximation method. Accuracy of IBD estimation can influence the power to detect linkage [10]. We considered using Markov chain Monte Carlo-based and exact methods for IBD estimation but encountered difficulties when attempting to analyze the large number of markers in the SNP maps, i.e., programs either skipped larger families or performed computations too slowly. It was encouraging, however, to see that our multipoint results from the highest density SNP map fit the expected distribution well. Perhaps the increased information content compensated for the loss of information in the multipoint IBD approximation.
