A map of the positions of the genotyped SNPs relative to the microsatellite markers was created with Fastlink. Variance component methods were used to recalculate LOD scores using SOLAR v4.0.7 with the identity by descent provided through pedigree information and estimating multipoint identity by descent sharing probabilities (Almasy and Blangero, 1998). Variance component linkage analysis uses correlation in the phenotype to partition out variance between relative pairs into the effects of the genes in the region of interest, additive genetic effects of other genes, and non-shared environmental variance. To account for the heterogeneity evident in the dataset, a calculation assuming locus heterogeneity was made using the HLOD (heterogeneity LOD) score to identify the cause of the lowered peak at the end of chromosome 10.
