We examined the two-point and multipoint genome-wide LOD score distributions of each marker set against the asymptotic null distribution using quantile-quantile (Q-Q) plots. Under the null hypothesis of no linkage, the likelihood ratio test statistic that is given by (2 ln 10) × LOD is expected to be distributed as a 1/2:1/2 mixture of a variable and a point mass at 0 [7]. To calculate empirical cutpoints for the maximum two-point and multipoint LOD scores for each marker set, we simulated 200–500 replicates of the chromosome 1 data using gene-dropping methods implemented in MERLIN version 0.10.2 [9]. Marker data are simulated under the null hypothesis of no linkage or association to the observed phenotype, keeping the marker informativeness, spacing, missing data patterns, and pedigree structure the same. These randomly generated datasets were then imported back into SOLAR for variance components analysis.
