indicated strong linkage signals on chromosome 7, and relatively strong linkage signals on chromosome 2. Results for these two chromosomes (excluding the erroneous genotypes) and one-LOD confidence intervals of these peaks are shown in Figure 1. In general, the peaks were better defined by the SNP scan, where peaks from the SNP scan had narrower 1-LOD intervals than those from the microsatellite scan (SNP 1-LOD interval was 20 cM, compared with a 40-cM 1-LOD interval with the microsatellites for the peak on chromosome 7 around 100 cM. For the peak on chromosome 7 around 60 cM, the SNP 1-LOD interval was 9 cM, compared with a 16-cM 1-LOD interval with the microsatellites. One-LOD intervals for the peaks on chromosome 2 around 10 cM had similar width for the SNPs and the microsatellites.) The NPL scores decreased in the SNP 1-cM scan for all but one region on chromosome 2 at about 18 cM compared to those from the SNP full set scan. With the NPL cutoff of 2, several regions on chromosomes 2, 7, and 12 that were significant in the SNP full set scan were no longer significant in the SNP subset scan. We also noted that the effect
