We have compared the genome-wide linkage analyses based on the microsatellites and the SNPs. We used the software MERLIN to conduct nonparametric linkage analysis to map regions associated with alcoholism on 22 autosomal chromosomes. The results from the two scans had good concordance in general, although more significant signals were obtained using the SNPs versus the microsatellites. Both scans suggested strong linkage evidence on chromosomes 2 and 7, where the two scans agreed especially well. The microsatellite scan had a peak at the marker D7S820 at 107.5 cM with an NPL score of 2.56 on chromosome 7, and the SNP scan had a peak at the marker tsc0046246 at 100.9 cM with an NPL score of 2.81. For chromosome 2, the microsatellite scan had a peak at the marker D2S1329 at 4.9 cM with an NPL score of 2.13, and the SNP scan had a peak at the marker tsc0056805 at 243.6 cM with an NPL score of 2.80. The differing results observed in the two scans were likely explained by the difference between the IC in the microsatellites and
