In this study we compared the linkage signals obtained through the use of limited number of microsatellites and two sets of relatively dense SNP maps in nonparametric multipoint linkage of age at onset of alcoholism across the 22 autosomal chromosomes. Although there was neither significant nor suggestive evidence of linkage [8] for age at onset of alcohol dependence from any of the three sets of genetic markers in this study, there were significant differences in the distributions and strength of linkage signals between microsatellites and the SNPs. We observed that the only linkage signal above 1.00 LOD score obtained with microsatellites (LOD = 1.43 at 243 cM) was on chromosome 1, and this was weaker than any of those obtained with Illumina (LOD = 1.67 at 215 cM) and Affymetrix (LOD = 1.80 at 230 cM) SNPs on the same chromosome. Furthermore, linkage signals detected with SNPs on other chromosomes ranged from LOD scores 1.33 to 1.95 at different positions on chromosomes 3, 4, 7, 16, 18, and 21. The highest LOD scores from SNPs are 1.95 on chromosome 7
