In the present analyses, linkage results were stronger overall for SNPs than for microsatellites. We found higher LOD scores and more narrowly defined linkage peaks with SNPs for both the quantitative and qualitative phenotypes (Figures 1 and 2). For the neurophysiology phenotype at the main linkage peak near 130 MB, the Illumina and Affymetrix markers produced LOD scores of 3.22 and 2.53, respectively, and the microsatellite markers gave a LOD score of 2.76. Using the sparse Illumina map the LOD score was 2.68. For the alcohol dependence phenotype at the linkage peak near 101 MB, the Illumina and Affymetrix markers gave LOD scores of 4.08 and 3.69, while the microsatellite markers had a LOD score of 3.09. The sparse Illumina map gave a LOD score of 4.11.
