These analyses provide a comparison of the use of microsatellite and SNP markers in linkage analysis for quantitative and qualitative phenotypes. For both phenotypes linkage results were stronger overall for SNPs than for microsatellites. Does this represent a true or a false increase in the evidence of linkage? The SNP maps have higher information content than microsatellite maps [8], and this may contribute to the higher LOD scores. However, there is also substantial pair-wise LD throughout the chromosome. Ignoring this and treating each SNP as an isolated marker may erroneously elevate sharing estimates. For the alcohol dependence phenotype, the LOD scores obtained using the dense and sparse Illumina maps were virtually the same, indicating that these scores were not artificially elevated by the LD near this location (only 2 of 17 markers were dropped for the sparse map). For the neurophysiology phenotype, the LOD scores using the microsatellite, Affymetrix, and sparse Illumina maps were nearly the same. The dense Illumina map gave a marginally higher LOD score, and this may reasonably be attributed to high LD in this region (7
