Microsatellites are commonly used as markers for linkage analysis. More recently, single-nucleotide polymorphisms (SNPs) have been increasingly used as genotyping markers due in part to lower cost and ease of use. This study compares SNP marker linkage results for qualitative and quantitative phenotypes to the corresponding microsatellite results. For this study we focused on chromosome 7, an area shown to have linkage and association for both alcohol dependence, a qualitative trait, and a neurophysiologic measure, a quantitative trait [1-4]. For the neurophysiologic measure, evidence of linkage and association has been demonstrated for chromosome 7 [2]. Alcohol dependence was examined by Foroud et al. [1] for evidence of linkage relative to two populations. The results of that study indicate evidence of linkage only on chromosome 7 for the samples both individually and combined. Because the Genetic Analysis Workshop 14 (GAW14) population is a mixture of these two samples, we restricted our analyses to chromosome 7.
