There is currently great interest in using SNPs in genetic linkage and association studies because of the abundance of SNPs as well as the availability of high-throughput genotyping technologies. Kruglyak [1] predicted in a theoretical study that maps with approximately two to three times the density of SNPs with a heterogeneity of 0.5 would be equivalent to the current microsatellites maps. With current high-throughput SNP genotyping technologies, it is now feasible and affordable to collect genotype data from tens of thousands of SNPs. John et al. [2] described the first whole-genome scans with linkage analysis of a complex disease, rheumatoid arthritis, to compare SNPs with microsatellites directly. In this paper, using the Collaborative Studies on Genetics of Alcoholism (COGA) data provided by Genetic Analysis Workshop 14 (GAW14), we compared the results based on whole-genome scans of 143 pedigrees using 315 microsatellites and 10,081 SNPs from Affymetrix across 22 autosomal chromosomes.
