In conclusion, variance-components linkage analysis using high-density SNP maps provided higher LOD scores compared with the standard microsatellite map. These results demonstrate that using dense SNP maps in linkage analysis is feasible and may increase power. However, the computational challenges are not trivial and will only increase as denser SNP sets become available. More widespread application of SNPs in linkage analysis will depend on further improvements to current statistical methods and associated software packages.
