How else can linkage disequilibrium be generated?
Other ways in which linkage disequilibrium can arise involve physical linkage, where the marker is found at a chromosomal locus that is near the genetic difference actually causing the disease. This is the kind of linkage disequilibrium that GWAS is searching for. While linkage disequilibrium is not the same as physical linkage, variants that are linked in the sense of being close together on the chromosome are much more likely to be associated than are physically unlinked variants, because a chromosomal recombination event would be required to separate them, and this does not happen very often, especially if the SNP and the disease gene are very close to one another. New mutations can remain associated with physically linked variants for hundreds of generations. So, if there is a strong association in a well matched sample between a SNP and the disease, the best guess is that there is a causative allele tightly linked physically to (and in linkage disequilibrium with) the SNP. The eff
