Many measures of LD have been proposed [17], though all are ultimately related to the difference between the observed frequency of co-occurrence for two alleles (i.e. a two-marker haplotype) and the frequency expected if the two markers are independent. The two commonly used measures of linkage disequilibrium are and [15], [17] shown in equations 1 and 2. In these equations, is the frequency of the haplotype, is the frequency of the allele, and is the frequency of the allele.(1) (2) is a population genetics measure that is related to recombination events between markers and is scaled between 0 and 1. A value of 0 indicates complete linkage equilibrium, which implies frequent recombination between the two markers and statistical independence under principles of Hardy-Weinberg equilibrium. A of 1 indicates complete LD, indicating no recombination between the two markers within the population. For the purposes of genetic analysis, LD is generally reported in terms of , a statistical measure of correlation. High values indicate that two SNPs convey similar information, as one allele of the first SNP is often observed with one
