Linkage disequilibrium

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Linkage disequilibrium measures the degree to which alleles at two loci are associated; it measures the non-random associations between alleles at two loci based on expectations relative to allele frequencies at two loci.

From Wikipedia:

In population genetics, linkage disequilibrium is the non-random association of alleles at two or more loci that descend from single, ancestral chromosomes. Linkage disequilibrium is wholly a measurement of proximal genomic space. It is necessary to refer to this as gametic phase disequilibrium or simply gametic disequilibrium because it is described through DNA recombination. In other words, linkage disequilibrium is the occurrence of some combinations of alleles or genetic markers in a population more often or less often than would be expected from a random formation of haplotypes from alleles based on their frequencies. It is a second order phenomenon derived from linkage, which is the presence of two or more loci on a chromosome with limited recombination between them. The amount of linkage disequilibrium depends on the difference between observed allelic frequencies and those expected from a homogenous, randomly distributed model. Populations where combinations of alleles or genotypes can be found in the expected proportions are said to be in linkage equilibrium.


The term linkage disequilibrium is misleading for two reasons: 1) Non-random associations of alleles at two loci can occur even if the two genes are unlinked 2) Just because two loci are linked, this does not mean that they will be in linkage disequilibrium.[1]


Alleles in linkage disequilibrium can reveal whether they have an epistatic interaction.[2]