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Linkage disequilibrium (LD) is the correlation between nearby variants such that the alleles at neighboring polymorphisms (observed on the same chromosome) are associated within a population more often than if they were unlinked.
How is linkage disequilibrium calculated?
When a new allele, B, appears by mutation, there are three haplotypes, the new one being AB or aB depending on which copy of b mutated. In both cases, D′ = 1 (D′ is the ratio of D (a measure of linkage disequilibrium) to its maximum possible absolute value, given the allele frequencies).
How can SNP haplotypes be determined?
With the current technology it is possible to get the genotype of an individual and to determine the positions of the SNPs. The genotype gives the bases at each SNP for both copies of the chromosome but loses the information of the origin.
What is linkage disequilibrium used for?
Linkage disequilibrium between two alleles is related to the time of the mutation events, genetic distance, and population history. It can be used to improve the power of cancer genetic association studies.
Is linkage disequilibrium good or bad?
In population genetics, linkage disequilibrium (LD) is the non-random association of alleles at different loci in a given population. As a result, the pattern of linkage disequilibrium in a genome is a powerful signal of the population genetic processes that are structuring it.
Does random mating cause linkage disequilibrium?
If random sampling produces by chance an excess of a haplotype in a generation, linkage disequilibrium will have arisen. If individuals with gene A1 tend to mate with B1 types rather than B2 types, A1B1 haplotypes will have excess frequency over that for random mating.
What is complete linkage disequilibrium?
Linkage disequilibrium (LD) is the nonrandom association of alleles of different loci. Unusually high local LD can indicate an allele that has recently increased to high frequency under strong selection. Several methods have been developed to detect selected loci and to estimate the age of alleles using patterns of LD.
What increases linkage disequilibrium?
Linkage disequilibrium is influenced by many factors, including selection, the rate of genetic recombination, mutation rate, genetic drift, the system of mating, population structure, and genetic linkage.
What are the possible consequences of linkage disequilibrium?
In this paper, we show that linkage disequilibrium (LD), which is the correlation of frequencies of genes at different loci, induced by random sampling during bottlenecks may cause a significant increase in genotypic variance and also a small increase in additive variance.