To use all functions of this page, please activate cookies in your browser.
my.bionity.com
With an accout for my.bionity.com you can always see everything at a glance – and you can configure your own website and individual newsletter.
 My watch list
 My saved searches
 My saved topics
 My newsletter
Linkage disequilibriumIn population genetics, linkage disequilibrium is the nonrandom association of alleles at two or more loci, not necessarily on the same chromosome. It is not the same as linkage, which describes the association of two or more loci on a chromosome with limited recombination between them. Linkage disequilibrium describes a situation in which some combinations of alleles or genetic markers occur more or less frequently in a population than would be expected from a random formation of haplotypes from alleles based on their frequencies. Nonrandom associations between polymorphisms at different loci are measured by the degree of linkage disequilibrium (LD). A comparison of different measures is provided by Devlin & Risch ^{[1]} Linkage disequilibrium is generally caused by genetic linkage and the rate of recombination; mutation rate; random drift or nonrandom mating; and population structure. For example, some organisms may show linkage disequilibrium (such as bacteria) because they reproduce asexually and there is no recombination (r=0) to break down the linkage disequilibrium: D'=(1r)D. It may be instructive to study genetic equilibrium, and its application in the HardyWeinberg principle. The International HapMap Project enables the study of LD in human populations online. The Ensembl project integrates HapMap data and such from dbSNP in general with other genetic information. Additional recommended knowledge
Linkage disequilibrium measure, δFormally, if we define pairwise LD, we consider indicator variables on alleles at two loci, say I_{1},I_{2}. We define the LD parameter δ (delta) as: Here p_{1},p_{2} denote the marginal allele frequencies at the two loci and h_{12} denotes the haplotype frequency in the joint distribution of both alleles. Various derivatives of this parameter have been developed. In the genetic literature the wording "two alleles are in LD" usually means to imply . Contrariwise, linkage equilibrium, denotes the case δ = 0. Linkage disequilibrium measure, DIf inspecting the two loci A and B with two alleles each—a twolocus, twoallele model—the following table denotes the frequencies of each combination:
Note that these are relative frequencies. One can use the above frequencies to determine the frequency of each of the alleles:
if the two loci and the alleles are independent from each other, then one can express the observation A1B1 as "A1 must be found and B1 must be found". The table above lists the frequencies for A_{1},p_{1}, and B_{1},q_{1}, hence the frequency of A_{1}B_{1}, x_{11}, equals according to the rules of elementary statistics x_{11} = p_{1} * q_{1}. A deviation of the observed frequencies from the expected is referred to as the linkage disequilibrium parameter^{[2]}, and is commonly denoted by a capital D ^{[3]} as defined by:
The following table illustrates the relationship between the haplotype and allele frequencies and D.
When extending these formula for diploid cells rather than investigating the gametes/haplotypes directly, the laid out principle prevails, the recombination rate between the two loci A and B must be taken into account, though, which is commonly denoted by the letter c. D is nice to calculate with but has the disadvantage of depending on the frequency of the alleles inspected. This is evident since frequencies are between 0 and 1. There can be no D observed if any locus has an allele frequency 0 or 1 and is maximal when frequencies are at 0.5. Lewontin (1964) suggested normalising D by dividing it with the theoretical maximum for the observed allele frequencies. Thus when When D < 0, . D_{max} is given by the smaller of p_{1}q_{2} and p_{2}q_{1}. D_{min} is given by the larger of − p_{1}q_{1} and − p_{2}q_{2} Another value is the correlation coefficient as also laid out in the initial paragraphs of this page, denoted as . This however is not adjusted to the loci having different allele frequencies. If it was, r, the square root of r^{2} if given the sign of D would be equivalent to D' ^{[4]} Another statistic used in a selective neutrality test is Tajima's D, to decide whether the mean number of differences between pairs of DNA sequences is compatible with the observed number of segregating sites in a sample. These are summary statistics (i.e. descriptive statistics summarizing the pattern of genetic diversity) that are computed from diploid samples of DNA sequences and which assume that the gametic phase is known. Analysis software
References
See also
Further reading


This article is licensed under the GNU Free Documentation License. It uses material from the Wikipedia article "Linkage_disequilibrium". A list of authors is available in Wikipedia. 