In population genetics, linkage disequilibrium is the non-random 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. Non-random associations between polymorphisms at different loci are measured by the degree of linkage disequilibrium (LD).

Linkage disequilibrium is generally caused by genetic linkage and the rate of recombination; rate of mutation; random drift or non-random mating; and population structure. For example, some organisms (such as bacteria) may show linkage disequilibrium because they reproduce asexually and there is no recombination to break down the linkage disequilibrium.

If we look at haplotypes for two loci A and B with two alleles each—a two-locus, two-allele model—the following table denotes the frequencies of each combination:

In the genetic literature the phrase "two alleles are in LD" usually means that $D e 0$. Contrariwise, "linkage equilibrium" denotes the case $D = 0$.

The following table illustrates the relationship between the haplotype frequencies and allele frequencies and D.

so thatwhere $D$ at the $n$-th generation is designated as $D_n$. Thus we haveIf $n o infty$, then $\left(1-c\right)^n o 0$ so that $D_n$ converges to zero.

If at some time we observe linkage disequilibrium, it will disappear in future due to recombination. However, the smaller the distance between the two loci, the smaller will be the rate of convergence of $D$ to zero.

Resources

A comparison of different measures of LD is provided by Devlin & Risch [cite journal|author=Devlin B., Risch N. |title=A Comparison of Linkage Disequilibrium Measures for Fine-Scale Mapping|journal=Genomics|year=1995|volume=29|pages=311–322|url=http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6WG1-45S9156-30-1&_cdi=6809&_user=128590&_orig=browse&_coverDate=09%2F30%2F1995&_sk=999709997&view=c&wchp=dGLbVtb-zSkzk&md5=71c2158ad4c51ae80b12a68c68814f78&ie=/sdarticle.pdf |doi=10.1006/geno.1995.9003]

The International HapMap Project enables the study of LD in human populations [http://www.hapmap.org/cgi-perl/gbrowse/hapmap/ online] . The Ensembl project integrates HapMap data and such from dbSNP in general with other genetic information.

Analysis software

* Haploview
* [http://www.affymetrix.com/support/developer/tools/devnettools.affx LdCompare] [cite journal|author=Hao K., Di X., Cawley S.|title=LdCompare: rapid computation of single- and multiple-marker r2 and genetic coverage|journal=Bioinformatics|year=2007|volume=23|pages=252–254|url=http://bioinformatics.oxfordjournals.org/cgi/reprint/23/2/252|doi=10.1093/bioinformatics/btl574|pmid=17148510] &mdash; open-source software for calculating LD.
* [http://www.pypop.org/ PyPop]
* [http://www.goldenhelix.com/SNP_Variation/HelixTree/linkage_disequilibrium_analysis.html HelixTree] - commercial software with interactive LD plot.

References

ee also

*Haploview
*Hardy-Weinberg principle
*Genealogical DNA test
*Tag SNP

*cite book| first=Philip W.| last=Hedrick| title=Genetics of Populations| year=2005 | edition=3rd| id=ISBN 0763747726| location=Sudbury, Boston, Toronto, London, Singapore | publisher=Jones and Bartlett Publishers

* [http://www.nslij-genetics.org/ld/ Bibliography: Linkage Disequilibrium Analysis] : a bibliography of more than one thousand articles on Linkage disequilibrium published since 1918.

Wikimedia Foundation. 2010.

### Look at other dictionaries:

• linkage disequilibrium — linkage disequilibrium. См. неравновесное сцепление. (Источник: «Англо русский толковый словарь генетических терминов». Арефьев В.А., Лисовенко Л.А., Москва: Изд во ВНИРО, 1995 г.) …   Молекулярная биология и генетика. Толковый словарь.

• linkage disequilibrium — noun A non random association of two or more alleles at two or more loci; normally caused by an interaction between genes, and often illustrated on a pairwise linkage disequilibrium diagram (HapMap) …   Wiktionary

• linkage disequilibrium — See: gametic phase disequilibrium …   Glossary of Biotechnology

• linkage disequilibrium — The occurrence of some genes together, more often than would be expected. Thus, in the HLA system of histocompatibility antigens, HLA A1 is commonly associated with B8 and DR3, and A2 with B7 and DR2, presumably because the combination confers… …   Dictionary of molecular biology

• linkage disequilibrium — the occurrence in a population of two linked alleles at a frequency higher than the expected equilibrium frequency (which is the product of the frequencies of the two alleles), suggesting a common mutation due to a founder effect …   Medical dictionary

• linkage disequilibrium —    The phenomenon of a specific allele of one locus being associated or linked to a specific allele or marker of another locus, on the same chromosome, with a greater frequency than expected by chance …   Forensic science glossary

• pairwise linkage disequilibrium diagram — noun A triangular graphical representation of linkage disequilibrium in which different colours represent different magnitudes of linkage between pairs of loci …   Wiktionary

• Disequilibrium — is a term used to describe the lack of or opposite of an equilibrium. in medicine: Disequilibrium (medicine) (DES) in cerebral palsy a syndrome described by Hagberg all[1] lack of equilibrioception in population genetics, linkage disequilibrium… …   Wikipedia

• disequilibrium — A disturbance or absence of equilibrium. genetic d. a state in the genetic composition of a population which under selection may be expected to change toward an equ …   Medical dictionary

• Transmission disequilibrium test — The transmission disequilibrium test (TDT) was proposed by [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve db=pubmed dopt=Abstract list uids=8447318 Spielman, McGinnis Ewens (1993)] as a family based association test for the presence… …   Wikipedia