Linkage disequilibrium

Linkage disequilibrium is the nonrandom association of alleles at different loci in a population. It reflects how often particular allele combinations occur relative to expectations from their individual frequencies.

Recombination: The exchange of genetic material between chromosomes, especially during meiosis. Recombination reshuffles alleles at different loci and generally erodes their associations.
Genome-wide association study: A study that tests genetic variants across the genome for statistical association with a trait or disease. Associated markers often tag causal variants through linkage disequilibrium.
Allele: One of two or more alternative forms of a genetic sequence at a particular position. Disequilibrium describes associations among alternative forms at different positions.
Physical linkage: The tendency of nearby genetic loci to be inherited together because recombination rarely separates them. Physical proximity is a cause of persistent associations, not the definition of disequilibrium.
Founder effect: A change in genetic variation when a new population is established by a small number of individuals. Founder events can create distinctive allele combinations that persist as disequilibrium.
Haplotype: A combination of alleles at nearby loci on the same chromosome, usually inherited together. Haplotypes are the allele combinations whose frequencies reveal linkage disequilibrium.
Tag SNP: A genetic variant chosen to represent nearby variants through correlated inheritance. Tag SNPs exploit local disequilibrium to survey many variants with fewer measurements.
Locus: A specific position or region in a genome. The definition compares alleles located at distinct loci.
Population stratification: The presence of subpopulations with different allele frequencies in a study sample. Mixtures of subpopulations can create apparent associations between otherwise unrelated loci.
Population bottleneck: A sharp reduction in population size that changes genetic variation through chance sampling. Bottlenecks can elevate and reshape allele associations through drift.

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