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In genetics, association mapping, also known as "linkage disequilibrium mapping", is a method of mapping quantitative trait loci (QTLs) that takes advantage of historic linkage disequilibrium to link phenotypes (observable characteristics) to genotypes (the genetic constitution of organisms), uncovering genetic associations. [1] [2]
In statistical genetics, linkage disequilibrium score regression (LDSR [1] or LDSC [2]) is a technique that aims to quantify the separate contributions of polygenic effects and various confounding factors, such as population stratification, based on summary statistics from genome-wide association studies (GWASs).
Once linkage disequilibrium has been calculated for a dataset, a visualization method is often chosen to display the linkage disequilibrium to make it more easily understandable. The most common method is to use a heatmap , where colors are used to indicate the loci with positive linkage disequilibrium, and linkage equilibrium.
Over time, a pair of markers or points on a chromosome in the population move from linkage disequilibrium to linkage equilibrium, as recombination events eventually occur between every possible point on the chromosome. [1] Two loci are said to be in linkage equilibrium (LE) if their inheritance is an
Measures of linkage disequilibrium are useful tools for gene and genome mapping. [5] A linkage between two genes may be due to their positions relative to each other in the genome or it may be due to selection acting to favor certain combinations of alleles. On a genomic scale, linkage disequilibrium plays a large analytical role.
In 2018, several genome-wide association studies are reaching a total sample size of over 1 million participants, including 1.1 million in a genome-wide study of educational attainment [39] follow by another in 2022 with 3 million individuals [40] and a study of insomnia containing 1.3 million individuals. [41]
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Initiation sites for recombination are usually identified by mapping crossing over events through pedigree analysis or through analysis of linkage disequilibrium. Linkage disequilibrium has identified more than 30,000 hotspots within the human genome. [3] In humans, the average number of crossover recombination events per hotspot is one ...