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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.
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. This example ...
Linkage disequilibrium (LD) is a term used in the study of population genetics for 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 is the phenomenon whereby two or more loci on a chromosome have reduced recombination between them because of their physical ...
Given loci and , the Linkage Disequilibrium between these loci, is denoted as = where is the frequency of the alternative allele at i and j co-occurring and and the frequency of the alternative allele at and respectively.
There are two main ways that the term "haplotype block" is defined: one based on whether a given genomic sequence displays higher linkage disequilibrium than a predetermined threshold, and one based on whether the sequence consists of a minimum number of single nucleotide polymorphisms (SNPs) that explain a majority of the common haplotypes in the sequence (or a lower-than-usual number of ...
The picture to the right serves to provide visual aid as to how a slice (NP) is taken from the nucleus and loci are searched for within the NP. Cosegregation used within other mathematical models (SLICE [3] and normalized linkage disequilibrium) assist in rendering 3-D visualizations as a smaller process of genome architecture mapping (GAM ...
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).
Therefore, the presence of strong linkage disequilibrium might indicate that there has been a recent selective sweep, and can be used to identify sites recently under selection. There have been many scans for selective sweeps in humans and other species, using a variety of statistical approaches and assumptions. [4]