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The approach involves using regression analysis to examine the relationship between linkage disequilibrium scores and the test statistics of the single-nucleotide polymorphisms (SNPs) from the GWAS. Here, the "linkage disequilibrium score" for a SNP "is the sum of LD r 2 measured with all other SNPs". [3]
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 ...
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.
In that case the signal produced from GWAS is an indirect (synthetic) association between one or more rare causal variants in linkage disequilibrium. It is important to recognize that this phenomenon is possible when selecting a group for tag SNPs.
Hence, GWAS is a non-candidate-driven approach, in contrast to gene-specific candidate-driven studies. GWA studies identify SNPs and other variants in DNA associated with a disease, but they cannot on their own specify which genes are causal. [1] [2] [3] The first successful GWAS published in 2002 studied myocardial infarction. [4]
Genetic correlations can arise due to: [19] linkage disequilibrium (two neighboring genes tend to be inherited together, each affecting a different trait); biological pleiotropy (a single gene having multiple otherwise unrelated biological effects, or shared regulation of multiple genes [39])
However, many of these associations can be developed throughout an individual due to linkage disequilibrium and the large size of the genome. Although GWAS provide valuable insight into identifying markers throughout the genome, a large portion of the SNPs are present in non-coding mRNA regions, and many have unknown functions that are ...
Linkage disequilibrium (LD) calculation; Identity by descent (IBD) and identity by state (IBS) matrix calculation; population stratification, such as a Principal component analysis; association analysis such as genome-wide association study for both basic case/control studies and quantitative traits; tests for epistasis