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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".
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]
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]
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 ...
The most commonly used approach, block-based method, exploits the principle of linkage disequilibrium observed within haplotype blocks. [12] Several algorithms have been devised to partition chromosomal regions into haplotype blocks which are based on haplotype diversity , LD , four-gamete test and information complexity and tag SNPs are ...
In contrast, there are alternative techniques which operate on summaries reported by GWASes without requiring the raw data [14] e.g. "LD score regression" [15] contrasts linkage disequilibrium statistics (available from public datasets like 1000 Genomes) with the public summary effect-sizes to infer heritability and estimate genetic ...
These factors include priorities in SNPs, relative risk of functional change in genes, and linkage disequilibrium among SNPs. [ 13 ] In addition, the availability of genetic information through online databases enables researchers to mine existing data and web-based resources for new candidate gene targets. [ 14 ]
In genetics, the transmission disequilibrium test (TDT) was proposed by Spielman, McGinnis and Ewens (1993) [1] as a family-based association test for the presence of genetic linkage between a genetic marker and a trait. It is an application of McNemar's test.