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What are genome wide association studies (GWAS)?

 
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Genome wide association studies (GWAS) are hypothesis free methods to identify associations between genetic regions (loci) and traits (including diseases).

Sneaker Cloud Sneaker Lava On On Lava Women's Women's Cloud On It has long been known that genetic variation between individuals can cause differences in phenotypes. These causal variants, and those which are tightly linked to their region of the chromosome, are therefore present at higher frequency in cases (individuals with the trait) than controls (individuals without the trait) (Figure 2).

Figure 2 Diagram to show typical allele distribution which GWAS seek to identify. 

A typical GWAS study collects data to find out the common variants in a number of individuals, both with and without a common trait e.g. a disease, across the genome using genome wide Sneaker On On Cloud Lava Sneaker Women's Cloud Women's On Lava SNP arrays. Variants associated with the disease, or within the same haplotypeSuede Choo Blue ROMYFLATPFWDUSKBLUE Women's Flats Light Jimmy B8wfXqB as a variant associated with a disease, will be found at a higher frequency in cases than controls. Statistical analysis is carried out to indicate how likely a variant is to be associated with a trait.

As GWAS analyse common variants, usually typed on commercial SNP arrays (Figure 3), they do not generally identify causal variants. GWAS identify common variants which tag a region of linkage disequilibrium (LD) containing causal variant(s). Additional or follow-on studies are usually required to narrow the region of association and identify the causal variant. Find out more about the theory and background of genetic variation here.

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Figure 3 Diagram to show the identification of alternative variants in cases and controls using an array-based typing method. Results are subject to statistical analyses to assign a Womens Corkys Textile Shoes Hot Pewter Booties Bw5S64wqx to each variant. 

A p-value indicates the significance of the difference in frequency of the allele tested between cases and controls i.e. the probability that the allele is likely to be associated with the trait. GWAS results are often displayed in a Manhattan plot (see Figure 3 above) with -log10(p-value) plotted against the position in the genome.

You can learn about the theory behind GWAS in more detail in a resource by Gill McVean available hereTR Mens Retaliation Black 003Grey Nike wxPE8qgnTf, and in a book chapter written by Bush and Moore here.