An illustration of a Manhattan plot depicting several strongly associated risk loci. Each dot represents a SNP, with the X-axis showing genomic location and Y-axis showing association level. This genetics and genomics in medicine strachan pdf is taken from a GWA study investigating microcirculation, so the tops indicates genetic variants that more often are found in individuals with constrictions in small blood vessels.
When applied to human data, GWA studies compare the DNA of participants having varying phenotypes for a particular trait or disease. Each person gives a sample of DNA, from which millions of genetic variants are read using SNP arrays. The associated SNPs are then considered to mark a region of the human genome that may influence the risk of disease. GWA studies investigate the entire genome, in contrast to methods that specifically test a small number of pre-specified genetic regions.
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. The first successful GWAS was published in 2005. It investigated patients with age-related macular degeneration and found two SNPs with significantly altered allele frequency compared to healthy controls.