7.1 Association studies

One of the central goals of human genetics is understanding the relationship between genotype and phenotype. Genome-wide association studies (GWAS) emerged ~20 years ago as a useful approach for discovering genetic variation that underlies variation in human traits.

To conduct GWAS, you:

Go through every variant in the genome
Ask if its allele frequency differs between individuals who have or don’t have a phenotype of interest
- For most variants (Fig. 1, SNP 1), there will be very little difference
Identify the variants with the largest association between genotype and phenotype (Fig. 1, SNP 2)

Fig. 1. In this GWAS cohort, SNP 2 is significantly associated with the phenotype.

The phenotype can be any measurable trait, whether it’s binary (ex: if someone has a disease) or continuous (ex: height).