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.
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).

All illustrations CC-BY.
All other materials CC-BY unless noted otherwise.