Allele frequency, penetrance, and disease.

Genome-wide association studies (GWAS) are effective in detecting common alleles that contribute to the inherited component of common multifactorial diseases. Typically, the alleles identified by this approach have modest effect sizes that cannot fully account for disease susceptibility. This discrepancy may exist because it is hard to identify rare alleles with a low to modest penetrance using GWAS. Penetrance is a measure of the proportion of individuals in a population carrying a particular allele that expresses the related phenotype. In contrast to multifactorial diseases, Mendelian diseases have a high penetrance and very rare allele frequency.