Population substructure due to assortative mating

The authors of this paper find that even in an ethnically homogeneous population, stratification can occur due to assortative mating.

The Effect of Assortative Mating upon Genetic Association Studies: Spurious Associations and Population Substructure in the Absence of Admixture

David T. Redden and David B. Allison

Behavior Genetics, Online First

Abstract: Spurious associations due to confounding factors are an often cited and intensely debated concern for genetic association studies. Great attention has been focused upon the specific threat of confounding due to population stratification. This emphasis has spurred the development of many statistical genetic methods to detect and correct for the potentially confounding effects of admixture. Unfortunately, this emphasis on admixture has led some authors to suggest that if ethnically homogenous populations are used, spurious associations are unlikely to occur. We show that under small and realistic degrees of assortative mating over time, spurious associations arise even in ethnically homogeneous populations. We demonstrate that structured association and genomic control tests can, under certain conditions, correct for these spurious associations. We conclude that investigators should not assume spurious associations will not occur in association studies using ethnically homogenous populations and recommend the use of genomic control methods and/or family-based association tests within genetic association studies.