Testing for differences in polygenic scores in the presence of confounding
Authors: Blanc Jennifer , Berg Jeremy J. 
Published: March 2023

Polygenic scores have become an important tool in human genetics, enabling the prediction of individuals’ phenotypes from their genotypes. Understanding how the pattern of differences in polygenic score predictions across individuals intersects with variation in ancestry can provide insights into the evolutionary forces acting on the trait in question, and is important for understanding health disparities. However, because most polygenic scores are computed using effect estimates from population samples, they are susceptible to confounding by both genetic and environmental effects that are correlated with ancestry. The extent to which this confounding drives patterns in the distribution of polygenic scores depends on patterns of population structure in both the original estimation panel and in the prediction/test panel. Here, we use theory from population and statistical genetics, together with simulations, to study the procedure of testing for an association between polygenic scores and axes of ancestry variation in the presence of confounding. We use a general model of genetic relatedness to describe how confounding in the estimation panel biases the distribution of polygenic scores in a way that depends on the degree of overlap in population structure between panels. We then show how this confounding can bias tests for associations between polygenic scores and important axes of ancestry variation in the test panel. Specifically, for any given test, there exists a single axis of population structure in the GWAS panel that needs to be controlled for in order to protect the test. Based on this result, we propose a new approach for directly estimating this axis of population structure in the GWAS panel. We then use simulations to compare the performance of this approach to the standard approach in which the principal components of the GWAS panel genotypes are used to control for stratification.

Author Summary

Complex traits are influenced by both genetics and the environment. Human geneticists increasingly use polygenic scores, calculated as the weighted sum of trait-associated alleles, to predict genetic effects on a phenotype. Differences in polygenic scores across groups would therefore seem to indicate differences in the genetic basis of the trait, which are of interest to researchers across disciplines. However, because polygenic scores are usually computed using effect sizes estimated using population samples, they are susceptible to confounding due to both the genetic background and the environment. Here, we use theory from population and statistical genetics, together with simulations, to study how environmental and background genetic effects can confound tests for association between polygenic scores and axes of ancestry variation. We then develop a simple method to protect these tests from confounding, which we evaluate, alongside standard methods, across a range of possible situations. Our work helps clarify how bias in the distribution of polygenic scores is produced and provides insight to researchers wishing to protect their analyses from confounding.