EraSOR: Erase Sample Overlap in polygenic score analyses

BackgroundPolygenic risk score (PRS) analyses are now routinely applied in biomedical research, with great hope that they will aid in our understanding of disease aetiology and contribute to personalized medicine. The continued growth of multi-cohort genome-wide association studies (GWASs) and large-scale biobank projects has provided researchers with a wealth of GWAS summary statistics and individual-level data suitable for performing PRS analyses. However, as the size of these studies increase, the risk of inter-cohort sample overlap and close relatedness increases. Ideally sample overlap would be identified and removed directly, but this is typically not possible due to privacy laws or consent agreements. This sample overlap, whether known or not, is a major problem in PRS analyses because it can lead to inflation of type 1 error and, thus, erroneous conclusions in published work. ResultsHere, for the first time, we report the scale of the sample overlap problem for PRS analyses by generating known sample overlap across sub-samples of the UK Biobank data, which we then use to produce GWAS and target data to mimic the effects of inter-cohort sample overlap. We demonstrate that inter-cohort overlap results in a significant and often substantial inflation in the observed PRS-trait association, coefficient of determination (R2) and false-positive rate. This inflation can be high even when the absolute number of overlapping individuals is small if this makes up a notable fraction of the target sample. We develop and introduce EraSOR (Erase Sample Overlap and Relatedness), a software for adjusting inflation in PRS prediction and association statistics in the presence of sample overlap or close relatedness between the GWAS and target samples. A key component of the EraSOR approach is inference of the degree of sample overlap from the intercept of a bivariate LD score regression applied to the GWAS and target data, making it powered in settings where both have sample sizes over 1,000 individuals. Through extensive benchmarking using UK Biobank and HapGen2 simulated genotype-phenotype data, we demonstrate that PRSs calculated using EraSOR-adjusted GWAS summary statistics are robust to inter-cohort overlap in a wide range of realistic scenarios and are even robust to high levels of residual genetic and environmental stratification. ConclusionThe results of all PRS analyses for which sample overlap cannot be definitively ruled out should be considered with caution given high type 1 error observed in the presence of even low overlap between base and target cohorts. Given the strong performance of EraSOR in eliminating inflation caused by sample overlap in PRS studies with large (>5k) target samples, we recommend that EraSOR be used in all future such PRS studies to mitigate the potential effects of inter-cohort overlap and close relatedness.