We conducted a phenome-wide association study (PheWAS) [63] of the PAU PRS by fitting a logistic regression model to 1,372 case/control phenotypes to estimate the odds of each diagnosis given the PAU polygenic score, controlling for sex, median age across the medical record, top 10 principal components of ancestry, and genotyping batch. We required the presence of at least two International Classification of Disease (ICD) codes that mapped to a PheWAS disease category (Phecode Map 1.2) to assign “case” status. A phenotype was required to have at least 100 cases to be included in the analysis. PheWAS analyses were run using the PheWAS R package [64]. Bonferroni correction was applied to test for significance (p < 0.05/1,372).
