We also conducted PheWAS in Yale–Penn, a deeply phenotyped cohort with comprehensive psychiatric assessments (SUDs and psychiatric disorders) and assessments for physical and psychosocial traits28. QC and creation of the PheWAS dataset have been described previously90. We calculated PRS for PAU in EUR and AUD in AFR (using summary statistics that leave out the Yale–Penn 3 and PGC sample, which includes Yale–Penn 1). We conducted PheWAS by fitting logistic regression models for binary traits and linear regression models for continuous traits. We used sex, age at recruitment and the top ten genetic PCs as covariates. We applied a Bonferroni correction to control for multiple comparisons.
