QC in all batches, then were imputed using the TOPMed Imputation Server with the TOPMed-r2 reference panel64,71. The core set used ∼441K, ∼232K and ∼280K markers for (1), (2) and (3), respectively. Association analysis was performed using SAIGE with the LOCO = TRUE flag; age, sex, ten PCs and two covariates that model the three imputation runs, which were used for the individuals. Participants of non-EUR ancestry (defined as >6 standard deviations from the PC1 and PC2 centroids) were excluded. Association analyses were limited to variants with a MAF ≥0.0001, minor allele count ≥5 and an R2 ≥ 0.1.
