After quality control, association testing using disease status (case or control) as the phenotype was performed on the variants under an additive logistic regression model implemented in Plink 1.9 [34]. PCs were calculated using Plink. The association tests were conducted on all 9,904 samples together for the full-cohort analysis, as well as on sets of samples stratified by sequencing center for the center-based association analyses. Variants were considered exome-wide statistically significant at the Bonferroni-corrected threshold of p < 0.05 / # tests, as in [19]. Only bi-allelic SNPs with a recalibrated variant quality score (VQSLOD) > 0 were retained for further analysis.

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