Genotype imputation of case-control cohorts was performed using the pre-phasing/imputation stepwise approach implemented in EAGLE 26 / MINIMAC37 (with 132 genomic windows of variable size and default parameters). The imputation reference consisted of 54,330 phased haplotypes with 36,678,882 variants from the publicly available HRC reference, release 1.18 Chromosome X imputation was conducted using individuals passing quality control for the autosomal analysis. ChrX imputation and association analysis was performed separately for males and females. For trio-based cohorts, families with multiple (N) affected offspring were split into N parent-offspring trios, duplicating the parental genotype information. Trios were phased with SHAPEIT 39. We created pseudo-controls based on the non-transmitted alleles from the parents. Phased case-pseudo-control genotypes were then taken forward to the IMPUTE4 algorithm10 into the above HRC reference panel.
