For each individual dataset, we performed sex-stratified and combined GWAS on imputed dosage files for autosomes and the X chromosome. In the sex-stratified analysis, dosages (i.e. number of chromosome copies) for the X chromosome in cases are equivalent to controls within each sex. However, in the sex-combined analysis, differences in dosage compensation between males (with one ChrX) and females (with two ChrX) should be considered. Thus, we verified that performing association analysis on ChrX dosage files produced consistent results compared with analysis of best-guess data in which ChrX was coded as 0/2 for males instead of 0/1 (--xchr-model 2 in PLINK).
