Genotyped data was first assessed in GenomeStudio using the GenCall algorithm (Illumina), however as the program is better at examining common variants, rare variants were then assessed using zCall [18], a rare-variant caller specially designed for microarrays. In accordance with the analytic pipeline developed in-house [19], the data from the initial genotype calling was subjected to further stringent quality control in PLINK [20] and PLINK2 [21]. The resulting dataset taken forward to imputation analysis consisted of 263084 autosomal SNPs, with MAF >5%, call rate >99% and which did not deviate from Hardy-Weinberg with p>1x10-5. A large number of SNPs were eliminated during this QC stage, as they were not polymorphic in the Chinese sample or were too rare; setting the MAF cutoff at 5% enabled us to include more of the common variants. Individuals with call rates of >99%, gender consistent with the heterozygosity of X chromosome SNPs and with genome-wide SNP heterozygosity within 2SD of the sample mean were retained, leaving a total of 504 samples (370 cases and 134 controls) available for genetic analyses.
