DNA was extracted from cerebellar tissues obtained from SMRI. Sample genotyping was conducted using Genome-Wide Human SNP Array 5.0, at Translational Genomics Research Institute (Tgen). BRLMM-p (Affymetrix) was used as the genotype calling algorithm. SNPs with call rates less than 99% were excluded from the analysis. SNPs showing departure from Hardy-Weinberg equilibrium (HWE) were filtered (p < 0.001). Of the remaining SNPs, only SNPs showing minor allele frequency (MAF) of at least 10% were carried forward for further analysis. These quality control filters yielded nearly 239,000 SNPs. We expanded on the earlier study 9 by performing imputation using MaCH v1.0 16, 17 to increase the density of interrogated SNPs. Only SNPs with MAF of at least 10% and Rsq (the squared correlation between imputed and true genotypes) > 0.3. 886,338 autosomal SNPs were analyzed for QTL mapping.
