Genotyping and Calculation of Polygenic Risk Scores

DNA samples were extracted from the whole blood of 386 patients and sequenced using an Illumina HiSeq X Ten Sequencer. Paired-end reads were aligned to the reference genome (hg38), and variants were called using the Genome Analysis Tool Kit.²⁵ We extracted the genotypes of the SNPs with the following quality control criteria: SNPs on nonautosomes, multiallelic, deviation from Hardy-Weinberg equilibrium (p < 1E-6), and high rates of missing genotypes (>0.05). PRS was computed using genotypes of 87 risk loci for PD after excluding 3 multiallelic loci.⁶ Each PRS was calculated by summing the risk alleles weighted by log-transformed odds ratios (ORs). We also applied PRSice-2,²⁶ which predicts PRS by applying multiple p-value thresholds, using publicly available summary statistics of the GWA study, which excluded data conducted by 23 and Me.