Whole-Exome and Whole-Genome Sequencing Pipeline

As shown in our previous study (15 (link)), the WES cohort used SureSelect Human All Exon Kit V6 (Agilent) to capture the whole-exome DNA, prepared the sample library, and then used Illumina HiSeq 10× for pair-end 2 × 150 bp sequencing. The average sequencing depth was 123×, achieving a coverage of at least 10× for 99.32% of the target region. WGS was performed using the Illumina Nova Sequencing platform in a pair-end 2 × 150 bp mode, and the average depth of coverage was about 12×. Sequencing data of both groups were processed and analyzed with the BWA-GATK-ANNOVAR pipeline (16 (link), 17 (link)). Quality control was conducted as described in our previous study (15 (link)). Samples would be removed if they had sex discrepancies, abnormal heterozygosity (>3 SD), pathogenic or likely pathogenic variants of PD-related genes, or unusual relatedness (descent > 0.15). In addition, we performed the principal component analysis (PCA) using PLINK v1.90 to assess potential population structure stratification. In subsequent analyses for the WGS cohort, gender, age, and the first five principal components of population stratification were used as covariates, whereas for the WES cohort (the control group included elderly people without neurological diseases), sex and the first five principal components for population stratification were used (18 (link)).