Data Sources
The genome-wide association study (GWAS) summary statistics data used in this study for PD were obtained from the FinnGen project (https://www.finngen.fi/en), led by the Finnish Biobank, which draws on longitudinal health registry data from the entire population of Finland since 1969.The GWAS summary data for PD contained 3,046 diagnosed cases and 195,395 control cases.
The GWAS summary data for IAs were obtained from a meta-analysis conducted by Bakker[14]et al. , which included uIAs and aSAH cases. The former included 7,495 diagnosed cases and 71,934 controls cases, while the latter included 5,140 diagnosed cases and 71,952 control cases. To mitigate population stratification bias, all GWAS summary data were included only from individuals of European ancestry. The research workflow was illustrated in Figure 1.
Selection of IVs
To estimate causal effects using genetic instruments, it is essential to meet the three key assumptions of IVs. Therefore, quality control measures were implemented. Firstly, since the number of independent SNPs with a strong association with PD at p < 5×10-8 was limited, we set the threshold at p < 5×10-5 to select a sufficient number of IVs. Secondly, to exclude SNPs in strong linkage disequilibrium (LD), the clump function was performed with default parameters. Thirdly, SNPs with a minor allele frequency (MAF) less than 0.01 were eliminated. Fourthly, the F statistic for each SNP was calculated using the following equation: F = R2× (N - 2) / (1 - R2). R2 represents the exposure variance for each IV interpretation. The filtering criterion was an F-test value > 10[15]. Fifthly, SNPs with allele inconsistency between exposure and outcome samples, as well as palindromic alleles were excluded. Lastly, the MR-PRESSO global test was applied to detect potential horizontal pleiotropy of SNPs, and SNPs with a p< 0.05 were excluded[16]. Finally, we obtained a set of high-quality SNPs.
Statistical Analysis
In this study, we employed multiple statistical analysis methods, including IVW, MR-Egger regression, and Weighted Median, to estimate the causal effects of exposure phenotypes on the outcome. The IVW method was the primary statistical approach used in this study. When all selected SNPs are valid IVs, the IVW method provides the most accurate results. MR-Egger regression method allows for consistent estimation of causal effects even in the presence of pleiotropy effects[17]. The Weighted Median method is applicable to some or as many as 50% of SNPs that are invalid IVs and gives consistent estimates[18].
Pleiotropic and sensitivity analysis
In this study, we employed various methods to detect the presence of pleiotropy in IVs. Firstly, the intercept term of MR-Egger regression can effectively indicate whether horizontal pleiotropy drives the results of the MR analysis[17]. Secondly, the asymmetry of the funnel plot can reflect the presence of horizontal pleiotropy in IVs[19]. Lastly, we conducted the MR-PRESSO test to assess the presence of pleiotropy in IVs[16]. To identify heterogeneity in IVs, we used both the IVW and MR-Egger regression to quantify heterogeneity by Cochran's Q statistic. Additionally, we performed leave-one-out analyses to examine the robustness and consistency of the MR analysis results.
In this study, the Bonferroni method was used to correct for p-values for multiple comparisons, i.e. P<0.006 (0.05/8) to show convincing evidence of causation. All analyses were conducted using the "TwoSampleMR"[19] and "MRPRESSO"[20] packages in R software version 4.3.1.