Table 2.

Canonical pathways significantly associated with PD risk through common variation in the discovery and replication phases after excluding PD known risk loci ± 1 Mb upstream and downstream

Gene set	Discovery					Replication
	PRS R2	Beta	SE	P	Num SNP	PRS R2	Beta	SE	P	Num SNP
Adaptive immune system (REACTOME)	0.0028	0.1560	0.0163	1.42E−21	397	0.0002	0.0438	0.0190	2.15E−02	182
Innate immune system (REACTOME)	0.0026	0.1522	0.0163	1.12E−20	621	0.0003	0.0475	0.0192	1.34E−02	332
Vesicle mediated transport (REACTOME)	0.0022	0.1398	0.0163	1.03E−17	515	0.0002	0.0439	0.0190	2.12E−02	259
Signaling by GPCR (REACTOME)	0.0019	0.1299	0.0163	1.86E−15	816	0.0002	0.0460	0.0190	1.58E−02	329
Metabolism of lipids (REACTOME)	0.0018	0.1265	0.0163	8.08E−15	538	0.0004	0.0547	0.0190	4.08E−03	275
Neutrophil degranulation (REACTOME)	0.0012	0.1026	0.0163	2.73E−10	259	0.0004	0.0593	0.0192	1.96E−03	143

PRS R² variance explained by polygenic risk score, SE standard error, P P-value, num_SNP number of SNPs included in each pathway analysis