PGS Catalog - PGS000902 / Parkinson's disease (Polygenic Score)

Polygenic Score (PGS) ID: PGS000902

Predicted Trait
Reported Trait	Parkinson's disease
Mapped Trait(s)	Parkinson disease (MONDO_0005180)

Released in PGS Catalog: Sept. 17, 2021

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Score Details

Score Construction
PGS Name	PRS90_PD
Development Method
Name	Genome-wide significant variants
Parameters	NR
Variants
Original Genome Build	NR
Number of Variants	90
Effect Weight Type	beta

PGS Source
PGS Catalog Publication (PGP) ID	PGP000235
Citation (link to publication)	Nalls MA et al. Lancet Neurol (2019)

Ancestry Distribution
Source of Variant Associations (GWAS)	Multi-ancestry (including European): 100% European Not Reported 1,474,097 individuals (100%)
Score Development/Training	Multi-ancestry (including European): 100% European Not Reported 1,473,098 individuals (100%)
PGS Evaluation	Multi-ancestry (including European): 75% European Not Reported Additional Diverse Ancestries Not Reported: 25% 4 Sample Sets

Development Samples

Source of Variant Associations (GWAS)

Study Identifiers	Sample Numbers	Sample Ancestry	Cohort(s)
—	1,474,097 individuals [ 56,306 cases , 1,417,791 controls ]	European, NR	6 cohorts 23andMe ,HBS ,IPDGC ,PDBP ,PPMI ,UKB

Score Development/Training

Study Identifiers	Sample Numbers	Sample Ancestry	Cohort(s)	Phenotype Definitions & Methods	Age of Study Participants	Participant Follow-up Time	Additional Ancestry Description	Additional Sample/Cohort Information
—	1,473,098 individuals [ 55,779 cases , 1,417,319 controls ]	European, NR	23andMe, IPDGC, PDBP, PPMI, UKB	Cases were individuals with Parkinson's disease (PD). In the 23andMe and PDWBS cohorts, PD cases were self-reported. In the UKB cohort PD cases were proxy cases defined by family history. All other cases were defined using the standard UK Brain Bank criteria with a modification to allow the inclusion of cases that had a family history of PD.	—	—	—	This dataset was used to identify effect weights for SNPS within PRS90_PD. Additional cases and controls for this dataset were obtained from (1) Baylor College of Medicine/University of Maryland, (2) Finnish Parkinson's, (3) McGill Parkinson's, (4) Oslo Parkinson's disease study, (5) System Genomics of Parkinson's Disease (SGPD), (6) Tubigen Parkinson's Disease cohort (Courage PD), (7) UK PDMED (CouragePD), Parkinson's DIsease Web-based Study (PDWBS).

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance Metric ID (PPM)	PGS Sample Set ID (PSS)	Performance Source	Trait	PGS Effect Sizes (per SD change)	Classification Metrics	Other Metrics	Covariates Included in the Model	PGS Performance: Other Relevant Information
PPM002665	PSS001174\| Multi-ancestry (including European)\| 999 individuals	PGP000235 \| Nalls MA et al. Lancet Neurol (2019)	Reported Trait: Parkinson's disease	—	AUROC: 0.651 [0.617, 0.684]	—	PCs(1-5), age, sex	Only 88 SNPs from the 90 SNP PRS were utilised. 2 SNPs were not included as they failed to pass quality control in the HBS cohort.
PPM018174	PSS010943\| Ancestry Not Reported\| 986 individuals	PGP000458 \| Pavelka L et al. NPJ Parkinsons Dis (2022) \|Ext.	Reported Trait: Age at onset of parkinson disease	—	—	Correlation: -0.11	—	—
PPM018547	PSS011016\| Multi-ancestry (including European)\| 3,427 individuals	PGP000479 \| Blauwendraat C et al. Mov Disord (2023) \|Ext.	Reported Trait: Parkinson's disease	OR: 1.575 [1.444, 1.717] β: 0.4541 (0.0443)	—	—	—	85 of 90 variants of PGS000902 was used excluding full GBA1 region, and two additional variants (chr10:119776815:G:A and chr19:2341049:C:T)
PPM018548	PSS011017\| Multi-ancestry (including European)\| 225 individuals	PGP000479 \| Blauwendraat C et al. Mov Disord (2023) \|Ext.	Reported Trait: Parkinson's disease with Gaucher Disease	OR: 1.687 [1.099, 2.589] β: 0.5228 (0.2186)	—	—	—	85 of 90 variants of PGS000902 was used excluding full GBA1 region, and two additional variants (chr10:119776815:G:A and chr19:2341049:C:T)

Evaluated Samples

PGS Sample Set ID (PSS)	Phenotype Definitions and Methods	Participant Follow-up Time	Sample Numbers	Age of Study Participants	Sample Ancestry	Additional Ancestry Description	Cohort(s)	Additional Sample/Cohort Information
PSS010943	—	—	986 individuals [ 430 cases , 556 controls ]	—	Not reported	—	NR	Luxembourg Parkinson's Study
PSS011016	—	—	444 individuals [ 335 cases , 109 controls ]	—	Other (Ashkenazi Jewish)	—	NR	—
PSS011016	—	—	2,983 individuals [ 2,050 cases , 933 controls ]	—	European	—	NR	—
PSS011017	—	—	152 individuals [ 18 cases , 134 controls ]	—	Other (Ashkenazi Jewish)	—	NR	—
PSS011017	—	—	73 individuals [ 8 cases , 65 controls ]	—	European	—	NR	—
PSS001174	Cases were individuals with Parkinson's disease (PD). Cases were defined using the standard UK Brain Bank criteria with a modification to allow the inclusion of cases that had a family history of PD.	—	999 individuals [ 527 cases , 472 controls ] , 52.75 % Male samples	—	European, NR	—	HBS	Sample overlap between this dataset and the dataset used to source SNPs for PRS90_PD.