Polygenic Score (PGS) ID: PGS000903

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 PRS1805_PD
Development Method
Name Clumping and Thresholding (C+T)
Parameters r^2 > 0.1 in a 250kb region, 10,000 permutations, p = 1.35e-03
Variants
Original Genome Build NR
Number of Variants 1,805
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
European: 33.3%
Multi-ancestry (including European): 33.3%
  • European
  • Not Reported
South Asian: 33.3%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
—
[
  • 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
—
[
  • 49,928 cases
  • , 1,411,453 controls
]
 European, NR 6 cohorts
  • 23andMe
  • ,HBS
  • ,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 PRS1809_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).
—
[
  • 5,851 cases
  • , 5,866 controls
]
 European, NR NR 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. — — — This dataset was used to train PRS1809_PD.

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
PPM002664 PSS001174|
Multi-ancestry (including European)|
999 individuals
 PGP000235 |
Nalls MA et al. Lancet Neurol (2019)
 Reported Trait: Parkinson's disease β: 0.709 (0.072) AUROC: 0.692 R²: 0.054
Odds Ratio (OR, top 25% vs bottom 25%): 6.25 [4.26, 9.28]		 PCs(1-5), age, sex —
PPM012831 PSS009572|
European Ancestry|
6,378 individuals
 PGP000281 |
Koch S et al. Genes (Basel) (2021)
|Ext.		 Reported Trait: Parkinson's disease — AUROC: 0.645 [0.63, 0.66] Nagelkerke’s Pseudo-R2: 0.348 sex, age and first three PCs Quality control led to the exclusion of 62 of the original 1805 PD-PRS SNPs
PPM012832 PSS009572|
European Ancestry|
6,378 individuals
 PGP000281 |
Koch S et al. Genes (Basel) (2021)
|Ext.		 Reported Trait: Parkinson's disease prognosis — — Sensitivity: 0.581 [0.479, 0.625]
Specificity: 0.625 [0.472, 0.725]		 — Cost of 1: optimal threshold for PD-PRS as determined by maximizing a weighted Youden index = 0.33
PPM012833 PSS009572|
European Ancestry|
6,378 individuals
 PGP000281 |
Koch S et al. Genes (Basel) (2021)
|Ext.		 Reported Trait: Parkinson's disease (age at onset) — AUROC: 0.59 [0.551, 0.629] Nagelkerke’s Pseudo-R2: 0.039 sex, age and first three PCs Quality control led to the exclusion of 62 of the original 1805 PD-PRS SNPs
PPM014928 PSS009933|
South Asian Ancestry|
90 individuals
 PGP000360 |
Kukkle PL et al. Adv Biol (Weinh) (2022)
|Ext.		 Reported Trait: Young onset Parkinson’s disease — — Odds ratio, OR (high vs low risk): 1.92 — —

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
PSS009572 — —
[
  • 1,914 cases
  • , 4,464 controls
]
,
54.0 % Male samples
 — European — DeNoPa, EPIPARK, KIEL, Other —
PSS009933 — — 90 individuals,
71.0 % Male samples
 Mean = 36.0 years South Asian
(Indian)		 — 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. —
[
  • 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.