PGS Publication: PGP000281

Publication Information (EuropePMC)
Title Validity and Prognostic Value of a Polygenic Risk Score for Parkinson's Disease.
PubMed ID 34946808(Europe PMC)
doi 10.3390/genes12121859
Publication Date Nov. 23, 2021
Journal Genes (Basel)
Author(s) Koch S, Laabs BH, Kasten M, Vollstedt EJ, Becktepe J, Brüggemann N, Franke A, Krämer UM, Kuhlenbäumer G, Lieb W, Mollenhauer B, Neis M, Trenkwalder C, Schäffer E, Usnich T, Wittig M, Klein C, König IR, Lohmann K, Krawczak M, Caliebe A.
Released in PGS Catalog: Feb. 16, 2022

Associated Polygenic Score(s)

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Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
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Not Reported

External PGS Evaluated By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution Scoring File (FTP Link)
PGS000903
(PRS1805_PD)
 PGP000235 |
Nalls MA et al. Lancet Neurol (2019)
 Parkinson's disease Parkinson disease 1,805
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000903/ScoringFiles/PGS000903.txt.gz

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) 		Evaluated Score 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
PPM012831 PGS000903
(PRS1805_PD)
 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 PGS000903
(PRS1805_PD)
 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 PGS000903
(PRS1805_PD)
 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

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 —