PGS Publication: PGP000235

Publication Information (EuropePMC)
Title Identification of novel risk loci, causal insights, and heritable risk for Parkinson's disease: a meta-analysis of genome-wide association studies.
PubMed ID 31701892(Europe PMC)
doi 10.1016/s1474-4422(19)30320-5
Publication Date Dec. 1, 2019
Journal Lancet Neurol
Author(s) Nalls MA, Blauwendraat C, Vallerga CL, Heilbron K, Bandres-Ciga S, Chang D, Tan M, Kia DA, Noyce AJ, Xue A, Bras J, Young E, von Coelln R, Simón-Sánchez J, Schulte C, Sharma M, Krohn L, Pihlstrøm L, Siitonen A, Iwaki H, Leonard H, Faghri F, Gibbs JR, Hernandez DG, Scholz SW, Botia JA, Martinez M, Corvol JC, Lesage S, Jankovic J, Shulman LM, Sutherland M, Tienari P, Majamaa K, Toft M, Andreassen OA, Bangale T, Brice A, Yang J, Gan-Or Z, Gasser T, Heutink P, Shulman JM, Wood NW, Hinds DA, Hardy JA, Morris HR, Gratten J, Visscher PM, Graham RR, Singleton AB, 23andMe Research Team, System Genomics of Parkinson's Disease Consortium, International Parkinson's Disease Genomics Consortium.
Released in PGS Catalog: Sept. 17, 2021

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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PGS Developed 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's disease 1,805
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000903/ScoringFiles/PGS000903.txt.gz
PGS000902
(PRS90_PD)
PGP000235 |
Nalls MA et al. Lancet Neurol (2019)
Parkinson's disease Parkinson's disease 90
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000902/ScoringFiles/PGS000902.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
PPM002664 PGS000903
(PRS1805_PD)
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 : 0.054
Odds Ratio (OR, top 25% vs bottom 25%): 6.25 [4.26, 9.28]
PCs(1-5), age, sex
PPM002665 PGS000902
(PRS90_PD)
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.

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
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.