PGS Catalog - Nalls MA, Lancet Neurol (2019) (Publication)

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)

PGS Developed By This Publication

Polygenic Score ID & Name	PGS Publication ID (PGP)	Reported Trait	Mapped Trait(s) (Ontology)	Number of Variants	Ancestry distribution GWAS Dev Eval	Scoring File (FTP Link)
PGS000902 (PRS90_PD)	PGP000235 \| Nalls MA et al. Lancet Neurol (2019)	Parkinson's disease	Parkinson disease	90		https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000902/ScoringFiles/PGS000902.txt.gz
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
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	R²: 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.	—	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.