Polygenic Score (PGS) ID: PGS000700

Predicted Trait
Reported Trait Urate [umol/L]
Mapped Trait(s) urate measurement (EFO_0004531)
Released in PGS Catalog: Feb. 3, 2021
Download Score FTP directory
Terms and Licenses
Creative Commons Attribution 4.0 International (CC BY 4.0)

Score Details

Score Construction
PGS Name snpnet.Urate
Development Method
Name snpnet
Parameters 1,080,968 variants as input (directly genotyped variants, imputed HLA allelotypes, and CNVs)
Variants
Original Genome Build hg19
Number of Variants 20,171
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000128
Citation (link to publication) Sinnott-Armstrong N et al. Nat Genet (2021)
Ancestry Distribution
Score Development/Training
European: 100%
255,256 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
10 Sample Sets

Development Samples

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
223,327 individuals European
(British)		 UKB — — — — Training
31,929 individuals European
(British)		 UKB — — — — Validation

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
PPM001428 PSS000777|
African Ancestry|
6,011 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Urate [umol/L] — — R²: 0.29536
Spearman's ρ: 0.24		 Age, sex, PCs(1-40) —
PPM001463 PSS000778|
East Asian Ancestry|
1,080 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Urate [umol/L] — — R²: 0.33805
Spearman's ρ: 0.269		 Age, sex, PCs(1-40) —
PPM001498 PSS000779|
European Ancestry|
23,561 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Urate [umol/L] — — R²: 0.42054
Spearman's ρ: 0.361		 Age, sex, PCs(1-40) —
PPM001533 PSS000780|
South Asian Ancestry|
7,328 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Urate [umol/L] — — R²: 0.32468
Spearman's ρ: 0.308		 Age, sex, PCs(1-40) —
PPM001568 PSS000781|
European Ancestry|
63,704 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Urate [umol/L] — — R²: 0.3966
Spearman's ρ: 0.378		 Age, sex, PCs(1-40) —
PPM007425 PSS007211|
African Ancestry|
6,093 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Urate — — R²: 0.23316 [0.21516, 0.25115]
Incremental R2 (full-covars): 0.00036
PGS R2 (no covariates): 0.04257 [0.03297, 0.05217]		 age, sex, UKB array type, Genotype PCs —
PPM007426 PSS007212|
East Asian Ancestry|
1,614 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Urate — — R²: 0.28286 [0.24672, 0.31901]
Incremental R2 (full-covars): 0.00043
PGS R2 (no covariates): 0.05737 [0.03597, 0.07876]		 age, sex, UKB array type, Genotype PCs —
PPM007427 PSS007213|
European Ancestry|
23,752 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Urate — — R²: 0.31443 [0.30488, 0.32398]
Incremental R2 (full-covars): 0.00063
PGS R2 (no covariates): 0.0839 [0.07731, 0.09049]		 age, sex, UKB array type, Genotype PCs —
PPM007428 PSS007214|
South Asian Ancestry|
7,418 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Urate — — R²: 0.22062 [0.20441, 0.23683]
Incremental R2 (full-covars): 0.00055
PGS R2 (no covariates): 0.07337 [0.06226, 0.08448]		 age, sex, UKB array type, Genotype PCs —
PPM007429 PSS007215|
European Ancestry|
64,383 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Urate — — R²: 0.27496 [0.26922, 0.2807]
Incremental R2 (full-covars): 0.00069
PGS R2 (no covariates): 0.10013 [0.09583, 0.10442]		 age, sex, UKB array type, Genotype PCs —

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
PSS000777 — — 6,011 individuals — African unspecified — UKB —
PSS000778 — — 1,080 individuals — East Asian — UKB —
PSS000779 — — 23,561 individuals — European Non-British White UKB —
PSS000780 — — 7,328 individuals — South Asian — UKB —
PSS000781 — — 63,704 individuals — European
(British)		 — UKB —
PSS007211 — — 6,093 individuals — African unspecified — UKB —
PSS007212 — — 1,614 individuals — East Asian — UKB —
PSS007213 — — 23,752 individuals — European non-white British ancestry UKB —
PSS007214 — — 7,418 individuals — South Asian — UKB —
PSS007215 — — 64,383 individuals — European white British ancestry UKB Testing cohort (heldout set)