Polygenic Score (PGS) ID: PGS000701

Predicted Trait
Reported Trait Urea [mmol/L]
Mapped Trait(s) serum urea measurement (EFO_0009795)
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.Urea
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 12,351
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
PPM001429 PSS000782|
African Ancestry|
6,015 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Urea [mmol/L] — — R²: 0.13035
Spearman's ρ: 0.111		 Age, sex, PCs(1-40) —
PPM001464 PSS000783|
East Asian Ancestry|
1,080 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Urea [mmol/L] — — R²: 0.12883
Spearman's ρ: 0.147		 Age, sex, PCs(1-40) —
PPM001499 PSS000784|
European Ancestry|
23,562 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Urea [mmol/L] — — R²: 0.15772
Spearman's ρ: 0.205		 Age, sex, PCs(1-40) —
PPM001534 PSS000785|
South Asian Ancestry|
7,336 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Urea [mmol/L] — — R²: 0.15556
Spearman's ρ: 0.174		 Age, sex, PCs(1-40) —
PPM001569 PSS000786|
European Ancestry|
63,745 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Urea [mmol/L] — — R²: 0.15214
Spearman's ρ: 0.223		 Age, sex, PCs(1-40) —
PPM007430 PSS007116|
African Ancestry|
6,097 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Urea — — R²: 0.09637 [0.08274, 0.11001]
Incremental R2 (full-covars): 0.00328
PGS R2 (no covariates): 0.00567 [0.00203, 0.00931]		 age, sex, UKB array type, Genotype PCs —
PPM007431 PSS007117|
East Asian Ancestry|
1,614 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Urea — — R²: 0.12047 [0.09154, 0.1494]
Incremental R2 (full-covars): 0.00765
PGS R2 (no covariates): 0.01582 [0.00409, 0.02754]		 age, sex, UKB array type, Genotype PCs —
PPM007432 PSS007118|
European Ancestry|
23,752 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Urea — — R²: 0.10315 [0.096, 0.11031]
Incremental R2 (full-covars): 0.01247
PGS R2 (no covariates): 0.03634 [0.03178, 0.0409]		 age, sex, UKB array type, Genotype PCs —
PPM007433 PSS007119|
South Asian Ancestry|
7,427 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Urea — — R²: 0.11244 [0.09926, 0.12562]
Incremental R2 (full-covars): 0.00839
PGS R2 (no covariates): 0.02026 [0.01408, 0.02643]		 age, sex, UKB array type, Genotype PCs —
PPM007434 PSS007120|
European Ancestry|
64,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Urea — — R²: 0.08868 [0.08459, 0.09278]
Incremental R2 (full-covars): 0.0137
PGS R2 (no covariates): 0.04033 [0.03742, 0.04324]		 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
PSS000782 — — 6,015 individuals — African unspecified — UKB —
PSS000783 — — 1,080 individuals — East Asian — UKB —
PSS000784 — — 23,562 individuals — European Non-British White UKB —
PSS000785 — — 7,336 individuals — South Asian — UKB —
PSS000786 — — 63,745 individuals — European
(British)		 — UKB —
PSS007116 — — 6,097 individuals — African unspecified — UKB —
PSS007117 — — 1,614 individuals — East Asian — UKB —
PSS007118 — — 23,752 individuals — European non-white British ancestry UKB —
PSS007119 — — 7,427 individuals — South Asian — UKB —
PSS007120 — — 64,425 individuals — European white British ancestry UKB Testing cohort (heldout set)