Polygenic Score (PGS) ID: PGS000695

Predicted Trait
Reported Trait Sodium in urine [mmol/L]
Mapped Trait(s)
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.Sodium_in_urine
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 5,833
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: 45.5%
African: 18.2%
East Asian: 18.2%
South Asian: 18.2%
11 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
PPM001423 PSS000749|
African Ancestry|
5,781 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Sodium in urine [mmol/L] — — R²: 0.0456
Spearman's ρ: 0.029		 Age, sex, PCs(1-40) —
PPM001458 PSS000750|
East Asian Ancestry|
1,044 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Sodium in urine [mmol/L] — — R²: 0.09743
Spearman's ρ: 0.068		 Age, sex, PCs(1-40) —
PPM001493 PSS000751|
European Ancestry|
22,812 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Sodium in urine [mmol/L] — — R²: 0.11027
Spearman's ρ: 0.077		 Age, sex, PCs(1-40) —
PPM001528 PSS000752|
South Asian Ancestry|
6,993 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Sodium in urine [mmol/L] — — R²: 0.06605
Spearman's ρ: 0.059		 Age, sex, PCs(1-40) —
PPM001563 PSS000753|
European Ancestry|
62,011 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Sodium in urine [mmol/L] — — R²: 0.09883
Spearman's ρ: 0.09		 Age, sex, PCs(1-40) —
PPM001588 PSS000836|
European Ancestry|
2,117 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Sodium in urine [mmol/L] — — Spearman's ρ: 0.059 Age, sex —
PPM007400 PSS007061|
African Ancestry|
6,233 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Sodium in urine — — R²: 0.05917 [0.04805, 0.07029]
Incremental R2 (full-covars): 5e-05
PGS R2 (no covariates): 0.00059 [-0.00059, 0.00177]		 age, sex, UKB array type, Genotype PCs —
PPM007401 PSS007062|
East Asian Ancestry|
1,643 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Sodium in urine — — R²: 0.08627 [0.06084, 0.11171]
Incremental R2 (full-covars): 0.00013
PGS R2 (no covariates): 0.00482 [-0.00173, 0.01137]		 age, sex, UKB array type, Genotype PCs —
PPM007402 PSS007063|
European Ancestry|
24,080 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Sodium in urine — — R²: 0.09373 [0.08684, 0.10062]
Incremental R2 (full-covars): 0.00019
PGS R2 (no covariates): 0.00572 [0.00385, 0.00758]		 age, sex, UKB array type, Genotype PCs —
PPM007403 PSS007064|
South Asian Ancestry|
7,459 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Sodium in urine — — R²: 0.05861 [0.04852, 0.0687]
Incremental R2 (full-covars): 0.00012
PGS R2 (no covariates): 0.00376 [0.00105, 0.00646]		 age, sex, UKB array type, Genotype PCs —
PPM007404 PSS007065|
European Ancestry|
65,531 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Sodium in urine — — R²: 0.07284 [0.06906, 0.07661]
Incremental R2 (full-covars): 0.00025
PGS R2 (no covariates): 0.00836 [0.00699, 0.00973]		 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
PSS000749 — — 5,781 individuals — African unspecified — UKB —
PSS000750 — — 1,044 individuals — East Asian — UKB —
PSS000751 — — 22,812 individuals — European Non-British White UKB —
PSS000752 — — 6,993 individuals — South Asian — UKB —
PSS000753 — — 62,011 individuals — European
(British)		 — UKB —
PSS007065 — — 65,531 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS007061 — — 6,233 individuals — African unspecified — UKB —
PSS007062 — — 1,643 individuals — East Asian — UKB —
PSS007063 — — 24,080 individuals — European non-white British ancestry UKB —
PSS007064 — — 7,459 individuals — South Asian — UKB —
PSS000836 — — 2,117 individuals — European Participants self-identifying as white MESA —