Trait: sodium measurement

Experimental Factor Ontology (EFO) Information
Identifier EFO_0009282
Description A quantitative measurement of the amount of sodium present in a sample.
Trait category
Other measurement
Synonyms 2 synonyms
  • Na measurement
  • sodium levels
Mapped term PMID:29403010

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
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)
PGS000695
(snpnet.Sodium_in_urine)
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Sodium in urine [mmol/L] urinary metabolite measurement,
sodium measurement		 5,833
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000695/ScoringFiles/PGS000695.txt.gz - Check Terms/Licenses
PGS002007
(portability-PLR_sodium_urine)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Sodium in urine sodium measurement 37,568
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002007/ScoringFiles/PGS002007.txt.gz
PGS002226
(portability-ldpred2_sodium_urine)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Sodium in urine sodium measurement 922,972
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002226/ScoringFiles/PGS002226.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
PPM001423 PGS000695
(snpnet.Sodium_in_urine)
 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 PGS000695
(snpnet.Sodium_in_urine)
 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 PGS000695
(snpnet.Sodium_in_urine)
 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 PGS000695
(snpnet.Sodium_in_urine)
 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 PGS000695
(snpnet.Sodium_in_urine)
 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 PGS000695
(snpnet.Sodium_in_urine)
 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 PGS000695
(snpnet.Sodium_in_urine)
 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 PGS000695
(snpnet.Sodium_in_urine)
 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 PGS000695
(snpnet.Sodium_in_urine)
 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 PGS000695
(snpnet.Sodium_in_urine)
 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 PGS000695
(snpnet.Sodium_in_urine)
 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 —
PPM010931 PGS002007
(portability-PLR_sodium_urine)
 PSS009266|
European Ancestry|
3,966 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sodium in urine — — Partial Correlation (partial-r): 0.089 [0.058, 0.1199] sex, age, birth date, deprivation index, 16 PCs —
PPM010932 PGS002007
(portability-PLR_sodium_urine)
 PSS008820|
European Ancestry|
6,423 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sodium in urine — — Partial Correlation (partial-r): 0.1028 [0.0785, 0.127] sex, age, birth date, deprivation index, 16 PCs —
PPM010933 PGS002007
(portability-PLR_sodium_urine)
 PSS008594|
Greater Middle Eastern Ancestry|
1,143 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sodium in urine — — Partial Correlation (partial-r): 0.0662 [0.0078, 0.1242] sex, age, birth date, deprivation index, 16 PCs —
PPM010934 PGS002007
(portability-PLR_sodium_urine)
 PSS008372|
South Asian Ancestry|
6,018 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sodium in urine — — Partial Correlation (partial-r): 0.0825 [0.0573, 0.1076] sex, age, birth date, deprivation index, 16 PCs —
PPM010935 PGS002007
(portability-PLR_sodium_urine)
 PSS008148|
East Asian Ancestry|
1,743 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sodium in urine — — Partial Correlation (partial-r): 0.0771 [0.03, 0.1239] sex, age, birth date, deprivation index, 16 PCs —
PPM010936 PGS002007
(portability-PLR_sodium_urine)
 PSS007936|
African Ancestry|
2,380 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sodium in urine — — Partial Correlation (partial-r): 0.0396 sex, age, birth date, deprivation index, 16 PCs —
PPM010937 PGS002007
(portability-PLR_sodium_urine)
 PSS009040|
African Ancestry|
3,769 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sodium in urine — — Partial Correlation (partial-r): 0.027 [-0.0051, 0.0589] sex, age, birth date, deprivation index, 16 PCs —
PPM010930 PGS002007
(portability-PLR_sodium_urine)
 PSS009492|
European Ancestry|
19,357 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sodium in urine — — Partial Correlation (partial-r): 0.1218 [0.1079, 0.1357] sex, age, birth date, deprivation index, 16 PCs —
PPM012654 PGS002226
(portability-ldpred2_sodium_urine)
 PSS009492|
European Ancestry|
19,357 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sodium in urine — — Partial Correlation (partial-r): 0.1412 [0.1274, 0.155] sex, age, birth date, deprivation index, 16 PCs —
PPM012655 PGS002226
(portability-ldpred2_sodium_urine)
 PSS009266|
European Ancestry|
3,966 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sodium in urine — — Partial Correlation (partial-r): 0.1046 [0.0737, 0.1354] sex, age, birth date, deprivation index, 16 PCs —
PPM012657 PGS002226
(portability-ldpred2_sodium_urine)
 PSS008594|
Greater Middle Eastern Ancestry|
1,143 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sodium in urine — — Partial Correlation (partial-r): 0.078 [0.0196, 0.1359] sex, age, birth date, deprivation index, 16 PCs —
PPM012658 PGS002226
(portability-ldpred2_sodium_urine)
 PSS008372|
South Asian Ancestry|
6,018 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sodium in urine — — Partial Correlation (partial-r): 0.1078 [0.0827, 0.1327] sex, age, birth date, deprivation index, 16 PCs —
PPM012659 PGS002226
(portability-ldpred2_sodium_urine)
 PSS008148|
East Asian Ancestry|
1,743 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sodium in urine — — Partial Correlation (partial-r): 0.0943 [0.0473, 0.1409] sex, age, birth date, deprivation index, 16 PCs —
PPM012660 PGS002226
(portability-ldpred2_sodium_urine)
 PSS007936|
African Ancestry|
2,380 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sodium in urine — — Partial Correlation (partial-r): 0.0148 [-0.0256, 0.0551] sex, age, birth date, deprivation index, 16 PCs —
PPM012661 PGS002226
(portability-ldpred2_sodium_urine)
 PSS009040|
African Ancestry|
3,769 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sodium in urine — — Partial Correlation (partial-r): 0.0336 [0.0016, 0.0656] sex, age, birth date, deprivation index, 16 PCs —
PPM012656 PGS002226
(portability-ldpred2_sodium_urine)
 PSS008820|
European Ancestry|
6,423 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sodium in urine — — Partial Correlation (partial-r): 0.1181 [0.0939, 0.1422] sex, age, birth date, deprivation index, 16 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
PSS009040 — — 3,769 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008148 — — 1,743 individuals — East Asian China (East Asia) UKB —
PSS000836 — — 2,117 individuals — European Participants self-identifying as white MESA —
PSS008820 — — 6,423 individuals — European Italy (South Europe) UKB —
PSS007936 — — 2,380 individuals — African American or Afro-Caribbean Carribean UKB —
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 —
PSS008594 — — 1,143 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009492 — — 19,357 individuals — European UK (+ Ireland) UKB —
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 —
PSS007065 — — 65,531 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS009266 — — 3,966 individuals — European Poland (NE Europe) UKB —
PSS008372 — — 6,018 individuals — South Asian India (South Asia) UKB —