Polygenic Score (PGS) ID: PGS002226

Predicted Trait
Reported Trait Sodium in urine
Mapped Trait(s) sodium measurement (EFO_0009282)
Additional Trait Information biological measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_sodium_urine
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 922,972
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 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
— 391,124 individuals European UKB — — — UK (+ Ireland) —

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
PPM012654 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 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 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 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 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 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 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 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 —
PSS008594 — — 1,143 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009266 — — 3,966 individuals — European Poland (NE Europe) UKB —
PSS009492 — — 19,357 individuals — European UK (+ Ireland) UKB —
PSS008148 — — 1,743 individuals — East Asian China (East Asia) UKB —
PSS008372 — — 6,018 individuals — South Asian India (South Asia) UKB —
PSS008820 — — 6,423 individuals — European Italy (South Europe) UKB —
PSS007936 — — 2,380 individuals — African American or Afro-Caribbean Carribean UKB —