Polygenic Score (PGS) ID: PGS002007

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-PLR_sodium_urine
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 37,568
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
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
391,124 individuals European UK (+ Ireland) UKB

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
PPM010931 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 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 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 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 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 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 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 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

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
PSS008820 6,423 individuals European Italy (South Europe) UKB
PSS008148 1,743 individuals East Asian China (East Asia) UKB
PSS008372 6,018 individuals South Asian India (South Asia) UKB
PSS009492 19,357 individuals European UK (+ Ireland) UKB
PSS007936 2,380 individuals African American or Afro-Caribbean Carribean UKB