Polygenic Score (PGS) ID: PGS001998

Predicted Trait
Reported Trait Phosphate
Mapped Trait(s) phosphate measurement (EFO_0010968)
Additional Trait Information biological measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-PLR_phosphate
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 47,793
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
PPM010859 PSS009482|
European Ancestry|
17,416 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phosphate Partial Correlation (partial-r): 0.2712 [0.2574, 0.2849] sex, age, birth date, deprivation index, 16 PCs
PPM010860 PSS009256|
European Ancestry|
3,587 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phosphate Partial Correlation (partial-r): 0.2829 [0.2524, 0.3128] sex, age, birth date, deprivation index, 16 PCs
PPM010861 PSS008810|
European Ancestry|
5,788 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phosphate Partial Correlation (partial-r): 0.2787 [0.2547, 0.3024] sex, age, birth date, deprivation index, 16 PCs
PPM010862 PSS008584|
Greater Middle Eastern Ancestry|
1,032 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phosphate Partial Correlation (partial-r): 0.3088 [0.252, 0.3635] sex, age, birth date, deprivation index, 16 PCs
PPM010863 PSS008362|
South Asian Ancestry|
5,480 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phosphate Partial Correlation (partial-r): 0.2425 [0.2174, 0.2673] sex, age, birth date, deprivation index, 16 PCs
PPM010864 PSS008139|
East Asian Ancestry|
1,562 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phosphate Partial Correlation (partial-r): 0.2335 [0.1858, 0.2802] sex, age, birth date, deprivation index, 16 PCs
PPM010865 PSS007926|
African Ancestry|
2,158 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phosphate Partial Correlation (partial-r): 0.1653 [0.1238, 0.2063] sex, age, birth date, deprivation index, 16 PCs
PPM010866 PSS009030|
African Ancestry|
3,396 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phosphate Partial Correlation (partial-r): 0.1139 [0.0804, 0.147] 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
PSS009030 3,396 individuals African unspecified Nigeria (West Africa) UKB
PSS008584 1,032 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009256 3,587 individuals European Poland (NE Europe) UKB
PSS008810 5,788 individuals European Italy (South Europe) UKB
PSS008362 5,480 individuals South Asian India (South Asia) UKB
PSS009482 17,416 individuals European UK (+ Ireland) UKB
PSS008139 1,562 individuals East Asian China (East Asia) UKB
PSS007926 2,158 individuals African American or Afro-Caribbean Carribean UKB