Polygenic Score (PGS) ID: PGS000692

Predicted Trait
Reported Trait Phosphate [mmol/L]
Mapped Trait(s) phosphate measurement (EFO_0010968)
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.Phosphate
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 12,448
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
PPM001420 PSS000734|
African Ancestry|
5,568 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Phosphate [mmol/L] — — R²: 0.12827
Spearman's ρ: 0.115		 Age, sex, PCs(1-40) —
PPM001455 PSS000735|
East Asian Ancestry|
986 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Phosphate [mmol/L] — — R²: 0.20287
Spearman's ρ: 0.222		 Age, sex, PCs(1-40) —
PPM001490 PSS000736|
European Ancestry|
21,497 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Phosphate [mmol/L] — — R²: 0.22656
Spearman's ρ: 0.253		 Age, sex, PCs(1-40) —
PPM001525 PSS000737|
South Asian Ancestry|
6,685 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Phosphate [mmol/L] — — R²: 0.20962
Spearman's ρ: 0.226		 Age, sex, PCs(1-40) —
PPM001560 PSS000738|
European Ancestry|
58,167 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Phosphate [mmol/L] — — Spearman's ρ: 0.255
R²: 0.23753		 Age, sex, PCs(1-40) —
PPM001587 PSS000828|
European Ancestry|
2,081 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Phosphate [mmol/L] — — Spearman's ρ: 0.248 Age, sex —
PPM007385 PSS007181|
African Ancestry|
5,650 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Phosphate — — R²: 0.0376 [0.02853, 0.04667]
Incremental R2 (full-covars): 0.01325
PGS R2 (no covariates): 0.01546 [0.00951, 0.02141]		 age, sex, UKB array type, Genotype PCs —
PPM007386 PSS007182|
East Asian Ancestry|
1,473 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Phosphate — — R²: 0.10627 [0.07866, 0.13388]
Incremental R2 (full-covars): 0.01785
PGS R2 (no covariates): 0.03634 [0.01893, 0.05375]		 age, sex, UKB array type, Genotype PCs —
PPM007387 PSS007183|
European Ancestry|
21,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Phosphate — — R²: 0.10387 [0.0967, 0.11104]
Incremental R2 (full-covars): 0.05604
PGS R2 (no covariates): 0.05717 [0.05157, 0.06277]		 age, sex, UKB array type, Genotype PCs —
PPM007388 PSS007184|
South Asian Ancestry|
6,778 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Phosphate — — R²: 0.09621 [0.0838, 0.10862]
Incremental R2 (full-covars): 0.0525
PGS R2 (no covariates): 0.05371 [0.044, 0.06342]		 age, sex, UKB array type, Genotype PCs —
PPM007389 PSS007185|
European Ancestry|
58,977 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Phosphate — — R²: 0.11827 [0.11369, 0.12284]
Incremental R2 (full-covars): 0.05726
PGS R2 (no covariates): 0.05777 [0.05435, 0.06119]		 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
PSS007181 — — 5,650 individuals — African unspecified — UKB —
PSS007182 — — 1,473 individuals — East Asian — UKB —
PSS007183 — — 21,704 individuals — European non-white British ancestry UKB —
PSS007184 — — 6,778 individuals — South Asian — UKB —
PSS000828 — — 2,081 individuals — European Participants self-identifying as white MESA —
PSS007185 — — 58,977 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS000734 — — 5,568 individuals — African unspecified — UKB —
PSS000735 — — 986 individuals — East Asian — UKB —
PSS000736 — — 21,497 individuals — European Non-British White UKB —
PSS000737 — — 6,685 individuals — South Asian — UKB —
PSS000738 — — 58,167 individuals — European
(British)		 — UKB —