Polygenic Score (PGS) ID: PGS000678

Predicted Trait
Reported Trait Creatinine [umol/L]
Mapped Trait(s) creatinine measurement (EFO_0004518)
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.Creatinine
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 21,027
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
PPM001406 PSS000667|
African Ancestry|
6,016 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Creatinine [umol/L] — — R²: 0.37051
Spearman's ρ: 0.146		 Age, sex, PCs(1-40) —
PPM001441 PSS000668|
East Asian Ancestry|
1,081 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Creatinine [umol/L] — — R²: 0.44314
Spearman's ρ: 0.229		 Age, sex, PCs(1-40) —
PPM001476 PSS000674|
European Ancestry|
23,576 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Creatinine [umol/L] — — R²: 0.3939
Spearman's ρ: 0.325		 Age, sex, PCs(1-40) —
PPM001511 PSS000675|
South Asian Ancestry|
7,339 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Creatinine [umol/L] — — R²: 0.40587
Spearman's ρ: 0.283		 Age, sex, PCs(1-40) —
PPM001546 PSS000676|
European Ancestry|
63,758 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Creatinine [umol/L] — — R²: 0.41565
Spearman's ρ: 0.337		 Age, sex, PCs(1-40) —
PPM001579 PSS000800|
European Ancestry|
2,129 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Creatinine [umol/L] — — Spearman's ρ: 0.24 Age, sex —
PPM007315 PSS007131|
African Ancestry|
6,097 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Creatinine — — R²: 0.1805 [0.16358, 0.19743]
Incremental R2 (full-covars): 0.00023
PGS R2 (no covariates): 0.0048 [0.00145, 0.00815]		 age, sex, UKB array type, Genotype PCs —
PPM007316 PSS007132|
East Asian Ancestry|
1,615 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Creatinine — — R²: 0.30903 [0.27263, 0.34543]
Incremental R2 (full-covars): 0.0006
PGS R2 (no covariates): 0.01099 [0.00116, 0.02081]		 age, sex, UKB array type, Genotype PCs —
PPM007317 PSS007133|
European Ancestry|
23,762 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Creatinine — — R²: 0.23065 [0.22147, 0.23982]
Incremental R2 (full-covars): 0.00126
PGS R2 (no covariates): 0.04345 [0.0385, 0.0484]		 age, sex, UKB array type, Genotype PCs —
PPM007318 PSS007134|
South Asian Ancestry|
7,427 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Creatinine — — R²: 0.2107 [0.19466, 0.22675]
Incremental R2 (full-covars): 0.00063
PGS R2 (no covariates): 0.02244 [0.01595, 0.02892]		 age, sex, UKB array type, Genotype PCs —
PPM007319 PSS007135|
European Ancestry|
64,433 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Creatinine — — R²: 0.23859 [0.23298, 0.24421]
Incremental R2 (full-covars): 0.00127
PGS R2 (no covariates): 0.04554 [0.04246, 0.04861]		 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
PSS007132 — — 1,615 individuals — East Asian — UKB —
PSS007133 — — 23,762 individuals — European non-white British ancestry UKB —
PSS007134 — — 7,427 individuals — South Asian — UKB —
PSS007135 — — 64,433 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS000667 — — 6,016 individuals — African unspecified — UKB —
PSS000668 — — 1,081 individuals — East Asian — UKB —
PSS000800 — — 2,129 individuals — European Participants self-identifying as white MESA —
PSS000674 — — 23,576 individuals — European Non-British White UKB —
PSS000675 — — 7,339 individuals — South Asian — UKB —
PSS000676 — — 63,758 individuals — European
(British)		 — UKB —
PSS007131 — — 6,097 individuals — African unspecified — UKB —