Polygenic Score (PGS) ID: PGS000682

Predicted Trait
Reported Trait eGFR [ml/min/1.73m2]
Mapped Trait(s) glomerular filtration rate (EFO_0005208)
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.eGFR
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 17,467
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
PPM001410 PSS000805|
African Ancestry|
6,016 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: eGFR [ml/min/1.73m2] — — R²: 0.17769
Spearman's ρ: 0.138		 Age, sex, PCs(1-40) —
PPM001445 PSS000806|
East Asian Ancestry|
1,081 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: eGFR [ml/min/1.73m2] — — R²: 0.21054
Spearman's ρ: 0.199		 Age, sex, PCs(1-40) —
PPM001480 PSS000807|
European Ancestry|
23,576 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: eGFR [ml/min/1.73m2] — — R²: 0.25538
Spearman's ρ: 0.299		 Age, sex, PCs(1-40) —
PPM001515 PSS000808|
South Asian Ancestry|
7,339 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: eGFR [ml/min/1.73m2] — — R²: 0.23182
Spearman's ρ: 0.252		 Age, sex, PCs(1-40) —
PPM001550 PSS000809|
European Ancestry|
63,758 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: eGFR [ml/min/1.73m2] — — R²: 0.24611
Spearman's ρ: 0.313		 Age, sex, PCs(1-40) —
PPM001592 PSS000810|
European Ancestry|
2,129 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: eGFR [ml/min/1.73m2] — — Spearman's ρ: 0.219 Age, sex —
PPM007335 PSS006911|
African Ancestry|
6,016 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: eGFR — — R²: 0.01637 [0.01025, 0.02249]
Incremental R2 (full-covars): 0.01318
PGS R2 (no covariates): 0.01368 [0.00807, 0.01929]		 age, sex, UKB array type, Genotype PCs —
PPM007336 PSS006912|
East Asian Ancestry|
1,578 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: eGFR — — R²: 0.03595 [0.01863, 0.05327]
Incremental R2 (full-covars): 0.01715
PGS R2 (no covariates): 0.0203 [0.00707, 0.03352]		 age, sex, UKB array type, Genotype PCs —
PPM007337 PSS006913|
European Ancestry|
23,574 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: eGFR — — R²: 0.06443 [0.05853, 0.07033]
Incremental R2 (full-covars): 0.06277
PGS R2 (no covariates): 0.06321 [0.05736, 0.06906]		 age, sex, UKB array type, Genotype PCs —
PPM007338 PSS006914|
South Asian Ancestry|
7,288 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: eGFR — — R²: 0.03876 [0.03038, 0.04714]
Incremental R2 (full-covars): 0.03269
PGS R2 (no covariates): 0.03296 [0.02519, 0.04073]		 age, sex, UKB array type, Genotype PCs —
PPM007339 PSS006915|
European Ancestry|
63,753 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: eGFR — — R²: 0.07514 [0.07131, 0.07897]
Incremental R2 (full-covars): 0.07513
PGS R2 (no covariates): 0.07525 [0.07142, 0.07908]		 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
PSS000807 — — 23,576 individuals — European Non-British White UKB —
PSS000808 — — 7,339 individuals — South Asian — UKB —
PSS000809 — — 63,758 individuals — European
(British)		 — UKB —
PSS000810 — — 2,129 individuals — European Participants self-identifying as white MESA —
PSS006911 — — 6,016 individuals — African unspecified — UKB —
PSS006912 — — 1,578 individuals — East Asian — UKB —
PSS006913 — — 23,574 individuals — European non-white British ancestry UKB —
PSS006914 — — 7,288 individuals — South Asian — UKB —
PSS006915 — — 63,753 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS000805 — — 6,016 individuals — African unspecified — UKB —
PSS000806 — — 1,081 individuals — East Asian — UKB —