Polygenic Score (PGS) ID: PGS000884

Predicted Trait
Reported Trait Estimated glomerular filtration rate
Mapped Trait(s) glomerular filtration rate (EFO_0005208)
Additional Trait Information Log transformed eGFR
Released in PGS Catalog: Oct. 7, 2021
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name eGFR_PTPRS
Development Method
Name Pruning and Thresholding (P+T)
Parameters r2 threshold = 0.1; p-value threshold = 0.05
Variants
Original Genome Build GRCh37
Number of Variants 40,042
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000229
Citation (link to publication) Yu Z et al. J Am Soc Nephrol (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 81.8%
East Asian: 14.4%
South Asian: 1.8%
African: 1.5%
Hispanic or Latin American: 0.4%
1,159,871 individuals (100%)
Score Development/Training
European: 96.1%
South Asian: 2%
African: 1.6%
East Asian: 0.3%
45,158 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
949,116 individuals European CKDGen, UKB
166,997 individuals East Asian CKDGen, UKB
21,338 individuals South Asian CKDGen, UKB
17,459 individuals African unspecified CKDGen, UKB
4,961 individuals Hispanic or Latin American CKDGen, UKB
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
43,413 individuals European UKB log transformed eGFR based on 2012 CKD-EPI creatinine equation
715 individuals African unspecified UKB log transformed eGFR based on 2012 CKD-EPI creatinine equation
888 individuals South Asian UKB log transformed eGFR based on 2012 CKD-EPI creatinine equation
142 individuals East Asian UKB log transformed eGFR based on 2012 CKD-EPI creatinine equation

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
PPM002533 PSS001143|
European Ancestry|
8,886 individuals
PGP000229 |
Yu Z et al. J Am Soc Nephrol (2021)
Reported Trait: Incident chronic kidney disease HR: 1.3 age at baseline, sex, center, first 10 genetic principal components, education, baseline body mass index, baseline smoking status, baseline history of hypertension, diabetes, and coronary heart disease
PPM002534 PSS001143|
European Ancestry|
8,886 individuals
PGP000229 |
Yu Z et al. J Am Soc Nephrol (2021)
Reported Trait: Incident end stage kidney disease HR: 1.28 age at baseline, sex, center, first 10 genetic principal components, education, baseline body mass index, baseline smoking status, baseline history of hypertension, diabetes, and coronary heart disease
PPM002535 PSS001143|
European Ancestry|
8,886 individuals
PGP000229 |
Yu Z et al. J Am Soc Nephrol (2021)
Reported Trait: Incident kidney failure HR: 1.2 age at baseline, sex, center, first 10 genetic principal components, education, baseline body mass index, baseline smoking status, baseline history of hypertension, diabetes, and coronary heart disease
PPM002536 PSS001143|
European Ancestry|
8,886 individuals
PGP000229 |
Yu Z et al. J Am Soc Nephrol (2021)
Reported Trait: Incident acute kidney injury HR: 1.04 age at baseline, sex, center, first 10 genetic principal components, education, baseline body mass index, baseline smoking status, baseline history of hypertension, diabetes, and coronary heart disease
PPM002537 PSS001143|
European Ancestry|
8,886 individuals
PGP000229 |
Yu Z et al. J Am Soc Nephrol (2021)
Reported Trait: Estimated glomerular filtration rate (eGFR) : 0.0599 age at baseline, sex, center, first 10 genetic principal components

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
PSS001143 log transformed eGFR based on 2012 CKD-EPI creatinine equation Mean = 30.0 years 8,886 individuals,
0.47 % Male samples
Mean = 54.3 years European ARIC