PGS Publication: PGP000229

Publication Information (EuropePMC)
Title Polygenic Risk Scores for Kidney Function and Their Associations with Circulating Proteome, and Incident Kidney Diseases.
PubMed ID 34548389(Europe PMC)
doi 10.1681/asn.2020111599
Publication Date Sept. 21, 2021
Journal J Am Soc Nephrol
Author(s) Yu Z, Jin J, Tin A, Köttgen A, Yu B, Chen J, Surapaneni A, Zhou L, Ballantyne C, Hoogeveen R, Arking D, Chatterjee N, Grams M, Coresh J.
Released in PGS Catalog: Oct. 7, 2021

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000885
(eGFR_TOPSNPPRS)
 PGP000229 |
Yu Z et al. J Am Soc Nephrol (2021)
 Estimated glomerular filtration rate glomerular filtration rate 1,460
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000885/ScoringFiles/PGS000885.txt.gz
PGS000883
(eGFR_LDpredPRS)
 PGP000229 |
Yu Z et al. J Am Soc Nephrol (2021)
 Estimated glomerular filtration rate glomerular filtration rate 1,477,661
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000883/ScoringFiles/PGS000883.txt.gz
PGS000884
(eGFR_PTPRS)
 PGP000229 |
Yu Z et al. J Am Soc Nephrol (2021)
 Estimated glomerular filtration rate glomerular filtration rate 40,042
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000884/ScoringFiles/PGS000884.txt.gz

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) 		Evaluated Score 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
PPM002529 PGS000883
(eGFR_LDpredPRS)
 PSS001143|
European Ancestry|
8,886 individuals
 PGP000229 |
Yu Z et al. J Am Soc Nephrol (2021)
 Reported Trait: Incident end stage kidney disease HR: 1.24 — — 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 —
PPM002531 PGS000883
(eGFR_LDpredPRS)
 PSS001143|
European Ancestry|
8,886 individuals
 PGP000229 |
Yu Z et al. J Am Soc Nephrol (2021)
 Reported Trait: Incident acute kidney injury HR: 1.05 — — 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 —
PPM002532 PGS000883
(eGFR_LDpredPRS)
 PSS001143|
European Ancestry|
8,886 individuals
 PGP000229 |
Yu Z et al. J Am Soc Nephrol (2021)
 Reported Trait: Estimated glomerular filtration rate (eGFR) — — R²: 0.0713 age at baseline, sex, center, first 10 genetic principal components —
PPM002533 PGS000884
(eGFR_PTPRS)
 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 PGS000884
(eGFR_PTPRS)
 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 PGS000884
(eGFR_PTPRS)
 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 PGS000884
(eGFR_PTPRS)
 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 PGS000884
(eGFR_PTPRS)
 PSS001143|
European Ancestry|
8,886 individuals
 PGP000229 |
Yu Z et al. J Am Soc Nephrol (2021)
 Reported Trait: Estimated glomerular filtration rate (eGFR) — — R²: 0.0599 age at baseline, sex, center, first 10 genetic principal components —
PPM002538 PGS000885
(eGFR_TOPSNPPRS)
 PSS001143|
European Ancestry|
8,886 individuals
 PGP000229 |
Yu Z et al. J Am Soc Nephrol (2021)
 Reported Trait: Incident chronic kidney disease HR: 1.25 — — 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 —
PPM002539 PGS000885
(eGFR_TOPSNPPRS)
 PSS001143|
European Ancestry|
8,886 individuals
 PGP000229 |
Yu Z et al. J Am Soc Nephrol (2021)
 Reported Trait: Incident end stage kidney disease HR: 1.12 — — 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 —
PPM002540 PGS000885
(eGFR_TOPSNPPRS)
 PSS001143|
European Ancestry|
8,886 individuals
 PGP000229 |
Yu Z et al. J Am Soc Nephrol (2021)
 Reported Trait: Incident kidney failure HR: 1.13 — — 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 —
PPM002541 PGS000885
(eGFR_TOPSNPPRS)
 PSS001143|
European Ancestry|
8,886 individuals
 PGP000229 |
Yu Z et al. J Am Soc Nephrol (2021)
 Reported Trait: Incident acute kidney injury HR: 1.0 — — 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 —
PPM002542 PGS000885
(eGFR_TOPSNPPRS)
 PSS001143|
European Ancestry|
8,886 individuals
 PGP000229 |
Yu Z et al. J Am Soc Nephrol (2021)
 Reported Trait: Estimated glomerular filtration rate (eGFR) — — R²: 0.0478 age at baseline, sex, center, first 10 genetic principal components —
PPM002528 PGS000883
(eGFR_LDpredPRS)
 PSS001143|
European Ancestry|
8,886 individuals
 PGP000229 |
Yu Z et al. J Am Soc Nephrol (2021)
 Reported Trait: Incident chronic kidney disease HR: 1.32 AUROC: 0.677 — 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 —
PPM002530 PGS000883
(eGFR_LDpredPRS)
 PSS001143|
European Ancestry|
8,886 individuals
 PGP000229 |
Yu Z et al. J Am Soc Nephrol (2021)
 Reported Trait: Incident kidney failure HR: 1.17 — — 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 —

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 —