PGS Catalog - PGS000884 / Estimated glomerular filtration rate (Polygenic Score)

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)	—	—	R²: 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	—