Polygenic Score (PGS) ID: PGS002237

Predicted Trait
Reported Trait Chronic kidney disease (stage 3 or greater)
Mapped Trait(s) chronic kidney disease (EFO_0003884)
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name GPS_CKD
Development Method
Name Pruning and Thresholding (P+T)
Parameters R2=0.2 and P-vale=0.03
Variants
Original Genome Build GRCh37
Number of Variants 471,316
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000269
Citation (link to publication) Khan A et al. Nat Med (2022)
Ancestry Distribution
Score Development/Training
European: 100%
279,819 individuals (100%)
PGS Evaluation
European: 28.6%
Multi-ancestry (including European): 28.6%
  • European
  • Not Reported
African: 14.3%
Hispanic or Latin American: 14.3%
Additional Asian Ancestries: 14.3%
7 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
—
[
  • 28,047 cases
  • , 251,772 controls
]
,
0.46 % Male samples
 European UKB eGFR used for phentyoing CKD staging Mean = 56.65 years — — —

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
PPM012722 PSS009508|
European Ancestry|
141,247 individuals
 PGP000269 |
Khan A et al. Nat Med (2022)
 Reported Trait: Chronic Kidney Disease (stage 3 or greater) OR: 1.49 [1.47, 1.5] AUROC: 0.75 — Age, Sex, Diabetes and 4 PCs —
PPM012723 PSS009506|
African Ancestry|
14,544 individuals
 PGP000269 |
Khan A et al. Nat Med (2022)
 Reported Trait: Chronic Kidney Disease (stage 3 or greater) OR: 1.32 AUROC: 0.78 — Age, Sex, Diabetes and 4 PCs —
PPM012724 PSS009509|
Hispanic or Latin American Ancestry|
4,264 individuals
 PGP000269 |
Khan A et al. Nat Med (2022)
 Reported Trait: Chronic Kidney Disease (stage 3 or greater) OR: 1.42 [1.29, 1.57] AUROC: 0.88 — Age, Sex, Diabetes and 4 PCs —
PPM012725 PSS009507|
Additional Asian Ancestries|
10,087 individuals
 PGP000269 |
Khan A et al. Nat Med (2022)
 Reported Trait: Chronic Kidney Disease (stage 3 or greater) OR: 1.56 [1.43, 1.69] AUROC: 0.79 — Age, Sex, Diabetes and 4 PCs —
PPM018706 PSS011075|
European Ancestry|
11,813 individuals
 PGP000495 |
Bakshi A et al. Kidney Int (2023)
|Ext.		 Reported Trait: Chronic kidney disease (eGFR <60 ml/min per 1.73 m2 or UACR >3.0 mg/mmol) OR: 1.24 [1.19, 1.3] AUROC: 0.68 [0.67, 0.69] — age, sex, alcohol, smoking, hypertension, diabetes, body mass index, nonsteroidal anti-inflammatory drug and angiotensin-converting enzyme inhibitor/angiotensin receptor blocker use, and visit year —
PPM018707 PSS011075|
European Ancestry|
11,813 individuals
 PGP000495 |
Bakshi A et al. Kidney Int (2023)
|Ext.		 Reported Trait: Chronic kidney disease (eGFR <60 ml/min per 1.73 m2) OR: 1.51 [1.43, 1.59] AUROC: 0.71 [0.7, 0.73] — age, sex, alcohol, smoking, hypertension, diabetes, body mass index, nonsteroidal anti-inflammatory drug and angiotensin-converting enzyme inhibitor/angiotensin receptor blocker use, and visit year —
PPM018708 PSS011075|
European Ancestry|
11,813 individuals
 PGP000495 |
Bakshi A et al. Kidney Int (2023)
|Ext.		 Reported Trait: Chronic kidney disease (eGFR <45 ml/min per 1.73 m2) OR: 1.47 [1.32, 1.65] AUROC: 0.78 [0.75, 0.8] — age, sex, alcohol, smoking, hypertension, diabetes, body mass index, nonsteroidal anti-inflammatory drug and angiotensin-converting enzyme inhibitor/angiotensin receptor blocker use, and visit year —
PPM020420 PSS011354|
Multi-ancestry (including European)|
1,144 individuals
 PGP000552 |
Mantovani A et al. Aliment Pharmacol Ther (2023)
|Ext.		 Reported Trait: Estimated glomerular filtration rate β: -10.0 (1.32) — — sex, age, height, waist circumference, systolic blood pressure, ALT aminotransferase, Fasting insulin, albuminuria, LDL-cholesterol, lipid-lowering treatment, ethnicity, PNPLA3 rs738409 p.I148M —
PPM020421 PSS011355|
Multi-ancestry (including European)|
144 individuals
 PGP000552 |
Mantovani A et al. Aliment Pharmacol Ther (2023)
|Ext.		 Reported Trait: Estimated glomerular filtration rate β: -8.1 (4.23) — — sex, height, systolic blood pressure, LDL-cholesterol, ALT aminotransferase, albuminuria, PNPLA3 rs738409 p.I148M —

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
PSS011354 — — 1,144 individuals,
36.5 % Male samples
 Mean = 54.0 years
Sd = 6.0 years		 European, Not reported European (>90%), Not reported NR Liver-Bible-2022
PSS011355 — Median = 17.0 months 144 individuals — European, Not reported European, Not reported NR Liver-Bible-2022
PSS009506 eGFR<60 mL/min/1.73m2 used to define CKD (stage 3 or greater) —
[
  • 4,268 cases
  • , 10,276 controls
]
,
0.61 % Male samples
 Mean = 61.0 years African unspecified — 7 cohorts
  • BioMe
  • ,GenHAT
  • ,HYPERGEN
  • ,REGARDS
  • ,UKB
  • ,WPC
  • ,eMERGE
 —
PSS009507 eGFR<60 mL/min/1.73m2 used to define CKD (stage 3 or greater) —
[
  • 969 cases
  • , 9,118 controls
]
,
0.51 % Male samples
 Mean = 58.0 years Asian unspecified — BioMe, UKB, eMERGE —
PSS009508 eGFR<60 mL/min/1.73m2 used to define CKD (stage 3 or greater) —
[
  • 23,364 cases
  • , 117,883 controls
]
,
0.5 % Male samples
 Mean = 61.59 years European — BioMe, UKB, eMERGE —
PSS009509 eGFR<60 mL/min/1.73m2 used to define CKD (stage 3 or greater) —
[
  • 1,386 cases
  • , 2,878 controls
]
,
0.51 % Male samples
 Mean = 64.0 years Hispanic or Latin American — BioMe, UKB, eMERGE —
PSS011075 — — 11,813 individuals,
45.8 % Male samples
 Mean = 75.0 years
Sd = 4.2 years		 European — ASPREE —