Polygenic Score (PGS) ID: PGS005090

Predicted Trait
Reported Trait Chronic kidney disease (stage 3 or higher)
Mapped Trait(s) chronic kidney disease (EFO_0003884)
Additional Trait Information APOL1 risk status
Released in PGS Catalog: Oct. 29, 2024
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Score Details

Score Construction
PGS Name CKD_PRS_AA
Development Method
Name PRS-CS
Parameters phi shrinkage parameter = 1
Variants
Original Genome Build hg19
Number of Variants 1,142,436
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000683
Citation (link to publication) Jones AC et al. J Am Soc Nephrol (2024)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 79.6%
African: 20.4%
280,722 individuals (100%)
PGS Evaluation
African: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST008747
Europe PMC: 31451708
 223,386 individuals European MVP, REGARDS
GWAS Catalog: GCST008747
Europe PMC: 31451708
 57,336 individuals African American or Afro-Caribbean MVP, REGARDS

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
PPM022177 PSS011829|
African Ancestry|
67,819 individuals
 PGP000683 |
Jones AC et al. J Am Soc Nephrol (2024)
 Reported Trait: Chronic kidney disease OR: 1.41 [1.14, 1.76] AUROC: 0.9 R²: 0.1 age, sex, diabetes, PC1-PC10 —

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
PSS011829 CKD (stage 3 or higher) per KDIGO staging —
[
  • 103 cases
  • , 1,759 controls
]
,
37.0 % Male samples
 Mean = [18.0, 99.0] years African American or Afro-Caribbean
(African American)		 — HYPERGEN —