Polygenic Score (PGS) ID: PGS000728

Predicted Trait
Reported Trait Chronic kidney disease
Mapped Trait(s) chronic kidney disease (EFO_0003884)
Released in PGS Catalog: Feb. 23, 2021
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Score Details

Score Construction
PGS Name CKD_PGS
Variants
Original Genome Build GRCh37
Number of Variants 1,958,860
Development Method
Name LD-thinning
Parameters UKB was used for thinning (bi-allelic SNPs, MAF > 1%, INFO > 0.4, excluding palindromic SNPs); r2 threshold = 0.9
PGS Source
PGS Catalog Publication (PGP) ID PGP000137
Citation (link to publication) Ritchie SC et al. bioRxiv (2019) Preprint
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
625,219 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST008065
Europe PMC: 31152163
625,219 individuals European

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
PPM001669 PSS000870|
European Ancestry|
3,037 individuals
PGP000137 |
Ritchie SC et al. bioRxiv (2019)
|Pre
Reported Trait: Estimated Glomerular Filtration Rate (eGFR) β: -0.9 [-1.45, -0.36] age, sex, 10 genetic PCs

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
PSS000870 Serum creatinine was quantified by Metabolon HD4 metabolomics in mg/dL units, and adjusted for sample measurement batch, sample measurement plate, and days between blood draw and sample processing. Subsequently, eGFR was quantified from serum creatinine using the CKD-EPI equation 3,037 individuals,
51.0 % Male samples
Median = 44.0 years
Iqr = [30.5, 54.7] years
European INTERVAL