Polygenic Score (PGS) ID: PGS003290

Predicted Trait
Reported Trait Estimated glomerular filtration rate (Cystatin C)
Mapped Trait(s)
Additional Trait Information eGFRcys; Quantitative
Released in PGS Catalog: Nov. 23, 2022
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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 ExPRSweb_CysC_CKDGen-1000Genomes-DiscoveryMeta-eGFRcys_PT_MGI_20211120
Development Method
Name Pruning and Thresholding (P+T)
Parameters LD Clumping (using Plink to calculate LD, MAF >= 1%, r^2 <= 0.1) & P-value threshold <=1.00e-05
Variants
Original Genome Build GRCh37
Number of Variants 48
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000393
Citation (link to publication) Ma Y et al. Am J Hum Genet (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
110,527 individuals (100%)
Score Development/Training
European: 100%
19,026 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST004293
 110,527 individuals European NR
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
— 19,026 individuals European MGI Cystatin C (LOINC: 33863-2); Quantitative — — — —

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
PPM015745 PSS010020|
European Ancestry|
19,504 individuals
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Reported Trait: eGFR β: -0.0298 (0.0525) — R²: 2e-05 SEX,AGE,Batch,PC1,PC2,PC3,PC4 —

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
PSS010020 Estimated GFR, Non-Black (LOINC: 48642-3); Quantitative — 19,504 individuals — European — MGI —