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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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 CKD_PGS
Development Method
Name LD thinning
Parameters UKB was used for thinning (bi-allelic SNPs, MAF > 1%, INFO > 0.4, excluding palindromic SNPs);...  r2 threshold = 0.9Show more
Variants
Original Genome Build GRCh37
Number of Variants 1,958,860
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000137
Citation (link to publication) Ritchie SC et al. Nat Metab (2021)
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)
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Study Identifiers
Sample Numbers
Sample Ancestry
Cohort(s)
GWAS Catalog: GCST008065
Europe PMC: 31152163
625,219 individualsEuropean48 cohorts
  • ADVANCE_TRIAL
  • ,AFTER_EU
  • ,AGES
  • ,Airwave
  • ,BBJ
  • ,BioMe
  • ,CHNS
  • ,CHRIS
  • ,CHS
  • ,CoLaus
  • ,DC
  • ,DIACORE
  • ,ERF
  • ,FHS
  • ,FINRISK
  • ,FamHS
  • ,GS:SFHS
  • ,INGI-FVG
  • ,JHS
  • ,JUPITER
  • ,KORA
  • ,LIFE-Adult
  • ,LIFE-HEART
  • ,LLFS
  • ,LOLIPOP
  • ,LURIC
  • ,LifeLines
  • ,MDC-CC
  • ,MESA
  • ,MyCode
  • ,OGP
  • ,PIVUS
  • ,PREVEND
  • ,QIMR
  • ,RS
  • ,SAAR
  • ,SCES
  • ,SHIP
  • ,SIMES
  • ,SINDI
  • ,SOLID-TIMI_52
  • ,STABILITY
  • ,TwinGene
  • ,UKB
  • ,ULSAM
  • ,Vanderbilt
  • ,WGHS
  • ,deCODE
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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.

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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
PPM001669PSS000870|
European Ancestry|
3,037 individuals
PGP000137 |
Ritchie SC et al. Nat Metab (2021)
Reported Trait: Estimated Glomerular Filtration Rate (eGFR)β: -0.9 [-1.45, -0.36]——age, sex, 10 genetic PCs—
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Evaluated Samples

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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
PSS000870Serum creatinine was quantified by Metabolon HD4 metabolomics in mg/dL units, and adjusted for sampl... e measurement batch, sample measurement plate, and days between blood draw and sample processing. Subsequently, eGFR was quantified from serum creatinine using the CKD-EPI equationShow more—3,037 individuals,
51.0 % Male samples
Median = 44.0 years
IQR = [30.5, 54.7] years		European—INTERVAL—
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