Polygenic Score (PGS) ID: PGS004045

Predicted Trait
Reported Trait Chronic kidney disease (CKD)
Mapped Trait(s) chronic kidney disease (EFO_0003884)
Released in PGS Catalog: Dec. 19, 2023
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Score Details

Score Construction
PGS Name ldpred2.CV.GCST008059.CKD
Development Method
Name LDpred2.CV
Parameters p:0.018,h2:0.0539,nosparse
Variants
Original Genome Build GRCh38
Number of Variants 1,050,295
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000517
Citation (link to publication) Monti R et al. Am J Hum Genet (2024)
Ancestry Distribution
Score Development/Training
European: 100%
13,496 individuals (100%)
PGS Evaluation
European: 66.7%
South Asian: 33.3%
6 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
— 13,496 individuals European UKB — — — — —

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
PPM019685 PSS011216|
European Ancestry|
199,274 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Chronic kidney disease or dialysis OR: 1.242 [1.20468213, 1.28047135]
β: 0.21672 [0.18621574, 0.24722825]		 AUROC: 0.55911 [0.55023739, 0.56797892] R²: 0.00866 [0.00640403, 0.01139544] 0 beta = sd_trait/sd_pgs = pearson correlation
PPM019686 PSS011228|
European Ancestry|
383,843 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Chronic kidney disease or dialysis OR: 1.19906 [1.17464211, 1.2239762]
β: 0.18153 [0.16096351, 0.20210474]		 AUROC: 0.5508 [0.54489488, 0.55670431] R²: 0.00608 [0.00470563, 0.00760115] 0 beta = sd_trait/sd_pgs = pearson correlation
PPM019688 PSS011239|
South Asian Ancestry|
44,057 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Chronic kidney disease or dialysis OR: 1.1551 [1.08886145, 1.22537065]
β: 0.14419 [0.08513261, 0.20324337]		 AUROC: 0.54134 [0.52407167, 0.55860959] R²: 0.00407 [0.00127295, 0.00787491] 0 beta = log(or)/sd_pgs
PPM019690 PSS011255|
European Ancestry|
66,865 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Chronic kidney disease or dialysis OR: 1.18451 [1.14041448, 1.23030035]
β: 0.16933 [0.13139177, 0.20725833]		 AUROC: 0.549 [0.53797079, 0.56002041] R²: 0.00527 [0.00319058, 0.0079898] 0 beta = log(or)/sd_pgs
PPM019692 PSS011283|
South Asian Ancestry|
9,326 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Chronic kidney disease or dialysis OR: 1.27638 [1.16349632, 1.40020791]
β: 0.24403 [0.15142954, 0.33662073]		 AUROC: 0.56537 [0.53845702, 0.59228784] R²: 0.01155 [0.00425064, 0.0225531] 0 beta = log(or)/sd_pgs
PPM019694 PSS011269|
European Ancestry|
90,274 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Chronic kidney disease or dialysis OR: 1.37553 [1.32885232, 1.42384795]
β: 0.31884 [0.28431565, 0.35336303]		 AUROC: 0.58851 [0.57882039, 0.59820663] R²: 0.01871 [0.01517095, 0.0232003] 0 beta = log(or)/sd_pgs

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
PSS011239 — —
[
  • 1,131 cases
  • , 42,926 controls
]
 — South Asian — G&H —
PSS011216 — —
[
  • 4,224 cases
  • , 195,050 controls
]
 — European — EB —
PSS011283 — —
[
  • 478 cases
  • , 8,848 controls
]
 — South Asian — UKB —
PSS011255 — —
[
  • 2,802 cases
  • , 64,063 controls
]
 — European — HUNT —
PSS011228 N14_CHRONKIDNEYDIS, ICD10: N18, ICD9: 585, include dialysis (ICD10 Z992|Y841) —
[
  • 9,314 cases
  • , 374,529 controls
]
 — European — FinnGen —
PSS011269 — —
[
  • 3,374 cases
  • , 86,900 controls
]
 — European — UKB —