Polygenic Score (PGS) ID: PGS004004

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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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 lassosum.auto.GCST008059.CKD
Development Method
Name lassosum.auto
Parameters s0.2,lambda0.00335981828628378
Variants
Original Genome Build GRCh38
Number of Variants 15,373
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
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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 individualsEuropeanUKB—————
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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
PPM019791PSS011216|
European Ancestry|
199,274 individuals
PGP000517 |
Monti R et al. Am J Hum Genet (2024)
Reported Trait: Chronic kidney disease or dialysisOR: 1.21322 [1.17679487, 1.25076374]
β: 0.19327 [0.16279453, 0.22375436]		AUROC: 0.5533 [0.54444893, 0.56214449]R²: 0.0069 [0.00494085, 0.00942766]0beta = log(or)/sd_pgs
PPM019792PSS011228|
European Ancestry|
383,843 individuals
PGP000517 |
Monti R et al. Am J Hum Genet (2024)
Reported Trait: Chronic kidney disease or dialysisOR: 1.1667 [1.14294429, 1.19094092]
β: 0.15418 [0.13360764, 0.17474368]		AUROC: 0.54321 [0.53730061, 0.54912911]R²: 0.00439 [0.00324186, 0.00567621]0beta = log(or)/sd_pgs
PPM019794PSS011239|
South Asian Ancestry|
44,057 individuals
PGP000517 |
Monti R et al. Am J Hum Genet (2024)
Reported Trait: Chronic kidney disease or dialysisOR: 1.14563 [1.07984697, 1.21542573]
β: 0.13596 [0.07681934, 0.19509441]		AUROC: 0.53841 [0.52122049, 0.55559138]R²: 0.00361 [0.0010689, 0.00745491]0beta = log(or)/sd_pgs
PPM019796PSS011255|
European Ancestry|
66,865 individuals
PGP000517 |
Monti R et al. Am J Hum Genet (2024)
Reported Trait: Chronic kidney disease or dialysisOR: 1.17435 [1.13067765, 1.21971447]
β: 0.16072 [0.12281715, 0.19861679]		AUROC: 0.54591 [0.53491235, 0.55689954]R²: 0.00476 [0.00282819, 0.00739137]0beta = log(or)/sd_pgs
PPM019798PSS011283|
South Asian Ancestry|
9,326 individuals
PGP000517 |
Monti R et al. Am J Hum Genet (2024)
Reported Trait: Chronic kidney disease or dialysisOR: 1.17987 [1.07574801, 1.29405974]
β: 0.1654 [0.07301624, 0.25778436]		AUROC: 0.54599 [0.51853554, 0.57344894]R²: 0.00532 [0.000857, 0.01375478]0beta = log(or)/sd_pgs
PPM019800PSS011269|
European Ancestry|
90,274 individuals
PGP000517 |
Monti R et al. Am J Hum Genet (2024)
Reported Trait: Chronic kidney disease or dialysisβ: 0.28325 [0.24886546, 0.31762566]
OR: 1.32743 [1.28256946, 1.37386187]		AUROC: 0.5783 [0.56845467, 0.5881504]R²: 0.01488 [0.01154959, 0.01893036]0beta = log(or)/sd_pgs
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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
PSS011216——
[
  • 4,224 cases
  • , 195,050 controls
]
—European—EB—
PSS011228N14_CHRONKIDNEYDIS, ICD10: N18, ICD9: 585, include dialysis (ICD10 Z992|Y841)—
[
  • 9,314 cases
  • , 374,529 controls
]
—European—FinnGen—
PSS011239——
[
  • 1,131 cases
  • , 42,926 controls
]
—South Asian—G&H—
PSS011255——
[
  • 2,802 cases
  • , 64,063 controls
]
—European—HUNT—
PSS011269——
[
  • 3,374 cases
  • , 86,900 controls
]
—European—UKB—
PSS011283——
[
  • 478 cases
  • , 8,848 controls
]
—South Asian—UKB—
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