Polygenic Score (PGS) ID: PGS001272

Predicted Trait
Reported Trait Chronic renal failure (time-to-event)
Mapped Trait(s) chronic kidney disease (EFO_0003884)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1302
Released in PGS Catalog: Oct. 21, 2021
Download Score FTP directory
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 GBE_HC1302
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 158
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
269,704 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 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
—
[
  • 9,555 cases
  • , 260,149 controls
]
 European UKB — — — white British ancestry —

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
PPM008858 PSS004248|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE chronic renal failure — AUROC: 0.72548 [0.69772, 0.75323] R²: 0.09414
Incremental AUROC (full-covars): -0.00175
PGS R2 (no covariates): 8e-05
PGS AUROC (no covariates): 0.49007 [0.45724, 0.52289]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008859 PSS004249|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE chronic renal failure — AUROC: 0.76389 [0.67406, 0.85372] R²: 0.0985
Incremental AUROC (full-covars): 0.00241
PGS R2 (no covariates): 0.00158
PGS AUROC (no covariates): 0.53553 [0.42884, 0.64222]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008860 PSS004250|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE chronic renal failure — AUROC: 0.73046 [0.71142, 0.74949] R²: 0.07894
Incremental AUROC (full-covars): 0.00093
PGS R2 (no covariates): 0.00109
PGS AUROC (no covariates): 0.52368 [0.50018, 0.54718]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008861 PSS004251|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE chronic renal failure — AUROC: 0.73226 [0.70793, 0.7566] R²: 0.10347
Incremental AUROC (full-covars): -0.00037
PGS R2 (no covariates): 0.00031
PGS AUROC (no covariates): 0.51162 [0.48335, 0.5399]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008862 PSS004252|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE chronic renal failure — AUROC: 0.70402 [0.69403, 0.71401] R²: 0.06815
Incremental AUROC (full-covars): 0.00281
PGS R2 (no covariates): 0.00203
PGS AUROC (no covariates): 0.53623 [0.52445, 0.548]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

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
PSS004252 — —
[
  • 2,373 cases
  • , 65,052 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS004248 — —
[
  • 323 cases
  • , 6,174 controls
]
 — African unspecified — UKB —
PSS004249 — —
[
  • 26 cases
  • , 1,678 controls
]
 — East Asian — UKB —
PSS004250 — —
[
  • 610 cases
  • , 24,295 controls
]
 — European non-white British ancestry UKB —
PSS004251 — —
[
  • 416 cases
  • , 7,415 controls
]
 — South Asian — UKB —