Polygenic Score (PGS) ID: PGS001250

Predicted Trait
Reported Trait Calculus of kidney and ureter (time-to-event)
Mapped Trait(s)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1304
Released in PGS Catalog: Oct. 21, 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 GBE_HC1304
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 341
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
—
[
  • 4,110 cases
  • , 265,594 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
PPM008759 PSS004253|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE calculus of kidney and ureter — AUROC: 0.63458 [0.56104, 0.70812] R²: 0.02267
Incremental AUROC (full-covars): -4e-05
PGS R2 (no covariates): 0.00013
PGS AUROC (no covariates): 0.50619 [0.43811, 0.57426]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008760 PSS004254|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE calculus of kidney and ureter — AUROC: 0.66992 [0.57144, 0.7684] R²: 0.05343
Incremental AUROC (full-covars): 0.02085
PGS R2 (no covariates): 0.01881
PGS AUROC (no covariates): 0.61787 [0.49482, 0.74092]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008761 PSS004255|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE calculus of kidney and ureter — AUROC: 0.6584 [0.63099, 0.68582] R²: 0.03459
Incremental AUROC (full-covars): 0.00159
PGS R2 (no covariates): 0.00193
PGS AUROC (no covariates): 0.53735 [0.50853, 0.56617]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008762 PSS004256|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE calculus of kidney and ureter — AUROC: 0.66463 [0.62056, 0.7087] R²: 0.03629
Incremental AUROC (full-covars): 0.01093
PGS R2 (no covariates): 0.0077
PGS AUROC (no covariates): 0.57305 [0.52667, 0.61943]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008763 PSS004257|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE calculus of kidney and ureter — AUROC: 0.66491 [0.64839, 0.68143] R²: 0.03503
Incremental AUROC (full-covars): 0.01494
PGS R2 (no covariates): 0.00592
PGS AUROC (no covariates): 0.56681 [0.54876, 0.58486]		 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
PSS004253 — —
[
  • 56 cases
  • , 6,441 controls
]
 — African unspecified — UKB —
PSS004254 — —
[
  • 25 cases
  • , 1,679 controls
]
 — East Asian — UKB —
PSS004255 — —
[
  • 384 cases
  • , 24,521 controls
]
 — European non-white British ancestry UKB —
PSS004256 — —
[
  • 146 cases
  • , 7,685 controls
]
 — South Asian — UKB —
PSS004257 — —
[
  • 989 cases
  • , 66,436 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)