Polygenic Score (PGS) ID: PGS001025

Predicted Trait
Reported Trait Nonrheumatic aortic valve disorders (time-to-event)
Mapped Trait(s) aortic valve disease (EFO_0009531)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC951
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_HC951
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 36
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
—
[
  • 2,517 cases
  • , 267,187 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
PPM007888 PSS004736|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE nonrheumatic aortic valve disorders — AUROC: 0.82312 [0.77164, 0.87459] R²: 0.11205
Incremental AUROC (full-covars): -0.00433
PGS R2 (no covariates): 0.00601
PGS AUROC (no covariates): 0.42408 [0.32798, 0.52019]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007889 PSS004737|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE nonrheumatic aortic valve disorders — AUROC: 0.85035 [0.70276, 0.99795] R²: 0.20912
Incremental AUROC (full-covars): 0.0036
PGS R2 (no covariates): 0.00383
PGS AUROC (no covariates): 0.57568 [0.385, 0.76636]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007890 PSS004738|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE nonrheumatic aortic valve disorders — AUROC: 0.7688 [0.74115, 0.79645] R²: 0.09382
Incremental AUROC (full-covars): 0.00229
PGS R2 (no covariates): 0.00416
PGS AUROC (no covariates): 0.55883 [0.52408, 0.59358]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007891 PSS004739|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE nonrheumatic aortic valve disorders — AUROC: 0.7872 [0.73952, 0.83487] R²: 0.10086
Incremental AUROC (full-covars): 2e-05
PGS R2 (no covariates): 0.00021
PGS AUROC (no covariates): 0.49071 [0.41731, 0.5641]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007892 PSS004740|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE nonrheumatic aortic valve disorders — AUROC: 0.72257 [0.70467, 0.74046] R²: 0.05934
Incremental AUROC (full-covars): 0.00304
PGS R2 (no covariates): 0.00268
PGS AUROC (no covariates): 0.5466 [0.52408, 0.56913]		 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
PSS004736 — —
[
  • 36 cases
  • , 6,461 controls
]
 — African unspecified — UKB —
PSS004737 — —
[
  • 10 cases
  • , 1,694 controls
]
 — East Asian — UKB —
PSS004738 — —
[
  • 262 cases
  • , 24,643 controls
]
 — European non-white British ancestry UKB —
PSS004739 — —
[
  • 65 cases
  • , 7,766 controls
]
 — South Asian — UKB —
PSS004740 — —
[
  • 654 cases
  • , 66,771 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)