Polygenic Score (PGS) ID: PGS000957

Predicted Trait
Reported Trait Essential (primary hypertension) (time-to-event)
Mapped Trait(s) essential hypertension (MONDO_0001134)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC932
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_HC932
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 11,276
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
—
[
  • 67,086 cases
  • , 202,618 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
PPM007609 PSS004711|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE essential (primary hypertension) — AUROC: 0.71865 [0.70527, 0.73203] R²: 0.17042
Incremental AUROC (full-covars): -0.00133
PGS R2 (no covariates): 0.00389
PGS AUROC (no covariates): 0.53092 [0.51597, 0.54587]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007610 PSS004712|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE essential (primary hypertension) — AUROC: 0.7519 [0.72118, 0.78262] R²: 0.18828
Incremental AUROC (full-covars): 0.01726
PGS R2 (no covariates): 0.02831
PGS AUROC (no covariates): 0.59059 [0.55566, 0.62552]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007611 PSS004713|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE essential (primary hypertension) — AUROC: 0.74724 [0.74015, 0.75433] R²: 0.19436
Incremental AUROC (full-covars): 0.02015
PGS R2 (no covariates): 0.03223
PGS AUROC (no covariates): 0.60027 [0.59183, 0.6087]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007612 PSS004714|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE essential (primary hypertension) — AUROC: 0.73072 [0.71892, 0.74253] R²: 0.19598
Incremental AUROC (full-covars): 0.00857
PGS R2 (no covariates): 0.01913
PGS AUROC (no covariates): 0.56924 [0.55569, 0.58279]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007613 PSS004715|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE essential (primary hypertension) — AUROC: 0.72352 [0.71925, 0.72779] R²: 0.16706
Incremental AUROC (full-covars): 0.02959
PGS R2 (no covariates): 0.04055
PGS AUROC (no covariates): 0.60837 [0.60349, 0.61326]		 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
PSS004711 — —
[
  • 2,034 cases
  • , 4,463 controls
]
 — African unspecified — UKB —
PSS004712 — —
[
  • 298 cases
  • , 1,406 controls
]
 — East Asian — UKB —
PSS004713 — —
[
  • 5,400 cases
  • , 19,505 controls
]
 — European non-white British ancestry UKB —
PSS004714 — —
[
  • 2,513 cases
  • , 5,318 controls
]
 — South Asian — UKB —
PSS004715 — —
[
  • 16,689 cases
  • , 50,736 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)