Polygenic Score (PGS) ID: PGS001320

Predicted Trait
Reported Trait Hypertension
Mapped Trait(s) hypertension (EFO_0000537)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC215
Released in PGS Catalog: Oct. 21, 2021
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Score Details

Score Construction
PGS Name GBE_HC215
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 13,791
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
—
[
  • 91,884 cases
  • , 177,820 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
PPM009092 PSS004349|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hypertension — AUROC: 0.7113 [0.69875, 0.72385] R²: 0.17724
Incremental AUROC (full-covars): 0.00194
PGS R2 (no covariates): 0.01116
PGS AUROC (no covariates): 0.55174 [0.53775, 0.56573]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009093 PSS004350|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hypertension — AUROC: 0.75955 [0.7336, 0.78551] R²: 0.22552
Incremental AUROC (full-covars): 0.03121
PGS R2 (no covariates): 0.05514
PGS AUROC (no covariates): 0.62221 [0.59228, 0.65214]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009094 PSS004351|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hypertension — AUROC: 0.731 [0.72434, 0.73765] R²: 0.19145
Incremental AUROC (full-covars): 0.03394
PGS R2 (no covariates): 0.05533
PGS AUROC (no covariates): 0.62108 [0.61358, 0.62857]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009095 PSS004352|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hypertension — AUROC: 0.73444 [0.72324, 0.74564] R²: 0.21325
Incremental AUROC (full-covars): 0.02055
PGS R2 (no covariates): 0.03841
PGS AUROC (no covariates): 0.59979 [0.58706, 0.61252]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009096 PSS004353|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hypertension — AUROC: 0.7189 [0.71489, 0.72291] R²: 0.17852
Incremental AUROC (full-covars): 0.04424
PGS R2 (no covariates): 0.06493
PGS AUROC (no covariates): 0.62908 [0.62467, 0.63349]		 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
PSS004349 — —
[
  • 2,919 cases
  • , 3,578 controls
]
 — African unspecified — UKB —
PSS004350 — —
[
  • 446 cases
  • , 1,258 controls
]
 — East Asian — UKB —
PSS004351 — —
[
  • 7,648 cases
  • , 17,257 controls
]
 — European non-white British ancestry UKB —
PSS004352 — —
[
  • 3,161 cases
  • , 4,670 controls
]
 — South Asian — UKB —
PSS004353 — —
[
  • 22,882 cases
  • , 44,543 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)