Polygenic Score (PGS) ID: PGS000958

Predicted Trait
Reported Trait Essential hypertension
Mapped Trait(s) essential hypertension (MONDO_0001134)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC273
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_HC273
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 9,400
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
—
[
  • 60,911 cases
  • , 208,793 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
PPM007614 PSS004403|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Essential hypertension — AUROC: 0.72155 [0.708, 0.7351] R²: 0.17503
Incremental AUROC (full-covars): -0.00192
PGS R2 (no covariates): 0.00286
PGS AUROC (no covariates): 0.52821 [0.51311, 0.54331]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007615 PSS004404|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Essential hypertension — AUROC: 0.74478 [0.71204, 0.77751] R²: 0.16987
Incremental AUROC (full-covars): 0.01358
PGS R2 (no covariates): 0.01557
PGS AUROC (no covariates): 0.56972 [0.5318, 0.60763]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007616 PSS004405|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Essential hypertension — AUROC: 0.74583 [0.73846, 0.75319] R²: 0.1847
Incremental AUROC (full-covars): 0.01683
PGS R2 (no covariates): 0.02709
PGS AUROC (no covariates): 0.59474 [0.58596, 0.60351]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007617 PSS004406|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Essential hypertension — AUROC: 0.73161 [0.71966, 0.74357] R²: 0.19538
Incremental AUROC (full-covars): 0.00693
PGS R2 (no covariates): 0.01804
PGS AUROC (no covariates): 0.56789 [0.55414, 0.58165]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007618 PSS004407|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Essential hypertension — AUROC: 0.72364 [0.71923, 0.72805] R²: 0.16114
Incremental AUROC (full-covars): 0.02564
PGS R2 (no covariates): 0.03436
PGS AUROC (no covariates): 0.60148 [0.5964, 0.60656]		 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
PSS004403 — —
[
  • 1,956 cases
  • , 4,541 controls
]
 — African unspecified — UKB —
PSS004404 — —
[
  • 259 cases
  • , 1,445 controls
]
 — East Asian — UKB —
PSS004405 — —
[
  • 4,864 cases
  • , 20,041 controls
]
 — European non-white British ancestry UKB —
PSS004406 — —
[
  • 2,406 cases
  • , 5,425 controls
]
 — South Asian — UKB —
PSS004407 — —
[
  • 15,118 cases
  • , 52,307 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)