Polygenic Score (PGS) ID: PGS001324

Predicted Trait
Reported Trait Family history of high blood pressure
Mapped Trait(s) family history (EFO_0000493)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/FH1065
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_FH1065
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 13,862
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
—
[
  • 159,331 cases
  • , 110,373 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
PPM009112 PSS004044|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: High BP (FH) — AUROC: 0.59339 [0.57784, 0.60894] R²: 0.03128
Incremental AUROC (full-covars): -0.00542
PGS R2 (no covariates): 0.00353
PGS AUROC (no covariates): 0.53126 [0.51539, 0.54713]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009113 PSS004045|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: High BP (FH) — AUROC: 0.58604 [0.55827, 0.61382] R²: 0.03732
Incremental AUROC (full-covars): 0.02078
PGS R2 (no covariates): 0.01267
PGS AUROC (no covariates): 0.55693 [0.52875, 0.58511]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009114 PSS004046|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: High BP (FH) — AUROC: 0.58225 [0.5751, 0.5894] R²: 0.0275
Incremental AUROC (full-covars): 0.04455
PGS R2 (no covariates): 0.02262
PGS AUROC (no covariates): 0.5748 [0.56762, 0.58198]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009115 PSS004047|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: High BP (FH) — AUROC: 0.59484 [0.58159, 0.6081] R²: 0.0361
Incremental AUROC (full-covars): 0.0245
PGS R2 (no covariates): 0.01922
PGS AUROC (no covariates): 0.57095 [0.55751, 0.58438]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009116 PSS004048|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: High BP (FH) — AUROC: 0.5865 [0.58217, 0.59084] R²: 0.03045
Incremental AUROC (full-covars): 0.06315
PGS R2 (no covariates): 0.0284
PGS AUROC (no covariates): 0.58323 [0.57889, 0.58758]		 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
PSS004044 — —
[
  • 4,775 cases
  • , 1,722 controls
]
 — African unspecified — UKB —
PSS004045 — —
[
  • 1,063 cases
  • , 641 controls
]
 — East Asian — UKB —
PSS004046 — —
[
  • 14,691 cases
  • , 10,214 controls
]
 — European non-white British ancestry UKB —
PSS004047 — —
[
  • 5,302 cases
  • , 2,529 controls
]
 — South Asian — UKB —
PSS004048 — —
[
  • 39,694 cases
  • , 27,731 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)