Polygenic Score (PGS) ID: PGS001335

Predicted Trait
Reported Trait Vascular/heart problems diagnosed by doctor High BP
Mapped Trait(s) cardiovascular disease (EFO_0000319)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC4006150
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_BIN_FC4006150
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 14,076
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%
262,060 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
—
[
  • 74,133 cases
  • , 187,927 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
PPM009161 PSS003949|
African Ancestry|
6,259 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vascular/heart problems diagnosed by doctor High BP — AUROC: 0.70003 [0.68681, 0.71325] R²: 0.1567
Incremental AUROC (full-covars): 0.00805
PGS R2 (no covariates): 0.0187
PGS AUROC (no covariates): 0.56975 [0.5553, 0.58419]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009162 PSS003950|
East Asian Ancestry|
1,636 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vascular/heart problems diagnosed by doctor High BP — AUROC: 0.76033 [0.73318, 0.78748] R²: 0.20594
Incremental AUROC (full-covars): 0.02832
PGS R2 (no covariates): 0.05248
PGS AUROC (no covariates): 0.61998 [0.5877, 0.65226]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009163 PSS003951|
European Ancestry|
24,199 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vascular/heart problems diagnosed by doctor High BP — AUROC: 0.7249 [0.71777, 0.73204] R²: 0.17206
Incremental AUROC (full-covars): 0.04382
PGS R2 (no covariates): 0.06274
PGS AUROC (no covariates): 0.63418 [0.62624, 0.64212]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009164 PSS003952|
South Asian Ancestry|
7,284 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vascular/heart problems diagnosed by doctor High BP — AUROC: 0.72573 [0.71331, 0.73816] R²: 0.18575
Incremental AUROC (full-covars): 0.02654
PGS R2 (no covariates): 0.04646
PGS AUROC (no covariates): 0.61155 [0.59761, 0.62549]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009165 PSS003953|
European Ancestry|
65,564 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vascular/heart problems diagnosed by doctor High BP — AUROC: 0.7135 [0.70921, 0.71779] R²: 0.16154
Incremental AUROC (full-covars): 0.05215
PGS R2 (no covariates): 0.06872
PGS AUROC (no covariates): 0.63791 [0.63326, 0.64256]		 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
PSS003949 — —
[
  • 2,457 cases
  • , 3,802 controls
]
 — African unspecified — UKB —
PSS003950 — —
[
  • 344 cases
  • , 1,292 controls
]
 — East Asian — UKB —
PSS003951 — —
[
  • 6,197 cases
  • , 18,002 controls
]
 — European non-white British ancestry UKB —
PSS003952 — —
[
  • 2,258 cases
  • , 5,026 controls
]
 — South Asian — UKB —
PSS003953 — —
[
  • 18,574 cases
  • , 46,990 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)