Polygenic Score (PGS) ID: PGS001260

Predicted Trait
Reported Trait Angina
Mapped Trait(s) angina pectoris (EFO_0003913)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC132
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_HC132
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 2,562
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
—
[
  • 16,301 cases
  • , 253,403 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
PPM008805 PSS004263|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Angina — AUROC: 0.74858 [0.72225, 0.7749] R²: 0.10317
Incremental AUROC (full-covars): 0.00581
PGS R2 (no covariates): 0.0021
PGS AUROC (no covariates): 0.53477 [0.50036, 0.56918]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008806 PSS004264|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Angina — AUROC: 0.79053 [0.72587, 0.85519] R²: 0.12393
Incremental AUROC (full-covars): 0.00849
PGS R2 (no covariates): 0.01465
PGS AUROC (no covariates): 0.60534 [0.52229, 0.68839]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008807 PSS004265|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Angina — AUROC: 0.74298 [0.72979, 0.75617] R²: 0.1154
Incremental AUROC (full-covars): 0.00783
PGS R2 (no covariates): 0.01185
PGS AUROC (no covariates): 0.58108 [0.56544, 0.59672]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008808 PSS004266|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Angina — AUROC: 0.74658 [0.73013, 0.76304] R²: 0.14735
Incremental AUROC (full-covars): 0.00443
PGS R2 (no covariates): 0.00579
PGS AUROC (no covariates): 0.54578 [0.52572, 0.56585]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008809 PSS004267|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Angina — AUROC: 0.74167 [0.73419, 0.74914] R²: 0.11464
Incremental AUROC (full-covars): 0.01108
PGS R2 (no covariates): 0.01112
PGS AUROC (no covariates): 0.57435 [0.565, 0.58369]		 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
PSS004263 — —
[
  • 281 cases
  • , 6,216 controls
]
 — African unspecified — UKB —
PSS004264 — —
[
  • 41 cases
  • , 1,663 controls
]
 — East Asian — UKB —
PSS004265 — —
[
  • 1,341 cases
  • , 23,564 controls
]
 — European non-white British ancestry UKB —
PSS004266 — —
[
  • 876 cases
  • , 6,955 controls
]
 — South Asian — UKB —
PSS004267 — —
[
  • 3,927 cases
  • , 63,498 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)