Polygenic Score (PGS) ID: PGS001261

Predicted Trait
Reported Trait Angina pectoris (time-to-event)
Mapped Trait(s) angina pectoris (EFO_0003913)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC937
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_HC937
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 2,524
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
—
[
  • 16,580 cases
  • , 253,124 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
PPM008810 PSS004716|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE angina pectoris — AUROC: 0.74888 [0.72237, 0.77539] R²: 0.10279
Incremental AUROC (full-covars): 0.00677
PGS R2 (no covariates): 0.00325
PGS AUROC (no covariates): 0.54251 [0.50735, 0.57767]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008811 PSS004717|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE angina pectoris — AUROC: 0.79649 [0.73626, 0.85672] R²: 0.13398
Incremental AUROC (full-covars): 0.00843
PGS R2 (no covariates): 0.01725
PGS AUROC (no covariates): 0.61522 [0.5356, 0.69485]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008812 PSS004718|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE angina pectoris — AUROC: 0.74852 [0.73543, 0.76161] R²: 0.12116
Incremental AUROC (full-covars): 0.00796
PGS R2 (no covariates): 0.01228
PGS AUROC (no covariates): 0.58233 [0.56671, 0.59794]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008813 PSS004719|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE angina pectoris — AUROC: 0.74714 [0.73072, 0.76355] R²: 0.14768
Incremental AUROC (full-covars): 0.00461
PGS R2 (no covariates): 0.00594
PGS AUROC (no covariates): 0.54707 [0.52705, 0.56709]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008814 PSS004720|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE angina pectoris — AUROC: 0.742 [0.73458, 0.74942] R²: 0.11586
Incremental AUROC (full-covars): 0.01139
PGS R2 (no covariates): 0.01162
PGS AUROC (no covariates): 0.57494 [0.56568, 0.5842]		 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
PSS004716 — —
[
  • 275 cases
  • , 6,222 controls
]
 — African unspecified — UKB —
PSS004717 — —
[
  • 45 cases
  • , 1,659 controls
]
 — East Asian — UKB —
PSS004718 — —
[
  • 1,336 cases
  • , 23,569 controls
]
 — European non-white British ancestry UKB —
PSS004719 — —
[
  • 878 cases
  • , 6,953 controls
]
 — South Asian — UKB —
PSS004720 — —
[
  • 3,997 cases
  • , 63,428 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)