Polygenic Score (PGS) ID: PGS001262

Predicted Trait
Reported Trait Vascular/heart problems diagnosed by doctor Angina
Mapped Trait(s) angina pectoris (EFO_0003913)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC2006150
Released in PGS Catalog: Oct. 21, 2021
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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_FC2006150
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,852
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%
198,364 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
—
[
  • 8,757 cases
  • , 189,607 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
PPM008815 PSS003854|
African Ancestry|
3,985 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vascular/heart problems diagnosed by doctor Angina — AUROC: 0.82431 [0.7951, 0.85352] R²: 0.18928
Incremental AUROC (full-covars): 0.00472
PGS R2 (no covariates): 0.00244
PGS AUROC (no covariates): 0.54151 [0.4965, 0.58652]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008816 PSS003855|
East Asian Ancestry|
1,317 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vascular/heart problems diagnosed by doctor Angina — AUROC: 0.81573 [0.71999, 0.91148] R²: 0.18878
Incremental AUROC (full-covars): 0.01113
PGS R2 (no covariates): 0.00409
PGS AUROC (no covariates): 0.54123 [0.41196, 0.67049]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008817 PSS003856|
European Ancestry|
18,868 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vascular/heart problems diagnosed by doctor Angina — AUROC: 0.78043 [0.76461, 0.79624] R²: 0.14388
Incremental AUROC (full-covars): 0.00599
PGS R2 (no covariates): 0.01288
PGS AUROC (no covariates): 0.58632 [0.56598, 0.60667]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008818 PSS003857|
South Asian Ancestry|
5,473 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vascular/heart problems diagnosed by doctor Angina — AUROC: 0.8083 [0.78794, 0.82865] R²: 0.2132
Incremental AUROC (full-covars): 0.00447
PGS R2 (no covariates): 0.00511
PGS AUROC (no covariates): 0.54847 [0.52094, 0.57599]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008819 PSS003858|
European Ancestry|
49,472 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vascular/heart problems diagnosed by doctor Angina — AUROC: 0.80729 [0.79886, 0.81571] R²: 0.17468
Incremental AUROC (full-covars): 0.0098
PGS R2 (no covariates): 0.01304
PGS AUROC (no covariates): 0.58683 [0.57429, 0.59937]		 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
PSS003854 — —
[
  • 161 cases
  • , 3,824 controls
]
 — African unspecified — UKB —
PSS003855 — —
[
  • 21 cases
  • , 1,296 controls
]
 — East Asian — UKB —
PSS003856 — —
[
  • 784 cases
  • , 18,084 controls
]
 — European non-white British ancestry UKB —
PSS003857 — —
[
  • 430 cases
  • , 5,043 controls
]
 — South Asian — UKB —
PSS003858 — —
[
  • 2,098 cases
  • , 47,374 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)