Polygenic Score (PGS) ID: PGS000962

Predicted Trait
Reported Trait Chronic ischaemic heart disease (time-to-event)
Mapped Trait(s) Myocardial Ischemia (EFO_1001375)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC942
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_HC942
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 2,168
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
—
[
  • 20,305 cases
  • , 249,399 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
PPM007634 PSS004726|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE chronic ischaemic heart disease — AUROC: 0.7358 [0.70724, 0.76436] R²: 0.09751
Incremental AUROC (full-covars): 0.00137
PGS R2 (no covariates): 0.00275
PGS AUROC (no covariates): 0.53401 [0.49965, 0.56838]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007635 PSS004727|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE chronic ischaemic heart disease — AUROC: 0.76843 [0.69891, 0.83795] R²: 0.12929
Incremental AUROC (full-covars): 0.00772
PGS R2 (no covariates): 0.01452
PGS AUROC (no covariates): 0.60835 [0.52909, 0.68761]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007636 PSS004728|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE chronic ischaemic heart disease — AUROC: 0.77959 [0.76878, 0.7904] R²: 0.1649
Incremental AUROC (full-covars): 0.00919
PGS R2 (no covariates): 0.0145
PGS AUROC (no covariates): 0.58654 [0.57236, 0.60073]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007637 PSS004729|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE chronic ischaemic heart disease — AUROC: 0.76819 [0.75382, 0.78257] R²: 0.19358
Incremental AUROC (full-covars): 0.00859
PGS R2 (no covariates): 0.01217
PGS AUROC (no covariates): 0.56681 [0.54864, 0.58499]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007638 PSS004730|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE chronic ischaemic heart disease — AUROC: 0.76113 [0.75467, 0.7676] R²: 0.14665
Incremental AUROC (full-covars): 0.01428
PGS R2 (no covariates): 0.01869
PGS AUROC (no covariates): 0.59199 [0.58389, 0.60008]		 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
PSS004726 — —
[
  • 283 cases
  • , 6,214 controls
]
 — African unspecified — UKB —
PSS004727 — —
[
  • 48 cases
  • , 1,656 controls
]
 — East Asian — UKB —
PSS004728 — —
[
  • 1,680 cases
  • , 23,225 controls
]
 — European non-white British ancestry UKB —
PSS004729 — —
[
  • 1,095 cases
  • , 6,736 controls
]
 — South Asian — UKB —
PSS004730 — —
[
  • 5,072 cases
  • , 62,353 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)