Polygenic Score (PGS) ID: PGS001314

Predicted Trait
Reported Trait Acute myocardial infarction (time-to-event)
Mapped Trait(s) myocardial infarction (EFO_0000612)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC938
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_HC938
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,108
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
—
[
  • 10,021 cases
  • , 259,683 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
PPM009063 PSS004721|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE acute myocardial infarction — AUROC: 0.70154 [0.65456, 0.74852] R²: 0.05819
Incremental AUROC (full-covars): 0.00259
PGS R2 (no covariates): 0.00375
PGS AUROC (no covariates): 0.54944 [0.49708, 0.6018]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009064 PSS004722|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE acute myocardial infarction — AUROC: 0.75783 [0.66508, 0.85058] R²: 0.11318
Incremental AUROC (full-covars): -0.01214
PGS R2 (no covariates): 4e-05
PGS AUROC (no covariates): 0.50047 [0.38016, 0.62077]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009065 PSS004723|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE acute myocardial infarction — AUROC: 0.77705 [0.76156, 0.79255] R²: 0.12586
Incremental AUROC (full-covars): 0.00931
PGS R2 (no covariates): 0.01217
PGS AUROC (no covariates): 0.59003 [0.56941, 0.61066]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009066 PSS004724|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE acute myocardial infarction — AUROC: 0.77134 [0.75168, 0.791] R²: 0.14992
Incremental AUROC (full-covars): 0.00612
PGS R2 (no covariates): 0.00867
PGS AUROC (no covariates): 0.56612 [0.54027, 0.59198]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009067 PSS004725|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE acute myocardial infarction — AUROC: 0.76117 [0.75218, 0.77016] R²: 0.11781
Incremental AUROC (full-covars): 0.00966
PGS R2 (no covariates): 0.01066
PGS AUROC (no covariates): 0.57977 [0.56827, 0.59127]		 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
PSS004721 — —
[
  • 116 cases
  • , 6,381 controls
]
 — African unspecified — UKB —
PSS004722 — —
[
  • 21 cases
  • , 1,683 controls
]
 — East Asian — UKB —
PSS004723 — —
[
  • 766 cases
  • , 24,139 controls
]
 — European non-white British ancestry UKB —
PSS004724 — —
[
  • 492 cases
  • , 7,339 controls
]
 — South Asian — UKB —
PSS004725 — —
[
  • 2,531 cases
  • , 64,894 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)