Polygenic Score (PGS) ID: PGS001316

Predicted Trait
Reported Trait Myocardial infarction (algorithmically-defined)
Mapped Trait(s) myocardial infarction (EFO_0000612)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1574
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_HC1574
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,831
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
—
[
  • 11,070 cases
  • , 258,634 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
PPM009073 PSS004282|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: AD myocardial infarction — AUROC: 0.70025 [0.65881, 0.74169] R²: 0.06323
Incremental AUROC (full-covars): -0.00109
PGS R2 (no covariates): 0.00341
PGS AUROC (no covariates): 0.55032 [0.50157, 0.59907]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009074 PSS004283|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: AD myocardial infarction — AUROC: 0.77563 [0.69186, 0.85939] R²: 0.13082
Incremental AUROC (full-covars): -0.00431
PGS R2 (no covariates): 0.00883
PGS AUROC (no covariates): 0.56569 [0.44162, 0.68977]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009075 PSS004284|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: AD myocardial infarction — AUROC: 0.77999 [0.76527, 0.7947] R²: 0.13319
Incremental AUROC (full-covars): 0.0073
PGS R2 (no covariates): 0.00977
PGS AUROC (no covariates): 0.57998 [0.56066, 0.59929]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009076 PSS004285|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: AD myocardial infarction — AUROC: 0.76882 [0.75001, 0.78764] R²: 0.15463
Incremental AUROC (full-covars): 0.0037
PGS R2 (no covariates): 0.00504
PGS AUROC (no covariates): 0.54779 [0.52311, 0.57248]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009077 PSS004286|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: AD myocardial infarction — AUROC: 0.75963 [0.75098, 0.76829] R²: 0.12014
Incremental AUROC (full-covars): 0.01074
PGS R2 (no covariates): 0.01247
PGS AUROC (no covariates): 0.58557 [0.57459, 0.59655]		 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
PSS004284 — —
[
  • 872 cases
  • , 24,033 controls
]
 — European non-white British ancestry UKB —
PSS004285 — —
[
  • 567 cases
  • , 7,264 controls
]
 — South Asian — UKB —
PSS004286 — —
[
  • 2,790 cases
  • , 64,635 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS004282 — —
[
  • 150 cases
  • , 6,347 controls
]
 — African unspecified — UKB —
PSS004283 — —
[
  • 25 cases
  • , 1,679 controls
]
 — East Asian — UKB —