Predicted Trait | |
Reported Trait | Vascular/heart problems diagnosed by doctor Heart attack |
Mapped Trait(s) | myocardial infarction (EFO_0000612) |
Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC1006150 |
Score Construction | |
PGS Name | GBE_BIN_FC1006150 |
Development Method | |
Name | snpnet |
Parameters | NR |
Variants | |
Original Genome Build | GRCh37 |
Number of Variants | 1,030 |
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% 195,990 individuals (100%) |
PGS Evaluation | European: 40% African: 20% East Asian: 20% South Asian: 20% 5 Sample Sets |
Study Identifiers
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Sample Numbers
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Sample Ancestry
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Cohort(s)
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Phenotype Definitions & Methods
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Age of Study Participants
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Participant Follow-up Time
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Additional Ancestry Description
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Additional Sample/Cohort Information
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— | [
| European | UKB | — | — | — | white British ancestry | — |
PGS Performance Metric ID (PPM) |
PGS Sample Set ID (PSS) |
Performance Source
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Trait
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PGS Effect Sizes (per SD change) |
Classification Metrics
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Other Metrics
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Covariates Included in the Model
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PGS Performance: Other Relevant Information |
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PPM009078 | PSS003775| African Ancestry| 3,906 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Vascular/heart problems diagnosed by doctor Heart attack | — | AUROC: 0.72462 [0.66421, 0.78503] | R²: 0.08703 Incremental AUROC (full-covars): -0.01046 PGS R2 (no covariates): 0.0002 PGS AUROC (no covariates): 0.50663 [0.44094, 0.57232] | age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM009079 | PSS003776| East Asian Ancestry| 1,308 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Vascular/heart problems diagnosed by doctor Heart attack | — | AUROC: 0.78888 [0.66178, 0.91598] | R²: 0.10419 Incremental AUROC (full-covars): -0.00694 PGS R2 (no covariates): 0.00068 PGS AUROC (no covariates): 0.53242 [0.37336, 0.69148] | age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM009080 | PSS003777| European Ancestry| 18,556 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Vascular/heart problems diagnosed by doctor Heart attack | — | AUROC: 0.82479 [0.80685, 0.84274] | R²: 0.1758 Incremental AUROC (full-covars): 0.00552 PGS R2 (no covariates): 0.00895 PGS AUROC (no covariates): 0.5766 [0.55039, 0.60282] | age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM009081 | PSS003778| South Asian Ancestry| 5,342 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Vascular/heart problems diagnosed by doctor Heart attack | — | AUROC: 0.82696 [0.80387, 0.85004] | R²: 0.22573 Incremental AUROC (full-covars): 0.00709 PGS R2 (no covariates): 0.00972 PGS AUROC (no covariates): 0.57536 [0.54237, 0.60835] | age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM009082 | PSS003779| European Ancestry| 48,989 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Vascular/heart problems diagnosed by doctor Heart attack | — | AUROC: 0.82191 [0.8123, 0.83152] | R²: 0.18282 Incremental AUROC (full-covars): 0.01045 PGS R2 (no covariates): 0.01654 PGS AUROC (no covariates): 0.60058 [0.58663, 0.61453] | age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PGS Sample Set ID (PSS) |
Phenotype Definitions and Methods
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Participant Follow-up Time
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Sample Numbers
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Age of Study Participants
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Sample Ancestry
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Additional Ancestry Description
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Cohort(s)
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Additional Sample/Cohort Information
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PSS003775 | — | — | [
| — | African unspecified | — | UKB | — |
PSS003776 | — | — | [
| — | East Asian | — | UKB | — |
PSS003777 | — | — | [
| — | European | non-white British ancestry | UKB | — |
PSS003778 | — | — | [
| — | South Asian | — | UKB | — |
PSS003779 | — | — | [
| — | European | white British ancestry | UKB | Testing cohort (heldout set) |