Polygenic Score (PGS) ID: PGS001317

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
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_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

Development Samples

Score Development/Training
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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
[
  • 6,356 cases
  • , 189,634 controls
]
EuropeanUKBwhite British ancestry
Showing 1 to 1 of 1 rows

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.

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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
PPM009078PSS003775|
African Ancestry|
3,906 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Vascular/heart problems diagnosed by doctor Heart attackAUROC: 0.72462 [0.66421, 0.78503]: 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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM009079PSS003776|
East Asian Ancestry|
1,308 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Vascular/heart problems diagnosed by doctor Heart attackAUROC: 0.78888 [0.66178, 0.91598]: 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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM009080PSS003777|
European Ancestry|
18,556 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Vascular/heart problems diagnosed by doctor Heart attackAUROC: 0.82479 [0.80685, 0.84274]: 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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM009081PSS003778|
South Asian Ancestry|
5,342 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Vascular/heart problems diagnosed by doctor Heart attackAUROC: 0.82696 [0.80387, 0.85004]: 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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM009082PSS003779|
European Ancestry|
48,989 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Vascular/heart problems diagnosed by doctor Heart attackAUROC: 0.82191 [0.8123, 0.83152]: 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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
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Evaluated Samples

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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
PSS003775
[
  • 82 cases
  • , 3,824 controls
]
African unspecifiedUKB
PSS003776
[
  • 11 cases
  • , 1,297 controls
]
East AsianUKB
PSS003777
[
  • 465 cases
  • , 18,091 controls
]
Europeannon-white British ancestryUKB
PSS003778
[
  • 299 cases
  • , 5,043 controls
]
South AsianUKB
PSS003779
[
  • 1,611 cases
  • , 47,378 controls
]
Europeanwhite British ancestryUKBTesting cohort (heldout set)
Showing 1 to 5 of 5 rows