Polygenic Score (PGS) ID: PGS004196

Predicted Trait
Reported Trait Coronary artery disease
Mapped Trait(s) coronary artery disease (EFO_0001645)
Additional Trait Information UK Biobank codes: non-cancer codes: 1075; ICD9: 410, 4109, 412, 4129; ICD10: I21, I210-I214, I219, I21X, I22, I220, I221, I228, I229, I23, I230-I236, I238, I241, I252; OPCS4: K401-K404, K411-K414, K451-K455, K491, K492, K498, K499, K502, K751-K754, K758, K759
Released in PGS Catalog: Dec. 15, 2023
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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 cad_1
Development Method
Name LASSO
Parameters To reduce the number of candidate SNPs to a computationally feasible set, a gwas was performed on th... e raw phenotype and the 50,000 snps with smallest p-value were retained. The raw phenotype was regressed on age, sex, and the top 20 UK Biobank PCs and a residual phenotype was then built. The LASSO model was trained using these 50k SNPs and the adjusted phenotype.Show more
Variants
Original Genome Build GRCh37
Number of Variants 3,892
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000520
Citation (link to publication) Raben TG et al. Sci Rep (2023)
Ancestry Distribution
Score Development/Training
European: 100%
200,000 individuals (100%)
PGS Evaluation
European: 100%
1 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
—
[
  • 21,091 cases
  • , 178,909 controls
]
,
47.9 % Male samples
EuropeanNRUK Biobank codes: non-cancer codes: 1075; ICD9: 410, 4109, 412, 4129; ICD10: I21, I210-I214, I219, I... 21X, I22, I220, I221, I228, I229, I23, I230-I236, I238, I241, I252; OPCS4: K401-K404, K411-K414, K451-K455, K491, K492, K498, K499, K502, K751-K754, K758, K759Show more—used UK self report 'white' category and then used an adjusted phenotype that includes a regression on the top 20 PCs—
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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
PPM020130PSS011296|
European Ancestry|
45,334 individuals
PGP000520 |
Raben TG et al. Sci Rep (2023)
Reported Trait: Coronary artery disease—AUROC: 0.74561—year of birth, sex—
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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
PSS01129622,667 sibling pairs—45,334 individuals—European—UKB—
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