Polygenic Score (PGS) ID: PGS000746

Predicted Trait
Reported Trait Coronary artery disease
Mapped Trait(s) coronary artery disease (EFO_0001645)
Released in PGS Catalog: March 22, 2021
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Score Details

Score Construction
PGS Name PRS_UKB
Variants
Original Genome Build hg19
Number of Variants 1,940
Development Method
Name LD clumping
Parameters p=1.23^-3, r^2=0.21
PGS Source
PGS Catalog Publication (PGP) ID PGP000152
Citation (link to publication) Gola D et al. Circ Genom Precis Med (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 75.3%
South Asian: 13.6%
East Asian: 6%
Hispanic or Latin American: 2.2%
African: 1.7%
Greater Middle Eastern: 1.2%
187,599 individuals (100%)
Score Development/Training
European: 100%
10,000 individuals (100%)
PGS Evaluation
European: 100%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST003116
Europe PMC: 26343387
11,323 individuals East Asian
GWAS Catalog: GCST003116
Europe PMC: 26343387
25,557 individuals South Asian
GWAS Catalog: GCST003116
Europe PMC: 26343387
2,268 individuals Greater Middle Eastern (Middle Eastern, North African or Persian)
GWAS Catalog: GCST003116
Europe PMC: 26343387
4,095 individuals Hispanic or Latin American
GWAS Catalog: GCST003116
Europe PMC: 26343387
141,217 individuals European
GWAS Catalog: GCST003116
Europe PMC: 26343387
3,139 individuals African American or Afro-Caribbean
Score Development/Training
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
CAD ascertainment was based on a composite of myocardial infarction or coronary revascularization. Myocardial infarction was based on ICD-9 codes 410.X, 411.X, 412.X, or 429.79, or ICD-10 codes I21.X, I22.X, I23.X, I24.1, or I25.2. Coronary revascularization was assessed based on OPCS-4 coded procedure for coronary artery bypass grafting (K40.1-40-4, K41.1-41.4, or K45.1-45.5), or coronary angioplasty with or without stenting (K49.1-49.2, K49.0-49.9, K50.2, K75.1-75.4, or K75.8-75.9)
[
  • 471 cases
  • , 9,529 controls
]
European UKB

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
PPM001836 PSS000931|
European Ancestry|
431,814 individuals
PGP000152 |
Gola D et al. Circ Genom Precis Med (2020)
Reported Trait: Coronary artery disease AUROC: 0.6133 [0.6094, 0.6172] Area under the Precision-Recall curve (AUPRC): 0.0752 [0.0745, 0.076]
PPM001834 PSS000929|
European Ancestry|
5,581 individuals
PGP000152 |
Gola D et al. Circ Genom Precis Med (2020)
Reported Trait: Coronary artery disease AUROC: 0.5143 [0.4992, 0.5294] Area under the Precision-Recall curve (AUPRC): 0.5607 [0.5593, 0.5621]
PPM001835 PSS000930|
European Ancestry|
27,048 individuals
PGP000152 |
Gola D et al. Circ Genom Precis Med (2020)
Reported Trait: Coronary artery disease AUROC: 0.6049 [0.5857, 0.6241] Area under the Precision-Recall curve (AUPRC): 0.046 [0.0454, 0.0466]

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
PSS000929 For GERMIFSI and GERMIFSII, CAD was defined as Myocardinal infarction before the age of 60 and 1 or more 1st- degree relative with CAD. In GERMIFSIII CAD was defined as myocardial infarction between the ages of 26 and 74. In GERMIFSIV, cases were based on a CAD diagnosis before age 65 in men or age 70 in women. In Luric, cases were ascertained as >50% angiographic confirmation of vascular obstruction in 1 or more coronary vessel
[
  • 2,919 cases
  • , 2,662 controls
]
European 6 cohorts
  • GERMIFSI
  • ,GERMIFSII
  • ,GERMIFSIII
  • ,GERMIFSIV
  • ,GERMIFSV
  • ,LURIC
PSS000930 CAD ascertainment was based on myocardial infarction diagnosis or death cause using ICD-10 codes I21.X, I22.X, I23.X, I24.1, or I25.2
[
  • 840 cases
  • , 26,208 controls
]
European EB
PSS000931 CAD ascertainment was based on a composite of myocardial infarction or coronary revascularization. Myocardial infarction was based on ICD-9 codes 410.X, 411.X, 412.X, or 429.79, or ICD-10 codes I21.X, I22.X, I23.X, I24.1, or I25.2. Coronary revascularization was assessed based on OPCS-4 coded procedure for coronary artery bypass grafting (K40.1-40-4, K41.1-41.4, or K45.1-45.5), or coronary angioplasty with or without stenting (K49.1-49.2, K49.0-49.9, K50.2, K75.1-75.4, or K75.8-75.9)
[
  • 21,025 cases
  • , 410,789 controls
]
European UKB