Polygenic Score (PGS) ID: PGS000019

Predicted Trait
Reported Trait Coronary artery disease
Mapped Trait(s) coronary artery disease (EFO_0001645)
Released in PGS Catalog: Oct. 14, 2019
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Score Details

Score Construction
PGS Name GRS_CAD
Variants
Original Genome Build NR
Number of Variants 192
Development Method
Name Genome-wide significant associations
Parameters FDR < 5%, r2 < 0.20
PGS Source
PGS Catalog Publication (PGP) ID PGP000009
Citation (link to publication) Paquette M et al. J Clin Lipidol (2017)
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%)
PGS Evaluation
European: 100%
2 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

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
PPM000038 PSS000023|
European Ancestry|
725 individuals
PGP000009 |
Paquette M et al. J Clin Lipidol (2017)
Reported Trait: Coronary artery disease in familial hypercholesterolemia patients OR: 1.66 [1.06, 2.62] age, gender, prior statin use, smoking, diabetes, hypertension, BMI, LDL-C, HDL-C, TGs, Lp(a), and type of LDLR mutation Performance metrics are from Model 2 (adjusted for cardiovascular risk factors)
PPM000039 PSS000024|
European Ancestry|
725 individuals
PGP000009 |
Paquette M et al. J Clin Lipidol (2017)
Reported Trait: Coronary artery disease in familial hypercholesterolemia patients OR: 1.8 [1.14, 2.85] age, gender, prior statin use, smoking, diabetes, hypertension, BMI, LDL-C, HDL-C, TGs, Lp(a), and type of LDLR mutation Performance metrics are from Model 2 (adjusted for cardiovascular risk factors)

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
PSS000023 CAD case endpoints were defined as: angina, myocardial infarction, coronary angioplasty, and coronary bypass surgery. Participants are described as Caucasian with diagnosed Familial hypercholesterolemia(FH; Dutch Lipid Criteria score >= 3 [possible, probable, or definite FH]) and carriers of classical French Canadian mutations in the LDLR gene including del .15 kb of the promoter and exon 1, del .5 kb of exons 2 and 3, W66G (exon 3), E207K (exon 4), Y468X (exon 10), and C646Y (exon 14).
[
  • 206 cases
  • , 519 controls
]
,
42.8 % Male samples
European CNMA Nutrition, Metabolism and Atherosclerosis Clinic (CNMA) of Institut de recherches cliniques de Montréal
PSS000024 Cerebrovascular disease (CVD) case endpoints were defined as: transient ischemic attack, stroke, and carotid endarterectomy. Participants are described as Caucasian with diagnosed Familial hypercholesterolemia(FH; Dutch Lipid Criteria score >= 3 [possible, probable, or definite FH]) and carriers of classical French Canadian mutations in the LDLR gene including del .15 kb of the promoter and exon 1, del .5 kb of exons 2 and 3, W66G (exon 3), E207K (exon 4), Y468X (exon 10), and C646Y (exon 14).
[
  • 231 cases
  • , 494 controls
]
,
42.8 % Male samples
European CNMA Nutrition, Metabolism and Atherosclerosis Clinic (CNMA) of Institut de recherches cliniques de Montréal