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(Variants and weights)

Polygenic Score (PGS) ID: PGS000019

Predicted Trait

Reported Trait: Coronary artery disease
Mapped Trait(s) (Experimental Factor Ontology (EFO) IDs): coronary artery disease

Score Details

Name: GRS_CAD

Original Genome Build: NR
Number of Variants: 192

PGS Development Method: Genome-wide significant associations
PGS Development Details/Relevant Parameters: FDR < 5%, r2 < 0.20

Citation: Paquette M et al. J Clin Lipidol (2017) | PGS Catalog Publication ID: PGP000009

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST003116
PubMed: 26343387
141,217 individuals European
GWAS Catalog: GCST003116
PubMed: 26343387
3,139 individuals African American or Afro-Caribbean
GWAS Catalog: GCST003116
PubMed: 26343387
4,095 individuals Hispanic or Latin American
GWAS Catalog: GCST003116
PubMed: 26343387
25,557 individuals South Asian
GWAS Catalog: GCST003116
PubMed: 26343387
2,268 individuals Greater Middle Eastern (Middle Eastern, North African or Persian)
GWAS Catalog: GCST003116
PubMed: 26343387
11,323 individuals East Asian

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 (PPM) ID PGS Catalog Sample Set (PSS) ID Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000038 PSS000023 Paquette M et al. (2017) Reported Trait: cases of 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 Paquette M et al. (2017) Reported Trait: cases of cardiovascular 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 Catalog Sample Set (PSS) ID Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers 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). 725 individuals
[ 206 cases, 519 controls]
0.428 % 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). 725 individuals
[ 231 cases, 494 controls]
0.428 % Male samples
European CNMA Nutrition, Metabolism and Atherosclerosis Clinic (CNMA) of Institut de recherches cliniques de Montréal