Download PGS
(Variants and weights)

Polygenic Score (PGS) ID: PGS000013

Predicted Trait

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

Score Details

Name: GPS_CAD

Original Genome Build: hg19
Number of Variants: 6,630,150

PGS Development Method: LDPred
PGS Development Details/Relevant Parameters: ρ = 0.001; LD panel = 503 1000G Europeans

Citation: Khera AV et al. Nat Genet (2018) | PGS Catalog Publication ID: PGP000006

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
Score Development/Training
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
CAD ascertainment was based on a composite of myocardial infarction or coronary revascularization. Myocardial infarction was based on self-report or hospital admission diagnosis, as performed centrally. This included individuals with ICD-9 codes of 410.X, 411.0, 412.X, or 429.79, or ICD-10 codes of I21.X, I22.X, I23.X, I24.1, or I25.2 in hospitalization records. Coronary revascularization was assessed based on an 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, K49.8–49.9, K50.2, K75.1–75.4, or K75.8–75.9). 120,280 individuals
[ 3,963 cases, 124,243 controls]
European UKB UKB Phase 1

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
PPM000022 PSS000015 Khera AV et al. (2018) Reported Trait: Coronary artery disease cases AUROC: 0.81 [0.81 - 0.81] Nagelkerke’s R2 (estimate of variance explained by the PGS after covariate adjustment): 0.04 age; sex; Ancestry PC 1-4; genotyping chip
PPM000030 PSS000021 Wünnemann F et al. (2019) Ext. Reported Trait: Prevalent coronary artery disease cases OR: 1.64 [1.48 - 1.81] AUROC: 0.72 [0.7 - 0.74] age, sex, first four genetic PCs
PPM000031 PSS000022 Wünnemann F et al. (2019) Ext. Reported Trait: Prevalent coronary artery disease cases OR: 1.55 [1.38 - 1.73] AUROC: 0.89 [0.88 - 0.91] age, sex, first four genetic PCs
PPM000032 PSS000019 Wünnemann F et al. (2019) Ext. Reported Trait: Prevalent coronary artery disease cases OR: 1.69 [1.44 - 1.99] AUROC: 0.84 [0.81 - 0.87] age, sex, first four genetic PCs, cohort recruitment centre
PPM000033 PSS000020 Wünnemann F et al. (2019) Ext. Reported Trait: Reccurent coronary artery disease events OR: 1.13 [1.06 - 1.22] age, sex, first four genetic PCs

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
PSS000015 CAD ascertainment was based on a composite of myocardial infarction or coronary revascularization. Myocardial infarction was based on self-report or hospital admission diagnosis, as performed centrally. This included individuals with ICD-9 codes of 410.X, 411.0, 412.X, or 429.79, or ICD-10 codes of I21.X, I22.X, I23.X, I24.1, or I25.2 in hospitalization records. Coronary revascularization was assessed based on an 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, K49.8–49.9, K50.2, K75.1–75.4, or K75.8–75.9). 288,978 individuals
[ 8,676 cases, 297,654 controls]
European UKB UKB Phase 2
PSS000019 Prevalent Coronary artery disease (CAD), where CAD is defined as previous diagnosis of myocardial infarction or revascularization procedures (percutaneous coronary intervention or coronary artery bypass grafting). 5,762 individuals
[ 173 cases, 5,589 controls]
41.2910447761194 % Male samples
European
(French Canadian)
CARTaGENE
PSS000020 Recurrent CAD event during the follow- up period (median follow-up time =3.9 years [range =1.1–7), where CAD is defined as previous diagnosis of myocardial infarction or revascularization procedures (percutaneous coronary intervention or coronary artery bypass grafting). 862 individuals
[ 446 cases, 416 controls]
European
(French Canadian)
MHI Phase 1
PSS000020 Recurrent CAD event during the follow- up period (median follow-up time =3.9 years [range =1.1–7), where CAD is defined as previous diagnosis of myocardial infarction or revascularization procedures (percutaneous coronary intervention or coronary artery bypass grafting). 2,333 individuals
[ 937 cases, 1,396 controls]
European
(French Canadian)
MHI Phase 2
PSS000021 Prevalent Coronary artery disease (CAD), where CAD is defined as previous diagnosis of myocardial infarction or revascularization procedures (percutaneous coronary intervention or coronary artery bypass grafting). 1,964 individuals
[ 974 cases, 976 controls]
72.69551934826883 % Male samples
European
(French Canadian)
MHI Phase 1
PSS000022 Prevalent Coronary artery disease (CAD), where CAD is defined as previous diagnosis of myocardial infarction or revascularization procedures (percutaneous coronary intervention or coronary artery bypass grafting). 3,309 individuals
[ 2,492 cases, 817 controls]
72.38319734058628 % Male samples
European
(French Canadian)
MHI Phase 2