Trait: coronary artery disease

Information

Experimental Factor Ontology ID: EFO_0000378

EFO Trait Description: Narrowing of the coronary arteries due to fatty deposits inside the arterial walls. The diagnostic criteria may include documented history of any of the following: documented coronary artery stenosis greater than or equal to 50% (by cardiac catheterization or other modality of direct imaging of the coronary arteries); previous coronary artery bypass surgery (CABG); previous percutaneous coronary intervention (PCI); previous myocardial infarction. (ACC) [NCIT: C26732]

Associated PGS

PGS 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 Evaluated Score 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 PGS000019 (GRS_CAD) 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 PGS000019 (GRS_CAD) 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)
PPM000030 PGS000013 (GPS_CAD) 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 PGS000013 (GPS_CAD) 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
PPM000033 PGS000013 (GPS_CAD) 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
PPM000034 PGS000018 (metaGRS_CAD) PSS000021 Wünnemann F et al. (2019) Ext. Reported Trait: Prevalent coronary artery disease cases OR: 1.74 [1.57 - 1.93] AUROC: 0.72 [0.7 - 0.75] age, sex, first four genetic PCs
PPM000035 PGS000018 (metaGRS_CAD) PSS000022 Wünnemann F et al. (2019) Ext. Reported Trait: Prevalent coronary artery disease cases OR: 1.6 [1.43 - 1.8] AUROC: 0.89 [0.88 - 0.91] age, sex, first four genetic PCs
PPM000037 PGS000018 (metaGRS_CAD) PSS000020 Wünnemann F et al. (2019) Ext. Reported Trait: Reccurent coronary artery disease events OR: 1.17 [1.08 - 1.26] age, sex, first four genetic PCs
PPM000032 PGS000013 (GPS_CAD) 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
PPM000036 PGS000018 (metaGRS_CAD) PSS000019 Wünnemann F et al. (2019) Ext. Reported Trait: Prevalent coronary artery disease cases OR: 1.75 [1.49 - 2.05] AUROC: 0.84 [0.81 - 0.87] age, sex, first four genetic PCs, cohort recruitment centre
PPM000016 PGS000011 (GRS50) PSS000010 Tada H et al. (2015) Reported Trait: incident coronary heart disease cases HR: 1.23 [1.18 - 1.28] age, sex, systolic blood pressure, hypertension treatment, smoking, apoB, apoA-I, prevalent diabetes
PPM000022 PGS000013 (GPS_CAD) 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
PPM000029 PGS000011 (GRS50) PSS000018 Inouye M et al. (2018) Ext. Reported Trait: Incident coronary artery disease HR: 1.263 [1.247 - 1.28] sex, genetic PCs (1-10), genotyping array
PPM000028 PGS000012 (GRS49K) PSS000018 Inouye M et al. (2018) Ext. Reported Trait: Incident coronary artery disease HR: 1.524 [1.498 - 1.551] sex, genetic PCs (1-10), genotyping array Used GRS46K (excludes A/T and C/G SNPs, with performance similar to GRS49K)
PPM000027 PGS000018 (metaGRS_CAD) PSS000018 Inouye M et al. (2018) Reported Trait: Incident coronary artery disease HR: 1.706 [1.682 - 1.73] AUROC: 0.79
C-index: 0.623 [0.615 - 0.631]
AUPRC: 0.161 sex, genetic PCs (1-10), genotyping array age-as-time-scale Cox regression
PPM000020 PGS000012 (GRS49K) PSS000011 Abraham G et al. (2016) Reported Trait: Incident coronary artery disease HR: 1.28 [1.18 - 1.38]
OR: 1.28 [1.17 - 1.41]
sex, sub-cohort, 5 genetic PCs Used only the 46,773 SNPs that were available in FHS
PPM000018 PGS000012 (GRS49K) PSS000012 Abraham G et al. (2016) Reported Trait: Incident coronary artery disease HR: 1.74 [1.61 - 1.86]
OR: 1.74 [1.61 - 1.89]
sex, sub-cohort, location (east/west), 5 genetic PCs Used only the 42,364 SNPs that were available in FINRISK

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
PSS000010 Incident CHD was defined as coronary revascularization, fatal or nonfatal myocardial infarction, or death due to ischemic heart disease. 23,595 individuals
[ 2,213 cases, 21,382 controls]
0.3802924348378894 % Male samples
European
(Swedish)
MDC Prospective study
PSS000011 The main outcome of interest was incident CHD event before age 75y. We used the definition of CHD as employed by the Framingham study, namely, one of • MI recognized, with diagnostic ECG (FHS event code #1) • MI recognized, without diagnostic ECG, with enzymes and history (#2) • MI recognized, without diagnostic ECG, with autopsy evidence (new event) (#3) • MI unrecognized, silent (#4) • MI unrecognized, not silent (#5) • Angina pectoris (AP), first episode only (#6) • Coronary insufficiency (CI), definite by both history and ECG (#7) • Questionable MI at exam 1 (#8) • Acute MI by autopsy, previously coded as 1 or 2 (#9) • Death, CHD sudden, with 1 hour (#21) • Death, CHD 1–23 hours, non sudden (#22) • Death, CHD 24-47 hours, non sudden (#23) • Death, CHD, 48 hours or more, non sudden (#24) 3,406 individuals
[ 587 cases, 2,819 controls]
45.0 % Male samples
European FHS FHS Original, FHS Offspring
PSS000012 Coronary heart disease (CHD) was defined as falling into any of the following categories: • I21 or I22 (ICD-10) / 410 (ICD-8/9) as the direct or as a contributing cause of death or I20-I25 (ICD-10) /410-414 (ICD-9) as the underlying cause of death • I21 or I22 (ICD-10) / 410 (ICD-8/9) as the main or secondary diagnosis at hospital discharge. • Coronary bypass surgery or coronary angioplasty at hospital discharge or identified from the Finnish registry of invasive cardiac procedures. 12,676 individuals
[ 757 cases, 11,919 controls]
46.0 % Male samples
European
(Finnish)
FINRISK FR92, FR97, FR02
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
PSS000018 CAD was defined as fatal or nonfatal myocardial infarction (MI) cases, percutaneous transluminal coronary angioplasty (PTCA), or coronary artery bypass grafting (CABG). Prevalent versus incident status was relative to the UKB enrollment assessment. In UKB self-reported data, cases were defined as having had a heart attack diagnosed by a doctor (data field #6150); “non-cancer illnesses that self-reported as heart attack” (data field #20002); or self-reported operation including PTCA, CABG, or triple heart bypass (data field #20004). In HES hospital episodes data and death registry data, MI was defined as hospital admission or cause of death due to ICD-9 410 to 412, or ICD-10 I21 to I24 or I25.2; CABG and PTCA were defined as hospital admission OPCS-4 K40 to K46, K49, K50.1,or K75. 482,629 individuals
[ 22,242 cases, 460,387 controls]
45.6 % Male samples
Other ~95% European ancestry samples, <5% non-European ancestry UKB
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
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