Polygenic Score (PGS) ID: PGS000018

Predicted Trait
Reported Trait Coronary artery disease
Mapped Trait(s) coronary artery disease (EFO_0000378)
Released in PGS: Oct. 14, 2019

Score Details

Score Construction
PGS Name metaGRS_CAD
Variants
Original Genome Build hg19
Number of Variants 1,745,180
Development Method
Name metaGRS
Parameters metaGRS log(HR) mixing weights: GRS46K=0.1278, FDR202=0.2359 and 1000Genomes=0.2400
PGS Source
PGS Catalog Publication (PGP) ID PGP000007
Citation (link to publication) Inouye M et al. J Am Coll Cardiol (2018)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST003116
EuropePMC: 26343387
11,323 individuals East Asian
GWAS Catalog: GCST003116
EuropePMC: 26343387
25,557 individuals South Asian
GWAS Catalog: GCST003116
EuropePMC: 26343387
2,268 individuals Greater Middle Eastern (Middle Eastern, North African or Persian)
GWAS Catalog: GCST003116
EuropePMC: 26343387
4,095 individuals Hispanic or Latin American
GWAS Catalog: GCST003116
EuropePMC: 26343387
141,217 individuals European
GWAS Catalog: GCST003116
EuropePMC: 26343387
3,139 individuals African American or Afro-Caribbean
EuropePMC: 23202125
[
  • 63,746 cases
  • , 130,681 controls
]
Other
Score Development/Training
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
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.
[
  • 1,000 cases
  • , 2,000 controls
]
Other ~95% European ancestry samples, <5% non-European ancestry 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 ID)
PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000027 PSS000018 PGP000007
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
PPM000034 PSS000021 PGP000008
Wünnemann F et al. (2019)
Ext.
Reported Trait: Coronary artery disease (prevalent) OR: 1.74[1.57, 1.93] AUROC: 0.72[0.7, 0.75] age, sex, first four genetic PCs
PPM000035 PSS000022 PGP000008
Wünnemann F et al. (2019)
Ext.
Reported Trait: Coronary artery disease (prevalent) OR: 1.6[1.43, 1.8] AUROC: 0.89[0.88, 0.91] age, sex, first four genetic PCs
PPM000036 PSS000019 PGP000008
Wünnemann F et al. (2019)
Ext.
Reported Trait: Coronary artery disease (prevalent) OR: 1.75[1.49, 2.05] AUROC: 0.84[0.81, 0.87] age, sex, first four genetic PCs, cohort recruitment centre
PPM000037 PSS000020 PGP000008
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
PPM000518 PSS000287 PGP000077
Timmerman N et al. (2019)
Ext. Pre
Reported Trait: Plaque vulnerability score β: 0.07[0.003, 0.137] Age, sex, surgery year, type of cerebrovascular symptoms, array, 4 genetic PCs
PPM000517 PSS000287 PGP000077
Timmerman N et al. (2019)
Ext. Pre
Reported Trait: Microvessels β: 0.037[-0.006, 0.08] Age, sex, surgery year, type of cerebrovascular symptoms, array, 4 genetic PCs
PPM000516 PSS000287 PGP000077
Timmerman N et al. (2019)
Ext. Pre
Reported Trait: Number of smoooth muscle cells β: -0.004[-0.038, 0.031] Age, sex, surgery year, type of cerebrovascular symptoms, array, 4 genetic PCs
PPM000515 PSS000287 PGP000077
Timmerman N et al. (2019)
Ext. Pre
Reported Trait: Number of macrophages β: 0.01[-0.015, 0.036] Age, sex, surgery year, type of cerebrovascular symptoms, array, 4 genetic PCs
PPM000514 PSS000287 PGP000077
Timmerman N et al. (2019)
Ext. Pre
Reported Trait: Moderate/heavy macrophages OR: 1.103[0.983, 1.237] Age, sex, surgery year, type of cerebrovascular symptoms, array, 4 genetic PCs
PPM000513 PSS000287 PGP000077
Timmerman N et al. (2019)
Ext. Pre
Reported Trait: Moderate/heavy smooth muscle cells OR: 1.004[0.88, 1.145] Age, sex, surgery year, type of cerebrovascular symptoms, array, 4 genetic PCs
PPM000512 PSS000287 PGP000077
Timmerman N et al. (2019)
Ext. Pre
Reported Trait: Presence of IPH OR: 1.126[0.999, 1.27] Age, sex, surgery year, type of cerebrovascular symptoms, array, 4 genetic PCs
PPM000511 PSS000287 PGP000077
Timmerman N et al. (2019)
Ext. Pre
Reported Trait: Presence of lipid core >10% OR: 1.171[1.026, 1.337] Age, sex, surgery year, type of cerebrovascular symptoms, array, 4 genetic PCs
PPM000510 PSS000287 PGP000077
Timmerman N et al. (2019)
Ext. Pre
Reported Trait: Moderate/heavy collagen OR: 1.064[0.919, 1.231] Age, sex, surgery year, type of cerebrovascular symptoms, array, 4 genetic PCs
PPM000509 PSS000287 PGP000077
Timmerman N et al. (2019)
Ext. Pre
Reported Trait: Moderate/heavy calficiations OR: 0.94[0.826, 1.07] Age, sex, surgery year, type of cerebrovascular symptoms, array, 4 genetic PCs
PPM000508 PSS000287 PGP000077
Timmerman N et al. (2019)
Ext. Pre
Reported Trait: Plaque vulnerability score OR: 0.198[0.003, 0.364] Age, sex, surgery year, type of cerebrovascular symptoms, array, 4 genetic PCs
PPM000507 PSS000287 PGP000077
Timmerman N et al. (2019)
Ext. Pre
Reported Trait: Microvessels Beta (top 20% vs. rest): 0.072[-0.037, 0.182] Age, sex, surgery year, type of cerebrovascular symptoms, array, 4 genetic PCs
PPM000506 PSS000287 PGP000077
Timmerman N et al. (2019)
Ext. Pre
Reported Trait: Number of smoooth muscle cells Beta (top 20% vs. rest): -0.056[-0.143, 0.031] Age, sex, surgery year, type of cerebrovascular symptoms, array, 4 genetic PCs
PPM000505 PSS000287 PGP000077
Timmerman N et al. (2019)
Ext. Pre
Reported Trait: Number of macrophages Beta (top 20% vs. rest): 0.55[-0.012, 0.121] Age, sex, surgery year, type of cerebrovascular symptoms, array, 4 genetic PCs
PPM000504 PSS000287 PGP000077
Timmerman N et al. (2019)
Ext. Pre
Reported Trait: Moderate/heavy macrophages Odds Ratio (OR; top 20% vs. rest): 1.49[1.118, 1.986] Age, sex, surgery year, type of cerebrovascular symptoms, array, 4 genetic PCs
PPM000503 PSS000287 PGP000077
Timmerman N et al. (2019)
Ext. Pre
Reported Trait: Moderate/heavy smooth muscle cells Odds Ratio (OR; top 20% vs. rest): 0.908[0.652, 1.265] Age, sex, surgery year, type of cerebrovascular symptoms, array, 4 genetic PCs
PPM000502 PSS000287 PGP000077
Timmerman N et al. (2019)
Ext. Pre
Reported Trait: Presence of IPH Odds Ratio (OR; top 20% vs. rest): 1.112[0.821, 1.506] Age, sex, surgery year, type of cerebrovascular symptoms, array, 4 genetic PCs
PPM000501 PSS000287 PGP000077
Timmerman N et al. (2019)
Ext. Pre
Reported Trait: Presence of lipid core >10% Odds Ratio (OR; top 20% vs. rest): 1.591[1.105, 2.291] Age, sex, surgery year, type of cerebrovascular symptoms, array, 4 genetic PCs
PPM000500 PSS000287 PGP000077
Timmerman N et al. (2019)
Ext. Pre
Reported Trait: Moderate/heavy collagen Odds Ratio (OR; top 20% vs. rest): 1.091[0.755, 1.577] Age, sex, surgery year, type of cerebrovascular symptoms, array, 4 genetic PCs
PPM000499 PSS000287 PGP000077
Timmerman N et al. (2019)
Ext. Pre
Reported Trait: Moderate/heavy calficiations Odds Ratio (OR; top 20% vs. rest): 1.001[0.754, 1.33] Age, sex, surgery year, type of cerebrovascular symptoms, array, 4 genetic PCs
PPM000498 PSS000287 PGP000077
Timmerman N et al. (2019)
Ext. Pre
Reported Trait: Secondary cardiovascular events HR: 1.15[1.02, 1.29] Age, sex, diabetes, BMI, smoking, hypercholesterolemia, array, 4 genetics PCs

Evaluated Samples

PGS Sample Set ID
(PSS ID)
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000287 (i) Secondary cardiovascular events (sCVE; incl myocardial infarction, stroke, ruptured abdominal aortic aneurysm, fatal cardiac failure, percuteneous of bypass surgery, leg amputation due to cardiovascular causes, cardiovascular death), (ii) atherosclerotic carotid plaque characteristics Mean = 3.0 years 1,319 individuals,
69.3 % Male samples
Mean = 68.8 years
Sd = 9.3 years
European
(Dutch)
AEGS1
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.
[
  • 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).
[
  • 173 cases
  • , 5,589 controls
]
,
41.29 % 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).
[
  • 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).
[
  • 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).
[
  • 974 cases
  • , 976 controls
]
,
72.7 % 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).
[
  • 2,492 cases
  • , 817 controls
]
,
72.38 % Male samples
European
(French Canadian)
MHI Phase 2