Polygenic Score (PGS) ID: PGS000018

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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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name metaGRS_CAD
Variants
Original Genome Build hg19
Number of Variants 1,745,179
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
]
 European, South Asian
Score Development/Training
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
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
]
 — European, NR ~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
PPM000597 PSS000336 PGP000083 Dikilitas O et al. (2020) Ext. Reported Trait: Incident coronary heart disease HR: 1.53 [1.23, 1.9] C-index: 0.683 — sex, eMERGE site, first five ancestry-specific principal components Age-as-time-scale Cox regression
PPM000594 PSS000332 PGP000083 Dikilitas O et al. (2020) Ext. Reported Trait: Incident coronary heart disease HR: 1.27 [1.13, 1.43] C-index: 0.663 — sex, eMERGE site, first five ancestry-specific principal components Age-as-time-scale Cox regression
PPM000591 PSS000334 PGP000083 Dikilitas O et al. (2020) Ext. Reported Trait: Incident coronary heart disease HR: 1.53 [1.46, 1.6] C-index: 0.719 — sex, eMERGE site, first five ancestry-specific principal components Age-as-time-scale Cox regression
PPM000616 PSS000334 PGP000083 Dikilitas O et al. (2020) Ext. Reported Trait: Incident coronary heart disease HR: 1.49 [1.43, 1.56] C-index: 0.75 — sex, eMERGE site, diabetes, hypertension, hyperlipidemia, statin use, first 5 ancestry-specific principal components Age-as-time-scale Cox regression
PPM000620 PSS000332 PGP000083 Dikilitas O et al. (2020) Ext. Reported Trait: Incident coronary heart disease HR: 1.25 [1.12, 1.41] C-index: 0.723 — sex, eMERGE site, diabetes, hypertension, hyperlipidemia, statin use, first 5 ancestry-specific principal components Age-as-time-scale Cox regression
PPM000624 PSS000336 PGP000083 Dikilitas O et al. (2020) Ext. Reported Trait: Incident coronary heart disease HR: 1.5 [1.21, 1.87] C-index: 0.725 — sex, eMERGE site, diabetes, hypertension, hyperlipidemia, statin use, first 5 ancestry-specific principal components Age-as-time-scale Cox regression
PPM001666 PSS000868 PGP000137 Ritchie SC et al. (2019) Ext. Pre Reported Trait: Incident myocardial infarction HR: 2.89 [1.66, 5.04] — — age, sex, 10 genetic PCs —
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 —
PPM000603 PSS000331 PGP000083 Dikilitas O et al. (2020) Ext. Reported Trait: Coronary heart disease (incident and prevalent) OR: 1.4 [1.3, 1.52] AUROC: 0.775 — age at first EHR record, duration of EHR, sex, eMERGE site, first five ancestry-specific principal components —
PPM000600 PSS000333 PGP000083 Dikilitas O et al. (2020) Ext. Reported Trait: Coronary heart disease (incident and prevalent) OR: 1.73 [1.68, 1.78] AUROC: 0.772 — age at first EHR record, duration of EHR, sex, eMERGE site, first five ancestry-specific principal components —
PPM000606 PSS000335 PGP000083 Dikilitas O et al. (2020) Ext. Reported Trait: Coronary heart disease (incident and prevalent) OR: 1.93 [1.67, 2.22] AUROC: 0.794 — age at first EHR record, duration of EHR, sex, eMERGE site, first five ancestry-specific principal components —

Evaluated Samples

PGS Sample Set ID
(PSS ID) 		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
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
 — European, NR ~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
PSS000331 CHD was defined as occurrence of either myocardial infarction (MI) or coronary revascularization events (such as percutaneous coronary intervention or coronary artery bypass grafting) using ICD codes. Individuals with MI were defined as those whose EHR included at least two related diagnostic codes on separate occasions within a 5-day window, and individuals with coronary revascularization were defined as those who had at least one relevant procedural code in the EHR. ICD codelists and phenotyping algorithm in PMID:27678441 and PMID:25717410 Median = 9.2 years
Iqr = [5.5, 13.0] years
[
  • 838 cases
  • , 6,759 controls
]
,
31.0 % Male samples
 Mean = 43.6 years
Sd = 12.5 years		 African American or Afro-Caribbean — 7 cohorts
  • BioVu
  • ,Columbia
  • ,KP
  • ,Mount Sinai
  • ,Nugene
  • ,PHB
  • ,eMERGE
 right censored at age 75 years or at the age of last observation (whichever was first)
PSS000332 CHD was defined as occurrence of either myocardial infarction (MI) or coronary revascularization events (such as percutaneous coronary intervention or coronary artery bypass grafting) using ICD codes. Individuals with MI were defined as those whose EHR included at least two related diagnostic codes on separate occasions within a 5-day window, and individuals with coronary revascularization were defined as those who had at least one relevant procedural code in the EHR. We identified the first CHD event and classified it as ‘‘incident’’ if the event occurred at least 6 months after the participant’s first record in the EHR and if there were no previous ICD-9-CM or ICD-10-CM codes associated with CHD. ICD codelists and phenotyping algorithm in PMID:27678441 and PMID:25717410 Median = 9.2 years
Iqr = [5.5, 13.0] years
[
  • 311 cases
  • , 6,759 controls
]
,
31.0 % Male samples
 Mean = 43.6 years
Sd = 12.5 years		 African American or Afro-Caribbean — 7 cohorts
  • BioVu
  • ,Columbia
  • ,KP
  • ,Mount Sinai
  • ,Nugene
  • ,PHB
  • ,eMERGE
 right censored at age 75 years or at the age of last observation (whichever was first)
PSS000333 CHD was defined as occurrence of either myocardial infarction (MI) or coronary revascularization events (such as percutaneous coronary intervention or coronary artery bypass grafting) using ICD codes. Individuals with MI were defined as those whose EHR included at least two related diagnostic codes on separate occasions within a 5-day window, and individuals with coronary revascularization were defined as those who had at least one relevant procedural code in the EHR. ICD codelists and phenotyping algorithm in PMID:27678441 and PMID:25717410 Median = 11.7 years
Iqr = [6.0, 18.5] years
[
  • 8,108 cases
  • , 37,537 controls
]
,
44.6 % Male samples
 Mean = 49.0 years
Sd = 14.1 years		 European — 11 cohorts
  • BioVu
  • ,CCHMC
  • ,Columbia
  • ,KP
  • ,MAYO
  • ,Marshfield
  • ,Mount Sinai
  • ,MyCode
  • ,Nugene
  • ,PHB
  • ,eMERGE
 right censored at age 75 years or at the age of last observation (whichever was first)
PSS000334 CHD was defined as occurrence of either myocardial infarction (MI) or coronary revascularization events (such as percutaneous coronary intervention or coronary artery bypass grafting) using ICD codes. Individuals with MI were defined as those whose EHR included at least two related diagnostic codes on separate occasions within a 5-day window, and individuals with coronary revascularization were defined as those who had at least one relevant procedural code in the EHR. We identified the first CHD event and classified it as ‘‘incident’’ if the event occurred at least 6 months after the participant’s first record in the EHR and if there were no previous ICD-9-CM or ICD-10-CM codes associated with CHD. ICD codelists and phenotyping algorithm in PMID:27678441 and PMID:25717410 Median = 11.7 years
Iqr = [6.0, 18.5] years
[
  • 2,221 cases
  • , 37,537 controls
]
,
44.6 % Male samples
 Mean = 49.0 years
Sd = 14.1 years		 European — 11 cohorts
  • BioVu
  • ,CCHMC
  • ,Columbia
  • ,KP
  • ,MAYO
  • ,Marshfield
  • ,Mount Sinai
  • ,MyCode
  • ,Nugene
  • ,PHB
  • ,eMERGE
 right censored at age 75 years or at the age of last observation (whichever was first)
PSS000335 CHD was defined as occurrence of either myocardial infarction (MI) or coronary revascularization events (such as percutaneous coronary intervention or coronary artery bypass grafting) using ICD codes. Individuals with MI were defined as those whose EHR included at least two related diagnostic codes on separate occasions within a 5-day window, and individuals with coronary revascularization were defined as those who had at least one relevant procedural code in the EHR. ICD codelists and phenotyping algorithm in PMID:27678441 and PMID:25717410 Median = 10.4 years
Iqr = [5.7, 14.7] years
[
  • 419 cases
  • , 2,074 controls
]
,
36.2 % Male samples
 Mean = 41.1 years
Sd = 13.2 years		 Hispanic or Latin American — 8 cohorts
  • BioVu
  • ,Columbia
  • ,KP
  • ,MAYO
  • ,Mount Sinai
  • ,Nugene
  • ,PHB
  • ,eMERGE
 right censored at age 75 years or at the age of last observation (whichever was first)
PSS000336 CHD was defined as occurrence of either myocardial infarction (MI) or coronary revascularization events (such as percutaneous coronary intervention or coronary artery bypass grafting) using ICD codes. Individuals with MI were defined as those whose EHR included at least two related diagnostic codes on separate occasions within a 5-day window, and individuals with coronary revascularization were defined as those who had at least one relevant procedural code in the EHR. We identified the first CHD event and classified it as ‘‘incident’’ if the event occurred at least 6 months after the participant’s first record in the EHR and if there were no previous ICD-9-CM or ICD-10-CM codes associated with CHD. ICD codelists and phenotyping algorithm in PMID:27678441 and PMID:25717410 Median = 10.4 years
Iqr = [5.7, 14.7] years
[
  • 120 cases
  • , 2,074 controls
]
,
36.2 % Male samples
 Mean = 41.1 years
Sd = 13.2 years		 Hispanic or Latin American — 8 cohorts
  • BioVu
  • ,Columbia
  • ,KP
  • ,MAYO
  • ,Mount Sinai
  • ,Nugene
  • ,PHB
  • ,eMERGE
 right censored at age 75 years or at the age of last observation (whichever was first)
PSS000868 CALIBER rule-based phenotyping algorithms (https://www.caliberresearch.org/portal). ICD-10: I21-I23, I24.1, I25.2 Median = 6.9 years
[
  • 15 cases
  • , 3,072 controls
]
,
51.0 % Male samples
 Median = 44.0 years
Iqr = [30.5, 54.7] years		 European — INTERVAL —