Predicted Trait | |
Reported Trait | Coronary artery disease |
Mapped Trait(s) | coronary artery disease (EFO_0001645) |
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) |
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 | [
|
European, South Asian |
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. | — | [
|
— | European, NR | ~95% European ancestry samples, <5% non-European ancestry | UKB | — |
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 | — |
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. | — | [ ,
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). | — | [ ,
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). | — | [
|
— | 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). | — | [
|
— | 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). | — | [ ,
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). | — | [ ,
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 |
[ ,
31.0 % Male samples |
Mean = 43.6 years Sd = 12.5 years |
African American or Afro-Caribbean | — | 7 cohorts
|
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 |
[ ,
31.0 % Male samples |
Mean = 43.6 years Sd = 12.5 years |
African American or Afro-Caribbean | — | 7 cohorts
|
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 |
[ ,
44.6 % Male samples |
Mean = 49.0 years Sd = 14.1 years |
European | — | 11 cohorts
|
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 |
[ ,
44.6 % Male samples |
Mean = 49.0 years Sd = 14.1 years |
European | — | 11 cohorts
|
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 |
[ ,
36.2 % Male samples |
Mean = 41.1 years Sd = 13.2 years |
Hispanic or Latin American | — | 8 cohorts
|
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 |
[ ,
36.2 % Male samples |
Mean = 41.1 years Sd = 13.2 years |
Hispanic or Latin American | — | 8 cohorts
|
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 | [ ,
51.0 % Male samples |
Median = 44.0 years Iqr = [30.5, 54.7] years |
European | — | INTERVAL | — |