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(Variants and weights)

Polygenic Score (PGS) ID: PGS000018

Predicted Trait

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

Score Details

Name: metaGRS_CAD

Original Genome Build: hg19
Number of Variants: 1,745,180

PGS Development Method: metaGRS
PGS Development Details/Relevant Parameters: metaGRS log(HR) mixing weights: GRS46K=0.1278, FDR202=0.2359 and 1000Genomes=0.2400

Citation: Inouye M et al. J Am Coll Cardiol (2018) | PGS Catalog Publication ID: PGP000007

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
PubMed: 23202125.0 194,427 individuals
[ 63,746 cases, 130,681 controls]
Other
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 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. 3,000 individuals
[ 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 (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
PPM000027 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
PPM000034 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 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
PPM000036 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
PPM000037 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

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
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