Polygenic Score (PGS) ID: PGS004237

Predicted Trait
Reported Trait Coronary Artery Disease
Mapped Trait(s) coronary artery disease (EFO_0001645)
Released in PGS Catalog: Dec. 15, 2023
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Score Details

Score Construction
PGS Name CAD_PRS_LDpred_UKB_Pub1
Development Method
Name LDpred
Parameters LDpred v1.0.08 / Rho parameter = 0.01 / LD reference panel = 1000 Genomes Consortium, 503 European Participants. Variants with info score R2 < 0.3 (i.e. quality of imputation), minor allele frequency (MAF) < 0.01, multi-allelic, insertion or deletions and with MAF discrepancies > 10% between all datasets were excluded. Only SNPs included in the Phase 3 HapMap Consortium (~1.2 million) were kept for the PRS derivation.
Variants
Original Genome Build GRCh37
Number of Variants 1,146,511
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000532
Citation (link to publication) Manikpurage HD et al. Circ Genom Precis Med (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 75.3%
South Asian: 13.6%
East Asian: 6%
Hispanic or Latin American: 2.2%
African: 1.7%
Greater Middle Eastern: 1.2%
187,599 individuals (100%)
Score Development/Training
European: 100%
5,000 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST003116
Europe PMC: 26343387
 141,217 individuals European NR
GWAS Catalog: GCST003116
Europe PMC: 26343387
 3,139 individuals African American or Afro-Caribbean NR
GWAS Catalog: GCST003116
Europe PMC: 26343387
 4,095 individuals Hispanic or Latin American NR
GWAS Catalog: GCST003116
Europe PMC: 26343387
 25,557 individuals South Asian NR
GWAS Catalog: GCST003116
Europe PMC: 26343387
 2,268 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) NR
GWAS Catalog: GCST003116
Europe PMC: 26343387
 11,323 individuals East Asian NR
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
—
[
  • 219 cases
  • , 4,781 controls
]
,
42.0 % Male samples
 European
(White British)		 UKB To define prevalent CAD, we selected participants with ICD-10 codes for MI (I21.X, I22.X, I23.X, I24.1, or I25.2), for other acute ischemic heart disease (I24.0, I24.8-9) and for atherosclerotic / chronic ischemic heart disease (I25.0-25.1, I25.5-25.9). Procedure codes for coronary artery bypass grafting (K40.1-40.4, K41.1-41.4, K45.1-45.5), for coronary angioplasty, with or without stenting (K49.1-49.2, K49.8-49.9, K50.2, K75.1-75.4, K75.8-75.9) were also added to the CAD definition. Mean = 55.97 years — — —

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) 		PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM020258 PSS011313|
European Ancestry|
403,422 individuals
 PGP000532 |
Manikpurage HD et al. Circ Genom Precis Med (2021)
 Reported Trait: Prevalent Coronary Artery Disease OR: 1.56 [1.56, 1.58] AUROC: 0.766 R²: 0.158 Age, Sex and Genetic Principal Components (1 to 10) —
PPM020259 PSS011313|
European Ancestry|
403,422 individuals
 PGP000532 |
Manikpurage HD et al. Circ Genom Precis Med (2021)
 Reported Trait: Prevalent Myocardial Infarction OR: 1.63 [1.6, 1.65] AUROC: 0.772 R²: 0.129 Age, Sex and Genetic Principal Components (1 to 10) —
PPM020260 PSS011313|
European Ancestry|
403,422 individuals
 PGP000532 |
Manikpurage HD et al. Circ Genom Precis Med (2021)
 Reported Trait: Prevalent Myocardial Infarction and Coronary Revascularization procedure OR: 1.73 [1.7, 1.76] AUROC: 0.789 R²: 0.162 Age, Sex and Genetic Principal Components (1 to 10) —
PPM020261 PSS011313|
European Ancestry|
403,422 individuals
 PGP000532 |
Manikpurage HD et al. Circ Genom Precis Med (2021)
 Reported Trait: Incident Myocardial Infarction HR: 1.53 [1.49, 1.56] C-index: 0.729 — Age, Sex and Genetic Principal Components (1 to 10) —
PPM020262 PSS011313|
European Ancestry|
403,422 individuals
 PGP000532 |
Manikpurage HD et al. Circ Genom Precis Med (2021)
 Reported Trait: Mortality HR: 1.08 [1.06, 1.09] — — Age, Sex and Genetic Principal Components (1 to 10) —

Evaluated Samples

PGS Sample Set ID
(PSS) 		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
PSS011313 To define prevalent CAD, we selected participants with ICD-10 codes for MI (I21.X, I22.X, I23.X, I24.1, or I25.2), for other acute ischemic heart disease (I24.0, I24.8-9) and for atherosclerotic / chronic ischemic heart disease (I25.0-25.1, I25.5-25.9). Procedure codes for coronary artery bypass grafting (K40.1-40.4, K41.1-41.4, K45.1-45.5), for coronary angioplasty, with or without stenting (K49.1-49.2, K49.8-49.9, K50.2, K75.1-75.4, K75.8-75.9) were also added to the CAD definition. Mean = 11.0 years
[
  • 32,475 cases
  • , 370,947 controls
]
,
46.0 % Male samples
 Mean = 56.93 years European
(White British)		 — UKB —