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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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 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 P... articipants. 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.Show more
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)
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Study Identifiers
Sample Numbers
Sample Ancestry
Cohort(s)
GWAS Catalog: GCST003116
Europe PMC: 26343387
141,217 individualsEuropeanNR
GWAS Catalog: GCST003116
Europe PMC: 26343387
3,139 individualsAfrican American or Afro-CaribbeanNR
GWAS Catalog: GCST003116
Europe PMC: 26343387
4,095 individualsHispanic or Latin AmericanNR
GWAS Catalog: GCST003116
Europe PMC: 26343387
25,557 individualsSouth AsianNR
GWAS Catalog: GCST003116
Europe PMC: 26343387
2,268 individualsGreater Middle Eastern (Middle Eastern, North African or Persian)NR
GWAS Catalog: GCST003116
Europe PMC: 26343387
11,323 individualsEast AsianNR
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Score Development/Training
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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)
UKBTo 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.Show moreMean = 55.97 years
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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.

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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
PPM020258PSS011313|
European Ancestry|
403,422 individuals
PGP000532 |
Manikpurage HD et al. Circ Genom Precis Med (2021)
Reported Trait: Prevalent Coronary Artery DiseaseOR: 1.56 [1.56, 1.58]AUROC: 0.766: 0.158Age, Sex and Genetic Principal Components (1 to 10)
PPM020259PSS011313|
European Ancestry|
403,422 individuals
PGP000532 |
Manikpurage HD et al. Circ Genom Precis Med (2021)
Reported Trait: Prevalent Myocardial InfarctionOR: 1.63 [1.6, 1.65]AUROC: 0.772: 0.129Age, Sex and Genetic Principal Components (1 to 10)
PPM020260PSS011313|
European Ancestry|
403,422 individuals
PGP000532 |
Manikpurage HD et al. Circ Genom Precis Med (2021)
Reported Trait: Prevalent Myocardial Infarction and Coronary Revascularization procedureOR: 1.73 [1.7, 1.76]AUROC: 0.789: 0.162Age, Sex and Genetic Principal Components (1 to 10)
PPM020261PSS011313|
European Ancestry|
403,422 individuals
PGP000532 |
Manikpurage HD et al. Circ Genom Precis Med (2021)
Reported Trait: Incident Myocardial InfarctionHR: 1.53 [1.49, 1.56]C-index: 0.729Age, Sex and Genetic Principal Components (1 to 10)
PPM020262PSS011313|
European Ancestry|
403,422 individuals
PGP000532 |
Manikpurage HD et al. Circ Genom Precis Med (2021)
Reported Trait: MortalityHR: 1.08 [1.06, 1.09]Age, Sex and Genetic Principal Components (1 to 10)
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Evaluated Samples

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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
PSS011313To 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.Show moreMean = 11.0 years
[
  • 32,475 cases
  • , 370,947 controls
]
,
46.0 % Male samples
Mean = 56.93 yearsEuropean
(White British)
UKB
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