Polygenic Score (PGS) ID: PGS004698

Predicted Trait
Reported Trait Coronary heart disease
Mapped Trait(s) coronary artery disease (EFO_0001645)
Additional Trait Information Multi-Ancestry
Released in PGS Catalog: March 18, 2024
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Score Details

Score Construction
PGS Name multi_anc_hg37PT
Development Method
Name Pruning and Thresholding (P+T)
Parameters P-value threshold<= 0.1, LD pruning window distance= 250 kb, R2<=0.8
Variants
Original Genome Build hg19
Number of Variants 542,218
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000602
Citation (link to publication) Smith JL et al. Circ Genom Precis Med (2024)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 70.7%
East Asian: 19.4%
African: 7%
Hispanic or Latin American: 2.8%
1,093,078 individuals (100%)
Score Development/Training
European: 64.2%
African: 19.4%
Hispanic or Latin American: 11.4%
Multi-ancestry (excluding European): 5%
  • East Asian
  • South Asian
87,724 individuals (100%)
PGS Evaluation
African: 20%
Hispanic or Latin American: 20%
East Asian: 20%
European: 20%
South Asian: 20%
5 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST90132305
Europe PMC: 35915156
 30,648 individuals Hispanic or Latin American BBJ, CARDIoGRAMplusC4D, MVP, UKB
GWAS Catalog: GCST90132305
Europe PMC: 35915156
 76,709 individuals African American or Afro-Caribbean BBJ, CARDIoGRAMplusC4D, MVP, UKB
GWAS Catalog: GCST90132305
Europe PMC: 35915156
 212,453 individuals East Asian BBJ, CARDIoGRAMplusC4D, MVP, UKB
GWAS Catalog: GCST90132305
Europe PMC: 35915156
 773,268 individuals European BBJ, CARDIoGRAMplusC4D, MVP, UKB
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
—
[
  • 24,041 cases
  • , 32,318 controls
]
 European MVP — — — — —
—
[
  • 3,980 cases
  • , 13,007 controls
]
 African unspecified MVP — — — — —
—
[
  • 1,800 cases
  • , 8,192 controls
]
 Hispanic or Latin American MVP — — — — —
—
[
  • 626 cases
  • , 3,760 controls
]
 East Asian, South Asian MVP — — — ~95% East Asian —

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
PPM020913 PSS011448|
European Ancestry|
52,702 individuals
 PGP000602 |
Smith JL et al. Circ Genom Precis Med (2024)
 Reported Trait: Incident coronary heart disease OR: 1.65 [1.59 -1.72) AUROC: 0.773 — age, sex, 10 PCs —
PPM020914 PSS011446|
African Ancestry|
17,008 individuals
 PGP000602 |
Smith JL et al. Circ Genom Precis Med (2024)
 Reported Trait: Incident coronary heart disease OR: 1.16 [1.11, 1.21] AUROC: 0.735 — age, sex, 10 PCs —
PPM020915 PSS011449|
Hispanic or Latin American Ancestry|
6,138 individuals
 PGP000602 |
Smith JL et al. Circ Genom Precis Med (2024)
 Reported Trait: Incident coronary heart disease OR: 1.38 [1.24, 1.54] AUROC: 0.699 — age, sex, 10 PCs —
PPM020916 PSS011447|
East Asian Ancestry|
22,751 individuals
 PGP000602 |
Smith JL et al. Circ Genom Precis Med (2024)
 Reported Trait: Incident coronary heart disease OR: 1.56 [1.5, 1.61] AUROC: 0.748 — age, sex, 10 PCs —
PPM020917 PSS011450|
South Asian Ancestry|
9,178 individuals
 PGP000602 |
Smith JL et al. Circ Genom Precis Med (2024)
 Reported Trait: Incident coronary heart disease OR: 2.75 [2.41, 3.14] AUROC: 0.786 — age, sex, 10 PCs —

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
PSS011446 — —
[
  • 1,359 cases
  • , 15,649 controls
]
 — African unspecified — ARIC, CHS, MESA, WHI, eMERGE —
PSS011447 — —
[
  • 6,321 cases
  • , 16,430 controls
]
 — East Asian — BBJ, OACIS, TaiChi —
PSS011448 — —
[
  • 4,970 cases
  • , 47,732 controls
]
 — European — ARIC, CHS, MESA, WHI, eMERGE —
PSS011449 — —
[
  • 314 cases
  • , 5,824 controls
]
 — Hispanic or Latin American — MESA, WHI, eMERGE —
PSS011450 — —
[
  • 517 cases
  • , 8,661 controls
]
 — South Asian — UKB —