Polygenic Score (PGS) ID: PGS000057

Predicted Trait
Reported Trait Coronary heart disease
Mapped Trait(s) coronary artery disease (EFO_0001645)
Released in PGS Catalog: Dec. 18, 2019
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Score Details

Score Construction
PGS Name CHD57
Variants
Original Genome Build hg19
Number of Variants 57
Development Method
Name Hard thresholding
Parameters Independent variants associated with CHD, with suitable proxies (r2 > 0.8) in the cohorts
PGS Source
PGS Catalog Publication (PGP) ID PGP000042
Citation (link to publication) Natarajan P et al. Circulation (2017)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 52.1%
Multi-ancestry (including European): 38.7%
  • European
  • South Asian
South Asian: 5.1%
East Asian: 2.3%
Hispanic or Latin American: 0.8%
African: 0.6%
Greater Middle Eastern: 0.5%
502,601 individuals (100%)
PGS Evaluation
Not Reported: 100%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
Europe PMC: 26934567
[
  • 42,335 cases
  • , 78,240 controls
]
European
GWAS Catalog: GCST003116
Europe PMC: 26343387
11,323 individuals East Asian
GWAS Catalog: GCST003116
Europe PMC: 26343387
25,557 individuals South Asian
GWAS Catalog: GCST003116
Europe PMC: 26343387
2,268 individuals Greater Middle Eastern (Middle Eastern, North African or Persian)
GWAS Catalog: GCST003116
Europe PMC: 26343387
4,095 individuals Hispanic or Latin American
GWAS Catalog: GCST003116
Europe PMC: 26343387
141,217 individuals European
GWAS Catalog: GCST003116
Europe PMC: 26343387
3,139 individuals African American or Afro-Caribbean
Europe PMC: 23202125
[
  • 63,746 cases
  • , 130,681 controls
]
European, South 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
PPM000144 PSS000091|
Ancestry Not Reported|
2,440 individuals
PGP000042 |
Natarajan P et al. Circulation (2017)
Reported Trait: Coronary heart disease (incident) HR (highest vs. lowest quintile of PGS): 1.66 [1.21, 2.29] age, sex, diabetes meliitus status, smoking status, LDL cholesterol, HDL cholesterol, systolic blood pressure, antihypertensive medication status, family history of CHD
PPM000145 PSS000090|
Ancestry Not Reported|
1,154 individuals
PGP000042 |
Natarajan P et al. Circulation (2017)
Reported Trait: Coronary artery calcification OR: 1.32 [1.04, 1.68] OR (highest vs. lowest quintile of PGS): 2.51 [1.08, 5.85] age, sex, diabetes meliitus status, smoking status, LDL cholesterol, HDL cholesterol, systolic blood pressure, antihypertensive medication status, family history of CHD
PPM000146 PSS000089|
Ancestry Not Reported|
4,392 individuals
PGP000042 |
Natarajan P et al. Circulation (2017)
Reported Trait: Carotid artery plaque burden β: 1.097 [1.022, 1.178] age, sex, diabetes meliitus status, smoking status, LDL cholesterol, HDL cholesterol, systolic blood pressure, antihypertensive medication status, family history of CHD

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
PSS000089 Total carotid plaque burden (mm2) 4,392 individuals Range = [55.0, 80.0] years NR BioImage
PSS000090 Total coronary arterial clacification (CAC) was coded as a a dichotomous outcome variable (CAC>0 versus CAC=0), and quantified by the Agatston method Mean = 15.0 years 1,154 individuals Range = [32.0, 47.0] years NR CARDIA
PSS000091 Nonfatal myocardial infarction or death from CHD Mean = 13.5 years
Sd = 2.8 years
2,440 individuals,
100.0 % Male samples
Mean = 55.1 years
Sd = 5.5 years
NR Participants were all men hypercholesterolemia but without a history of myocardial infarction, allocated to the placebo group