Polygenic Score (PGS) ID: PGS000059

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 CHD46
Variants
Original Genome Build NR
Number of Variants 46
Development Method
Name Literature-derived SNP selection
Parameters NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000044
Citation (link to publication) Hajek C et al. Circ Genom Precis Med (2018)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 51.4%
Multi-ancestry (including European): 36%
  • European
  • South Asian
South Asian: 7.5%
East Asian: 3.4%
Hispanic or Latin American: 0.8%
African: 0.6%
Greater Middle Eastern: 0.4%
540,176 individuals (100%)
PGS Evaluation
European: 100%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
Europe PMC: 23202125
[
  • 63,746 cases
  • , 130,681 controls
]
European, South Asian
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
GWAS Catalog: GCST000030
Europe PMC: 17478679
8,335 individuals European
GWAS Catalog: GCST000057
Europe PMC: 17634449
4,864 individuals European
GWAS Catalog: GCST000338
Europe PMC: 19198612
2,520 individuals European
GWAS Catalog: GCST000875
Europe PMC: 21088011
2,905 individuals European
GWAS Catalog: GCST000946
Europe PMC: 21239051
7,311 individuals European
GWAS Catalog: GCST000945
Europe PMC: 21239051
2,723 individuals European
GWAS Catalog: GCST001000
Europe PMC: 21378986
460 individuals East Asian
GWAS Catalog: GCST000999
Europe PMC: 21378988
14,790 individuals South Asian
(India, Pakistan)
GWAS Catalog: GCST000999
Europe PMC: 21378988
15,682 individuals European
Europe PMC: 21673312
[
  • 22,233 cases
  • , 64,762 controls
]
European
(European )
GWAS Catalog: GCST001079
Europe PMC: 21606135
5,031 individuals European
GWAS Catalog: GCST001587
Europe PMC: 22751097
6,534 individuals 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
PPM000150 PSS000094|
European Ancestry|
1,320 individuals
PGP000044 |
Hajek C et al. Circ Genom Precis Med (2018)
Reported Trait: Incident coronary heart disease HR (top vs. bottom quartiles of GRS): 0.76 [0.41, 1.39]
p-value (association between risk and incidence): 0.31
NR
PPM000149 PSS000095|
European Ancestry|
1,206 individuals
PGP000044 |
Hajek C et al. Circ Genom Precis Med (2018)
Reported Trait: Incident coronary heart disease HR (top vs. bottom quartiles of GRS): 1.92 [1.19, 3.11]
p-value (association between risk and incidence): 0.029
NR

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
PSS000094 Incident CHD was defined as myocardial infarction (MI), resuscitated cardiac arrest, definite or probable angina if followed by a revascularization and CHD death
[
  • 86 cases
  • , 1,234 controls
]
Mean = 62.6 years European Analysis restricted to "White participants" MESA
PSS000095 Incident CHD was defined as myocardial infarction (MI), resuscitated cardiac arrest, definite or probable angina if followed by a revascularization and CHD death
[
  • 144 cases
  • , 1,062 controls
]
Mean = 62.7 years European Analysis restricted to "White participants" MESA