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(Variants and weights)

Polygenic Score (PGS) ID: PGS000057

Predicted Trait

Reported Trait: Coronary heart disease
Mapped Trait(s) (Experimental Factor Ontology (EFO) IDs): coronary heart disease

Score Details

Name: CHD57

Original Genome Build: hg19
Number of Variants: 57

PGS Development Method: Hard thresholding
PGS Development Details/Relevant Parameters: Independent variants associated with CHD, with suitable proxies (r2 > 0.8) in the cohorts

Citation: Natarajan P et al. Circulation (2017) | PGS Catalog Publication ID: PGP000042

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST003116
PubMed: 26343387
11,323 individuals East Asian
GWAS Catalog: GCST003116
PubMed: 26343387
25,557 individuals South Asian
GWAS Catalog: GCST003116
PubMed: 26343387
2,268 individuals Greater Middle Eastern (Middle Eastern, North African or Persian)
GWAS Catalog: GCST003116
PubMed: 26343387
4,095 individuals Hispanic or Latin American
GWAS Catalog: GCST003116
PubMed: 26343387
141,217 individuals European
GWAS Catalog: GCST003116
PubMed: 26343387
3,139 individuals African American or Afro-Caribbean
PubMed: 23202125.0 194,427 individuals
[ 63,746 cases, 130,681 controls]
Other
(Combined analysis of European and South Asian ancestry individuals)
PubMed: 26934567.0 120,575 individuals
[ 42,335 cases, 78,240 controls]
European

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 (PPM) ID PGS Catalog Sample Set (PSS) ID Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000144 PSS000091 Natarajan P et al. (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 Natarajan P et al. (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 Natarajan P et al. (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 Catalog Sample Set (PSS) ID Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000089 Total carotid plaque burden (mm2) 4,392 individuals 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 1,154 individuals CARDIA
PSS000091 Nonfatal myocardial infarction or death from CHD 2,440 individuals
100.00 %% Male samples
Participants were all men hypercholesterolemia but without a history of myocardial infarction, allocated to the placebo group