Polygenic Score (PGS) ID: PGS000329

Predicted Trait
Reported Trait Coronary heart disease
Mapped Trait(s) coronary artery disease (EFO_0001645)
Released in PGS Catalog: Sept. 18, 2020
Download Score FTP directory
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 PRS_CHD
Development Method
Name LDpred
Parameters ρ = 0.003; LD radius = 4000; LD reference panel = 2,690 Finnish individuals [autosomal variants only]
Variants
Original Genome Build hg19
Number of Variants 6,423,165
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000100
Citation (link to publication) Mars N et al. Nat Med (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
408,458 individuals (100%)
Score Development/Training
European: 100%
21,813 individuals (100%)
PGS Evaluation
European: 100%
6 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST008370
Europe PMC: 30104761
 408,458 individuals European 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
— 21,813 individuals,
47.3 % Male samples
 European
(Finnish)		 FINRISK National registries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2018, whichever came first. Disease endpoints are defined in Table S9. Mean (Age At Baseline) = 48.0 years — — Used to select optimal threshold of ρ for all subsequent analyses. FINRISK surveys from 1992, 1997, 2002 and 2007

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
PPM000896 PSS000440|
European Ancestry|
20,165 individuals
 PGP000100 |
Mars N et al. Nat Med (2020)
 Reported Trait: Incident coronary heart disease — C-index: 0.82 — ASCVD risk calculator(age, sex, total cholesterol, HDL, SBP, blood-pressure-lowering medication, diabetes and smoking status), FINRISK cohort, genotyping array/batch, 10 ancestry PCs 10-year risk
PPM000891 PSS000440|
European Ancestry|
20,165 individuals
 PGP000100 |
Mars N et al. Nat Med (2020)
 Reported Trait: Incident coronary heart disease HR: 1.25 [1.18, 1.32] C-index: 0.832 — age, sex, FINRISK cohort, genotyping array/batch, 10 ancestry PCs 10-year risk
PPM000886 PSS000445|
European Ancestry|
135,300 individuals
 PGP000100 |
Mars N et al. Nat Med (2020)
 Reported Trait: Coronary heart disease (incident and prevalent cases) HR: 1.31 [1.29, 1.33] — — genotyping array/batch, 10 ancestry PCs, stratified by sex —
PPM017092 PSS010120|
European Ancestry|
4,218 individuals
 PGP000433 |
de La Harpe R et al. Eur J Prev Cardiol (2023)
|Ext.		 Reported Trait: Atherosclerotic cardiovascular disease (incident and prevalent) OR: 1.33 [1.2, 1.49] AUROC: 0.765 [0.74, 0.79] — sex, age —
PPM017093 PSS010122|
European Ancestry|
4,218 individuals
 PGP000433 |
de La Harpe R et al. Eur J Prev Cardiol (2023)
|Ext.		 Reported Trait: Coronary heart disease (incident and prevalent) OR: 1.59 [1.42, 1.77] AUROC: 0.779 [0.756, 0.803] — sex, age —
PPM017094 PSS010119|
European Ancestry|
3,383 individuals
 PGP000433 |
de La Harpe R et al. Eur J Prev Cardiol (2023)
|Ext.		 Reported Trait: Incident atherosclerotic cardiovascular disease HR: 1.29 [1.12, 1.47] — — sex, age, 10 principal components —
PPM017095 PSS010121|
European Ancestry|
3,383 individuals
 PGP000433 |
de La Harpe R et al. Eur J Prev Cardiol (2023)
|Ext.		 Reported Trait: Incident coronary heart disease HR: 1.57 [1.4, 1.77] — — sex, age, 10 principal components —

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
PSS010119 Atherosclerotic cardiovacular disease (ASCVD), comprising non-fatal acute myocardial infarction, death of cardiovascular origin (comprising sudden death, ischemic death) and fatal and non-fatal ischaemic stroke (including transient ischaemic attack) using relevant medical records and ICD codes. All events were adjudicated by two expert. More details in PMID: 33838036 Median = [10.7, 14.6] years
[
  • 190 cases
  • , 3,193 controls
]
,
45.0 % Male samples
 Mean = 52.3 years European — CoLaus right censored was death or latest evidence of good health, participant with statine therapy at baseline were excluded
PSS010120 Atherosclerotic cardiovacular disease (ASCVD), comprising non-fatal acute myocardial infarction, death of cardiovascular origin (comprising sudden death, ischemic death) and fatal and non-fatal ischaemic stroke (including transient ischaemic attack) using relevant medical records and ICD codes. All events were adjudicated by two expert. More details in PMID: 33838036 Median = [10.6, 14.6] years
[
  • 363 cases
  • , 3,855 controls
]
,
47.0 % Male samples
 Mean = 53.4 years European — CoLaus right censored was death or latest evidence of good health
PSS010121 Coronary artery disease (CAD), ccomprising either non-fatal myocardial infarction, death from coronary heart disease or symptomatic stable angina followed by a revascularization procedure, either by percutaneous coronary intervention (PCI), or by coronary artery bypass grafting (CABG) using relevant medical records and ICD codes. All events were adjudicated by two expert. More details in PMID: 33838036 Median = [10.7, 14.6] years
[
  • 195 cases
  • , 3,188 controls
]
,
45.0 % Male samples
 Mean = 52.3 years European — CoLaus right censored was death or latest evidence of good health, participant with statine therapy at baseline were excluded
PSS010122 Coronary artery disease (CAD), ccomprising either non-fatal myocardial infarction, death from coronary heart disease or symptomatic stable angina followed by a revascularization procedure, either by percutaneous coronary intervention (PCI), or by coronary artery bypass grafting (CABG) using relevant medical records and ICD codes. All events were adjudicated by two expert. More details in PMID: 33838036 Median = [10.6, 14.6] years
[
  • 388 cases
  • , 3,830 controls
]
,
47.0 % Male samples
 Mean = 53.4 years European — CoLaus right censored was death or latest evidence of good health
PSS000440 Coronary heart disease was defined as Myocardial infarction|Myocardial infarction, strict|Complications following myocardial infarction|Prior myocardial infactrion|Angina pectoris|Other coronary atherosclerosis|Coronary artery bypass graft**|Coronary angioplasty**. ICD9/10 codes are listed in Table S9. National registries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2018, whichever came first. —
[
  • 1,209 cases
  • , 18,956 controls
]
,
47.3 % Male samples
 Mean (Age At Baseline) = 48.0 years European
(Finnish)		 — FINRISK FINRISK surveys from 1992, 1997, 2002 and 2007
PSS000445 Coronary heart disease was defined as Myocardial infarction|Myocardial infarction, strict|Complications following myocardial infarction|Prior myocardial infactrion|Angina pectoris|Other coronary atherosclerosis|Coronary artery bypass graft**|Coronary angioplasty**. ICD9/10 codes are listed in Table S9. National registries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2018, whichever came first. —
[
  • 20,179 cases
  • , 115,121 controls
]
,
43.7 % Male samples
 Mean (Age At Baseline) = 59.2 years
Sd = 16.6 years		 European
(Finnish)		 — FinnGen —