PGS Catalog - PGS004596 / Coronary heart disease (Polygenic Score)

Polygenic Score (PGS) ID: PGS004596

Predicted Trait
Reported Trait	Coronary heart disease
Mapped Trait(s)	coronary artery disease (EFO_0001645)

Released in PGS Catalog: Jan. 26, 2024

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Score Details

Score Construction
PGS Name	PRS64_CHD
Development Method
Name	Genome-wide significant SNPs
Parameters	NR
Variants
Original Genome Build	NR
Number of Variants	64
Effect Weight Type	beta

PGS Source
PGS Catalog Publication (PGP) ID	PGP000576
Citation (link to publication)	Peng H et al. Nutrients (2023)

Ancestry Distribution
Source of Variant Associations (GWAS)	European: 75.3% South Asian: 13.6% East Asian: 6% Hispanic or Latin American: 2.2% African: 1.7% Greater Middle Eastern: 1.2% 187,599 individuals (100%)
PGS Evaluation	Multi-ancestry (including European): 100% European Not Reported 1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)

Study Identifiers	Sample Numbers	Sample Ancestry	Cohort(s)
GWAS Catalog: GCST003116 Europe PMC: 26343387	141,217 individuals	European	NR
GWAS Catalog: GCST003116 Europe PMC: 26343387	3,139 individuals	African American or Afro-Caribbean	NR
GWAS Catalog: GCST003116 Europe PMC: 26343387	4,095 individuals	Hispanic or Latin American	NR
GWAS Catalog: GCST003116 Europe PMC: 26343387	25,557 individuals	South Asian	NR
GWAS Catalog: GCST003116 Europe PMC: 26343387	2,268 individuals	Greater Middle Eastern (Middle Eastern, North African or Persian)	NR
GWAS Catalog: GCST003116 Europe PMC: 26343387	11,323 individuals	East Asian	NR

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
PPM020748	PSS011390\| Multi-ancestry (including European)\| 13,348 individuals	PGP000576 \| Peng H et al. Nutrients (2023)	Reported Trait: Incident coronary artery disease in breast cancer survivors	—	—	Hazard ratio (HR, top 50% vs bottom 50% of PRS): 1.36 [1.1, 1.67]	Age at diagnosis of breast cancer, race, Townsend Deprivation Index, diabetes, hypertension, antihypertensive medications, insulin treatment, lipid treatments, hormone replacement therapy, menopause, surgical treatment of breast cancer, genetic testing batches, 10 PCs	—
PPM020751	PSS011390\| Multi-ancestry (including European)\| 13,348 individuals	PGP000576 \| Peng H et al. Nutrients (2023)	Reported Trait: Incident coronary artery disease in breast cancer survivors with lifestyle	—	—	Hazard ratio (HR, unhealthy lifestyle and PRS in top 50% vs healthy lifestyle and PRS in bottom 50%): 0.37 [0.24, 0.56]	Age at diagnosis of breast cancer, race, Townsend Deprivation Index, diabetes, hypertension, antihypertensive medications, insulin treatment, lipid treatments, hormone replacement therapy, menopause, surgical treatment of breast cancer, genetic testing batches, 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
PSS011390	CVD ICD-10: I20-I25, I60-I64, G45	—	12,780 individuals, 0.0 % Male samples	—	European	—	UKB	Mean age of full combined ancestry cohort = 58.8 years (sd = 7.1)
PSS011390	CVD ICD-10: I20-I25, I60-I64, G45	—	568 individuals, 0.0 % Male samples	—	Not reported	—	UKB	Mean age of full combined ancestry cohort = 58.8 years (sd = 7.1)