Polygenic Score (PGS) ID: PGS000337

Predicted Trait
Reported Trait Coronary artery disease
Mapped Trait(s) coronary artery disease (EFO_0001645)
Released in PGS Catalog: Nov. 5, 2020
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Terms and Licenses
The use of data is limited for research purposes only. Identification of individuals is prohibited. The hum0014-v20 accession number should be cited in public publications and presentations.

Score Details

Score Construction
PGS Name MetaPRS_CAD
Development Method
Name P-value thresholding
Parameters p < 5e-2, r2 < 0.8
Variants
Original Genome Build hg19
Number of Variants 75,028
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000104
Citation (link to publication) Koyama S et al. Nat Genet (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
Not Reported: 45.5%
East Asian: 27.5%
European: 21.6%
South Asian: 3.9%
Hispanic or Latin American: 0.6%
African: 0.5%
Greater Middle Eastern: 0.3%
652,352 individuals (100%)
PGS Evaluation
East Asian: 85.7%
Greater Middle Eastern: 14.3%
7 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST010867
Europe PMC: 33020668
[
  • 25,892 cases
  • , 142,336 controls
]
,
53.63 % Male samples
 East Asian
(Japanese)		 BBJ
GWAS Catalog: GCST003116
Europe PMC: 26343387
 11,323 individuals East Asian 41 cohorts
  • ADVANCE
  • ,AGES
  • ,AIDHS
  • ,ARIC
  • ,BAS
  • ,BioMe
  • ,CARDIOGENICS
  • ,CAS
  • ,CCGB
  • ,COROGENE
  • ,DUKE_2
  • ,EGCUT
  • ,FGENTCARD
  • ,FHS
  • ,FINRISK
  • ,FamHS
  • ,GENRIC
  • ,GerMIFS
  • ,GoDARTS
  • ,HPS
  • ,HSDS
  • ,HSIEA
  • ,ITH
  • ,LIFE-HEART
  • ,LOLIPOP
  • ,LURIC
  • ,MAYO-VDB
  • ,MIGen
  • ,MedSTAR
  • ,OHGS
  • ,PIVUS
  • ,PROCARDIS
  • ,PROMIS
  • ,PROSPER
  • ,PennCATH
  • ,RS
  • ,SDS
  • ,TwinGene
  • ,ULSAM
  • ,WGHS
  • ,WTCCC
GWAS Catalog: GCST003116
Europe PMC: 26343387
 25,557 individuals South Asian 41 cohorts
  • ADVANCE
  • ,AGES
  • ,AIDHS
  • ,ARIC
  • ,BAS
  • ,BioMe
  • ,CARDIOGENICS
  • ,CAS
  • ,CCGB
  • ,COROGENE
  • ,DUKE_2
  • ,EGCUT
  • ,FGENTCARD
  • ,FHS
  • ,FINRISK
  • ,FamHS
  • ,GENRIC
  • ,GerMIFS
  • ,GoDARTS
  • ,HPS
  • ,HSDS
  • ,HSIEA
  • ,ITH
  • ,LIFE-HEART
  • ,LOLIPOP
  • ,LURIC
  • ,MAYO-VDB
  • ,MIGen
  • ,MedSTAR
  • ,OHGS
  • ,PIVUS
  • ,PROCARDIS
  • ,PROMIS
  • ,PROSPER
  • ,PennCATH
  • ,RS
  • ,SDS
  • ,TwinGene
  • ,ULSAM
  • ,WGHS
  • ,WTCCC
GWAS Catalog: GCST003116
Europe PMC: 26343387
 4,095 individuals Hispanic or Latin American 41 cohorts
  • ADVANCE
  • ,AGES
  • ,AIDHS
  • ,ARIC
  • ,BAS
  • ,BioMe
  • ,CARDIOGENICS
  • ,CAS
  • ,CCGB
  • ,COROGENE
  • ,DUKE_2
  • ,EGCUT
  • ,FGENTCARD
  • ,FHS
  • ,FINRISK
  • ,FamHS
  • ,GENRIC
  • ,GerMIFS
  • ,GoDARTS
  • ,HPS
  • ,HSDS
  • ,HSIEA
  • ,ITH
  • ,LIFE-HEART
  • ,LOLIPOP
  • ,LURIC
  • ,MAYO-VDB
  • ,MIGen
  • ,MedSTAR
  • ,OHGS
  • ,PIVUS
  • ,PROCARDIS
  • ,PROMIS
  • ,PROSPER
  • ,PennCATH
  • ,RS
  • ,SDS
  • ,TwinGene
  • ,ULSAM
  • ,WGHS
  • ,WTCCC
GWAS Catalog: GCST003116
Europe PMC: 26343387
 141,217 individuals European 41 cohorts
  • ADVANCE
  • ,AGES
  • ,AIDHS
  • ,ARIC
  • ,BAS
  • ,BioMe
  • ,CARDIOGENICS
  • ,CAS
  • ,CCGB
  • ,COROGENE
  • ,DUKE_2
  • ,EGCUT
  • ,FGENTCARD
  • ,FHS
  • ,FINRISK
  • ,FamHS
  • ,GENRIC
  • ,GerMIFS
  • ,GoDARTS
  • ,HPS
  • ,HSDS
  • ,HSIEA
  • ,ITH
  • ,LIFE-HEART
  • ,LOLIPOP
  • ,LURIC
  • ,MAYO-VDB
  • ,MIGen
  • ,MedSTAR
  • ,OHGS
  • ,PIVUS
  • ,PROCARDIS
  • ,PROMIS
  • ,PROSPER
  • ,PennCATH
  • ,RS
  • ,SDS
  • ,TwinGene
  • ,ULSAM
  • ,WGHS
  • ,WTCCC
GWAS Catalog: GCST005194
Europe PMC: 29212778
 296,525 individuals NR UKB
GWAS Catalog: GCST003116
Europe PMC: 26343387
 2,268 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) 40 cohorts
  • ADVANCE
  • ,AGES
  • ,AIDHS
  • ,ARIC
  • ,BAS
  • ,BioMe
  • ,CARDIOGENICS
  • ,CAS
  • ,CCGB
  • ,COROGENE
  • ,DUKE_2
  • ,EGCUT
  • ,FGENTCARD
  • ,FHS
  • ,FINRISK
  • ,FamHS
  • ,GENRIC
  • ,GerMIFS
  • ,GoDARTS
  • ,HPS
  • ,HSDS
  • ,HSIEA
  • ,ITH
  • ,LIFE-HEART
  • ,LOLIPOP
  • ,LURIC
  • ,MAYO-VDB
  • ,MIGen
  • ,MedSTAR
  • ,OHGS
  • ,PIVUS
  • ,PROCARDIS
  • ,PROMIS
  • ,PROSPER
  • ,PennCATH
  • ,RS
  • ,TwinGene
  • ,ULSAM
  • ,WGHS
  • ,WTCCC
GWAS Catalog: GCST003116
Europe PMC: 26343387
 3,139 individuals African American or Afro-Caribbean 41 cohorts
  • ADVANCE
  • ,AGES
  • ,AIDHS
  • ,ARIC
  • ,BAS
  • ,BioMe
  • ,CARDIOGENICS
  • ,CAS
  • ,CCGB
  • ,COROGENE
  • ,DUKE_2
  • ,EGCUT
  • ,FGENTCARD
  • ,FHS
  • ,FINRISK
  • ,FamHS
  • ,GENRIC
  • ,GerMIFS
  • ,GoDARTS
  • ,HPS
  • ,HSDS
  • ,HSIEA
  • ,ITH
  • ,LIFE-HEART
  • ,LOLIPOP
  • ,LURIC
  • ,MAYO-VDB
  • ,MIGen
  • ,MedSTAR
  • ,OHGS
  • ,PIVUS
  • ,PROCARDIS
  • ,PROMIS
  • ,PROSPER
  • ,PennCATH
  • ,RS
  • ,SDS
  • ,TwinGene
  • ,ULSAM
  • ,WGHS
  • ,WTCCC

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
PPM000909 PSS000456|
East Asian Ancestry|
49,230 individuals
 PGP000104 |
Koyama S et al. Nat Genet (2020)
 Reported Trait: Mortality (diseases of the circulatory system) HR: 1.10351 [1.057, 1.152] — — Sex, age, age^2, PCs (1-10), disease status —
PPM000908 PSS000454|
East Asian Ancestry|
49,230 individuals
 PGP000104 |
Koyama S et al. Nat Genet (2020)
 Reported Trait: All-cause Mortality HR: 1.03159 [1.011, 1.052] — — Sex, age, age^2, PCs (1-10), disease status —
PPM000911 PSS000457|
East Asian Ancestry|
49,230 individuals
 PGP000104 |
Koyama S et al. Nat Genet (2020)
 Reported Trait: Mortality (ischemic heart disease) HR: 1.2158 [1.109, 1.333] — — Sex, age, age^2, PCs (1-10), disease status —
PPM000912 PSS000455|
East Asian Ancestry|
49,230 individuals
 PGP000104 |
Koyama S et al. Nat Genet (2020)
 Reported Trait: Mortality (congestive heart failure) HR: 1.15604 [1.042, 1.2283] — — Sex, age, age^2, PCs (1-10), disease status —
PPM000910 PSS000458|
East Asian Ancestry|
49,230 individuals
 PGP000104 |
Koyama S et al. Nat Genet (2020)
 Reported Trait: Mortality (diseases of the respiratory system) HR: 1.07133 [1.012, 1.134] — — Sex, age, age^2, PCs (1-10), disease status —
PPM000907 PSS000459|
East Asian Ancestry|
10,999 individuals
 PGP000104 |
Koyama S et al. Nat Genet (2020)
 Reported Trait: Coronary artery disease OR: 1.84 [1.744, 1.943] AUROC: 0.674 [0.661, 0.687] R²: 0.087 [0.074, 0.101] — —
PPM015569 PSS009986|
Greater Middle Eastern Ancestry|
7,023 individuals
 PGP000386 |
Saad M et al. Circ Genom Precis Med (2022)
|Ext.		 Reported Trait: Coronary heart disease OR: 1.81 [1.66, 1.98] AUROC: 0.667 [0.649, 0.685] — — —

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
PSS009986 — —
[
  • 1,014 cases
  • , 6,009 controls
]
,
47.0 % Male samples
 — Greater Middle Eastern (Middle Eastern, North African or Persian)
(Qatari)		 — QBB —
PSS000454 Cause of death under ICD-10 code Median = 7.7 years
[
  • 9,816 cases
  • , 39,414 controls
]
 — East Asian
(Japanese)		 — BBJ —
PSS000455 Cause of death under ICD-10.CHF code Median = 7.7 years
[
  • 362 cases
  • , 48,868 controls
]
 — East Asian
(Japanese)		 — BBJ —
PSS000456 Cause of death under ICD-10.I codes Median = 7.7 years
[
  • 2,122 cases
  • , 47,108 controls
]
 — East Asian
(Japanese)		 — BBJ —
PSS000457 Cause of death under ICD-10.IHD code Median = 7.7 years
[
  • 464 cases
  • , 48,766 controls
]
 — East Asian
(Japanese)		 — BBJ —
PSS000458 Cause of death under ICD-10.J codes Median = 7.7 years
[
  • 1,193 cases
  • , 48,037 controls
]
 — East Asian
(Japanese)		 — BBJ —
PSS000459 CAD was defined as a composite of stable angina, unstable angina and myocardial infarction. The disease definitions are dependent on the physician's diagnosis based on general medical practices following relevant guidelines and according to the clinical symptoms and diagnotic tests. —
[
  • 1,827 cases
  • , 9,172 controls
]
,
84.0 % Male samples
 — East Asian
(Japanese)		 — BBJ —