Polygenic Score (PGS) ID: PGS002776

Predicted Trait
Reported Trait Incident coronary artery disease
Mapped Trait(s) coronary artery disease (EFO_0001645)
Released in PGS Catalog: Dec. 20, 2022
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Terms and Licenses
Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)

Score Details

Score Construction
PGS Name GTG_CAD_SCT
Development Method
Name Stacked clumping and thresholding (SCT)
Parameters SCT(bigsnpr) using default hyperparameters
Variants
Original Genome Build hg19
Number of Variants 390,782
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000365
Citation (link to publication) Wong CK et al. PLoS One (2022)
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%)
Score Development/Training
European: 100%
38,217 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
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
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
 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
 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
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
—
[
  • 6,370 cases
  • , 31,847 controls
]
,
67.0 % Male samples
 European UKB We used the disease definitions described in the supplement of Said et al (2018). PMID: 29955826 — — —

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
PPM014976 PSS009941|
European Ancestry|
16,374 individuals
 PGP000365 |
Wong CK et al. PLoS One (2022)
 Reported Trait: Incident coronary artery disease OR: 1.36 [1.31, 1.42] AUROC: 0.587 [0.576, 0.599] — — —

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
PSS009941 We used the disease definitions described in the supplement of Said et al (2018). PMID: 29955826 —
[
  • 2,729 cases
  • , 13,645 controls
]
,
46.0 % Male samples
 European — UKB —