Polygenic Score (PGS) ID: PGS000296

Predicted Trait
Reported Trait Coronary artery disease
Mapped Trait(s) coronary artery disease (EFO_0001645)
Released in PGS Catalog: Aug. 19, 2020
Download Score FTP directory
Terms and Licenses
Freely available to the academic community for research use. Parties interested in using the scores for commercial purposes should contact the Broad Office of Strategic Alliances and Partnering (partnering@broadinstitute.org).

Score Details

Score Construction
PGS Name GPS_CAD_SA
Development Method
Name LDpred
Parameters ρ = 0.003; LD panel = 503 1000G Europeans
Variants
Original Genome Build hg19
Number of Variants 6,630,150
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000090
Citation (link to publication) Wang M et al. J Am Coll Cardiol (2020)
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
South Asian: 100%
8,766 individuals (100%)
PGS Evaluation
South Asian: 66.7%
Greater Middle Eastern: 33.3%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
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
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
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
—
[
  • 398 cases
]
,
86.7 % Male samples
 South Asian UKB Ascertainment of coronary artery disease was based on self-report or hospital admission diagnosis. This included individuals with ICD-9 codes of 410.X, 411.0, 412.X, or 429.79, or ICD-10 codes of I21.X, I22.X, I23.X, I24.1, or I25.2 in hospitalization records. Coronary revascularization was assessed based on an OPCS-4 coded procedure for coronary artery bypass grafting (K40.1–40.4, K41.1–41.4, or K45.1–45.5), or coronary angioplasty with or without stenting (K49.1–49.2, K49.8–49.9, K50.2, K75.1–75.4, or K75.8–75.9). Mean = 60.6 years
IQR = [54.4, 66.1] years		 — — Used to select optimal LDpred thresholds
— 6,846 individuals,
52.1 % Male samples
 South Asian UKB Ascertainment of coronary artery disease was based on self-report or hospital admission diagnosis. This included individuals with ICD-9 codes of 410.X, 411.0, 412.X, or 429.79, or ICD-10 codes of I21.X, I22.X, I23.X, I24.1, or I25.2 in hospitalization records. Coronary revascularization was assessed based on an OPCS-4 coded procedure for coronary artery bypass grafting (K40.1–40.4, K41.1–41.4, or K45.1–45.5), or coronary angioplasty with or without stenting (K49.1–49.2, K49.8–49.9, K50.2, K75.1–75.4, or K75.8–75.9). Mean = 52.8 years
IQR = [46.3, 60.2] years		 — — Used to select optimal LDpred thresholds
1,522 individuals South Asian GenomeAsia100K — — — — Used to to generate a static ancestry-specific genetic ancestry space and to generate a fixed GPS reference distribution

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
PPM000743 PSS000365|
South Asian Ancestry|
491 individuals
 PGP000090 |
Wang M et al. J Am Coll Cardiol (2020)
 Reported Trait: Myocardial infarction (first-ever) OR: 1.6 [1.32, 1.94] AUROC: 0.6632 — age, sex, top 5 genetic PCs —
PPM000745 PSS000366|
South Asian Ancestry|
2,963 individuals
 PGP000090 |
Wang M et al. J Am Coll Cardiol (2020)
 Reported Trait: Coronary artery disease OR: 1.66 [1.53, 1.81] AUROC: 0.712 — age, sex, top 5 genetic PCs —
PPM000746 PSS000366|
South Asian Ancestry|
2,963 individuals
 PGP000090 |
Wang M et al. J Am Coll Cardiol (2020)
 Reported Trait: Coronary artery disease OR: 1.58 [1.42, 1.75] — — age, sex, top 5 genetic PCs, diabetes, hypertension, hypercholesterolemia, smoking, body mass index —
PPM000744 PSS000365|
South Asian Ancestry|
491 individuals
 PGP000090 |
Wang M et al. J Am Coll Cardiol (2020)
 Reported Trait: Myocardial infarction (first-ever) OR: 1.51 [1.22, 1.88] — — age, sex, top 5 genetic PCs, diabetes, hypertension, hypercholesterolemia, family history of heart disease, current smoking, family history of myocardial infarction —
PPM015570 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: 1.53 [1.42, 1.64] AUROC: 0.683 [0.665, 0.701] — — —

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
PSS000365 Case-control study of first-onset acute myocardial infarction — 244 individuals,
90.2 % Male samples
 Mean = 33.0 years
IQR = [30.0, 35.0] years		 South Asian — BRAVE —
PSS000366 Cases composed of men and women diagnosed with coronary artery disease. Controls were selected from consenting men and women without any form of heart disease. —
[
  • 1,800 cases
]
,
90.2 % Male samples
 Mean = 54.0 years
IQR = [46.0, 60.0] years		 South Asian — MedGenome —
PSS000366 Cases composed of men and women diagnosed with coronary artery disease. Controls were selected from consenting men and women without any form of heart disease. — 1,163 individuals,
76.4 % Male samples
 Mean = 55.0 years
IQR = [49.0, 62.0] years		 South Asian — MedGenome —
PSS009986 — —
[
  • 1,014 cases
  • , 6,009 controls
]
,
47.0 % Male samples
 — Greater Middle Eastern (Middle Eastern, North African or Persian)
(Qatari)		 — QBB —
PSS000365 Case-control study of first-onset acute myocardial infarction —
[
  • 247 cases
]
,
90.7 % Male samples
 Mean = 34.0 years
IQR = [30.0, 35.0] years		 South Asian — BRAVE —