Polygenic Score (PGS) ID: PGS002244

Predicted Trait
Reported Trait Coronary artery disease
Mapped Trait(s) coronary artery disease (EFO_0001645)
Released in PGS Catalog: April 13, 2022
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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 ldpred_cad
Development Method
Name LDpred
Parameters p = 0.003, LD radius = 2000, LD reference panel: European ancestry in 1000 Genomes
Variants
Original Genome Build GRCh37
Number of Variants 6,576,338
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000271
Citation (link to publication) Mars N et al. Cell Genom (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%
175,364 individuals (100%)
PGS Evaluation
European: 50%
African: 25%
Hispanic or Latin American: 8.3%
East Asian: 8.3%
South Asian: 8.3%
12 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
 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
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
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
—
[
  • 17,732 cases
  • , 157,632 controls
]
 European
(Finnish)		 FinnGen — — — — —

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
PPM012736 PSS009517|
European Ancestry|
110,597 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Coronary artery disease OR: 1.47 [1.43, 1.52] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012740 PSS009513|
East Asian Ancestry|
178,726 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Coronary artery disease OR: 1.32 [1.3, 1.34] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012744 PSS009525|
European Ancestry|
69,422 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Coronary artery disease OR: 1.44 [1.4, 1.48] — — birth year, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012752 PSS009529|
African Ancestry|
1,535 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Coronary artery disease OR: 1.1 [0.96, 1.26] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012756 PSS009541|
European Ancestry|
343,676 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Coronary artery disease OR: 1.64 [1.61, 1.67] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012761 PSS009537|
African Ancestry|
7,618 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Coronary artery disease OR: 1.32 [1.13, 1.54] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012766 PSS009545|
South Asian Ancestry|
7,628 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Coronary artery disease OR: 1.41 [1.3, 1.53] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012732 PSS009521|
European Ancestry|
258,402 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Coronary artery disease OR: 1.53 [1.5, 1.55] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012748 PSS009533|
European Ancestry|
25,696 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Coronary artery disease OR: 1.35 [1.29, 1.4] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM020276 PSS011318|
African Ancestry|
18,505 individuals
 PGP000536 |
Vassy JL et al. JAMA Cardiol (2023)
|Ext.		 Reported Trait: Incident myocardial infarction HR: 1.1 [1.02, 1.19] — — age, sex, and principal components of genetic ancestry —
PPM020277 PSS011319|
Hispanic or Latin American Ancestry|
6,785 individuals
 PGP000536 |
Vassy JL et al. JAMA Cardiol (2023)
|Ext.		 Reported Trait: Incident myocardial infarction HR: 1.26 [1.09, 1.46] — — age, sex, and principal components of genetic ancestry —
PPM020278 PSS011320|
European Ancestry|
53,861 individuals
 PGP000536 |
Vassy JL et al. JAMA Cardiol (2023)
|Ext.		 Reported Trait: Incident myocardial infarction HR: 1.23 [1.18, 1.29] — — age, sex, and principal components of genetic ancestry —

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
PSS009537 — —
[
  • 169 cases
  • , 7,449 controls
]
 — African unspecified — UKB —
PSS009541 — —
[
  • 17,986 cases
  • , 325,690 controls
]
 — European British UKB —
PSS009513 — —
[
  • 29,080 cases
  • , 149,646 controls
]
 — East Asian
(Japanese)		 — BBJ —
PSS009545 — —
[
  • 740 cases
  • , 6,888 controls
]
 — South Asian — UKB —
PSS009517 — —
[
  • 5,064 cases
  • , 105,533 controls
]
 — European
(Estonian)		 — EB —
PSS011318 — — 18,505 individuals,
81.9 % Male samples
 Mean = 55.4 years
Sd = 11.8 years		 African American or Afro-Caribbean — MVP —
PSS009521 — —
[
  • 25,706 cases
  • , 232,696 controls
]
 — European
(Finnish)		 — FinnGen —
PSS011319 — — 6,785 individuals,
86.5 % Male samples
 Mean = 52.6 years
Sd = 14.8 years		 Hispanic or Latin American — MVP —
PSS011320 — — 53,861 individuals,
88.2 % Male samples
 Mean = 59.3 years
Sd = 13.8 years		 European — MVP —
PSS009525 — —
[
  • 6,594 cases
  • , 62,828 controls
]
 — European Norwegian HUNT —
PSS009529 — —
[
  • 285 cases
  • , 1,250 controls
]
 — African American or Afro-Caribbean — MGBB —
PSS009533 — —
[
  • 3,206 cases
  • , 22,490 controls
]
 — European — MGBB —