Polygenic Score (PGS) ID: PGS000013

Predicted Trait
Reported Trait Coronary artery disease
Mapped Trait(s) coronary artery disease (EFO_0000378)
Released in PGS: Oct. 14, 2019

Score Details

Score Construction
PGS Name GPS_CAD
Variants
Original Genome Build hg19
Number of Variants 6,630,150
Development Method
Name LDPred
Parameters ρ = 0.001; LD panel = 503 1000G Europeans
PGS Source
PGS Catalog Publication (PGP) ID PGP000006
Citation (link to publication) Khera AV et al. Nat Genet (2018)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST003116
EuropePMC: 26343387
11,323 individuals East Asian
GWAS Catalog: GCST003116
EuropePMC: 26343387
25,557 individuals South Asian
GWAS Catalog: GCST003116
EuropePMC: 26343387
2,268 individuals Greater Middle Eastern (Middle Eastern, North African or Persian)
GWAS Catalog: GCST003116
EuropePMC: 26343387
4,095 individuals Hispanic or Latin American
GWAS Catalog: GCST003116
EuropePMC: 26343387
141,217 individuals European
GWAS Catalog: GCST003116
EuropePMC: 26343387
3,139 individuals African American or Afro-Caribbean
Score Development/Training
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
CAD ascertainment was based on a composite of myocardial infarction or coronary revascularization. Myocardial infarction was based on self-report or hospital admission diagnosis, as performed centrally. 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).
[
  • 3,963 cases
  • , 124,243 controls
]
European UKB UKB Phase 1

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 ID)
PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000022 PSS000015 PGP000006
Khera AV et al. (2018)
Reported Trait: Coronary artery disease AUROC: 0.81[0.81, 0.81] Nagelkerke’s R2 (estimate of variance explained by the PGS after covariate adjustment): 0.04 age; sex; Ancestry PC 1-4; genotyping chip
PPM000030 PSS000021 PGP000008
Wünnemann F et al. (2019)
Ext.
Reported Trait: Coronary artery disease (prevalent) OR: 1.64[1.48, 1.81] AUROC: 0.72[0.7, 0.74] age, sex, first four genetic PCs
PPM000031 PSS000022 PGP000008
Wünnemann F et al. (2019)
Ext.
Reported Trait: Coronary artery disease (prevalent) OR: 1.55[1.38, 1.73] AUROC: 0.89[0.88, 0.91] age, sex, first four genetic PCs
PPM000032 PSS000019 PGP000008
Wünnemann F et al. (2019)
Ext.
Reported Trait: Coronary artery disease (prevalent) OR: 1.69[1.44, 1.99] AUROC: 0.84[0.81, 0.87] age, sex, first four genetic PCs, cohort recruitment centre
PPM000033 PSS000020 PGP000008
Wünnemann F et al. (2019)
Ext.
Reported Trait: Reccurent coronary artery disease events OR: 1.13[1.06, 1.22] age, sex, first four genetic PCs
PPM000387 PSS000219 PGP000057
Homburger JR et al. (2019)
Ext.
Reported Trait: Coronary artery disease (personal history) AUROC: 0.6
PPM000383 PSS000219 PGP000057
Homburger JR et al. (2019)
Ext.
Reported Trait: Coronary artery disease (personal history) OR: 1.589[1.32, 1.92] AUROC: 0.86 age, sex
PPM000402 PSS000227 PGP000060
Khera AV et al. (2019)
Ext.
Reported Trait: Early-onset mycardial infarction (age ≤55 years) OR: 2.16[1.35, 1.59] Odds Ratio (OR; top 5% vs. rest): 3.33[0.82, 13.51] 4 genetic PCs
PPM000401 PSS000229 PGP000060
Khera AV et al. (2019)
Ext.
Reported Trait: Early-onset mycardial infarction (age ≤55 years) OR: 1.56[1.29, 1.88] Odds Ratio (OR; top 5% vs. rest): 3.38[2.03, 5.64] 4 genetic PCs
PPM000400 PSS000228 PGP000060
Khera AV et al. (2019)
Ext.
Reported Trait: Early-onset mycardial infarction (age ≤55 years) OR: 1.46[1.28, 1.66] Odds Ratio (OR; top 5% vs. rest): 2.02[1.29, 3.16] 4 genetic PCs
PPM000399 PSS000230 PGP000060
Khera AV et al. (2019)
Ext.
Reported Trait: Early-onset mycardial infarction (age ≤55 years) OR: 2.06[1.89, 2.25] Odds Ratio (OR; top 5% vs. rest): 5.09[3.82, 6.78] 4 genetic PCs

Evaluated Samples

PGS Sample Set ID
(PSS ID)
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000227
[
  • 40 cases
  • , 504 controls
]
Asian unspecified MESA, VIRGO Cases are from VIRGO, controls are from MESA
PSS000228
[
  • 336 cases
  • , 962 controls
]
African American or Afro-Caribbean MESA, VIRGO Cases are from VIRGO, controls are from MESA
PSS000229
[
  • 168 cases
  • , 751 controls
]
Hispanic or Latin American MESA, VIRGO Cases are from VIRGO, controls are from MESA
PSS000230
[
  • 1,537 cases
  • , 1,544 controls
]
European MESA, VIRGO Cases are from VIRGO, controls are from MESA
PSS000015 CAD ascertainment was based on a composite of myocardial infarction or coronary revascularization. Myocardial infarction was based on self-report or hospital admission diagnosis, as performed centrally. 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).
[
  • 8,676 cases
  • , 297,654 controls
]
European UKB UKB Phase 2
PSS000019 Prevalent Coronary artery disease (CAD), where CAD is defined as previous diagnosis of myocardial infarction or revascularization procedures (percutaneous coronary intervention or coronary artery bypass grafting).
[
  • 173 cases
  • , 5,589 controls
]
,
41.29 % Male samples
European
(French Canadian)
CARTaGENE
PSS000020 Recurrent CAD event during the follow- up period (median follow-up time =3.9 years [range =1.1–7), where CAD is defined as previous diagnosis of myocardial infarction or revascularization procedures (percutaneous coronary intervention or coronary artery bypass grafting).
[
  • 446 cases
  • , 416 controls
]
European
(French Canadian)
MHI Phase 1
PSS000020 Recurrent CAD event during the follow- up period (median follow-up time =3.9 years [range =1.1–7), where CAD is defined as previous diagnosis of myocardial infarction or revascularization procedures (percutaneous coronary intervention or coronary artery bypass grafting).
[
  • 937 cases
  • , 1,396 controls
]
European
(French Canadian)
MHI Phase 2
PSS000021 Prevalent Coronary artery disease (CAD), where CAD is defined as previous diagnosis of myocardial infarction or revascularization procedures (percutaneous coronary intervention or coronary artery bypass grafting).
[
  • 974 cases
  • , 976 controls
]
,
72.7 % Male samples
European
(French Canadian)
MHI Phase 1
PSS000022 Prevalent Coronary artery disease (CAD), where CAD is defined as previous diagnosis of myocardial infarction or revascularization procedures (percutaneous coronary intervention or coronary artery bypass grafting).
[
  • 2,492 cases
  • , 817 controls
]
,
72.38 % Male samples
European
(French Canadian)
MHI Phase 2
PSS000219 Phenotypic information was self-reported by the individual through an online, interactive health history tool
[
  • 126 cases
  • , 10,884 controls
]
,
17.1 % Male samples
European CG Samples are individuals whose healthcare provider had ordered a Color Genomics multi-gene panel test