Polygenic Score (PGS) ID: PGS002262

Predicted Trait
Reported Trait Coronary artery disease
Mapped Trait(s) coronary artery disease (EFO_0001645)
Additional Trait Information Integrating nine optimal trait-specific PRSs (CAD, stroke, BP, T2D, TC, LDL-C, TG, HDL-C and BMI)
Released in PGS Catalog: March 16, 2022
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Score Details

Score Construction
PGS Name metaPRS_CAD
Development Method
Name metaPRS (elasticnet)
Parameters 9 component PRS
Variants
Original Genome Build GRCh37
Number of Variants 540
Effect Weight Type metaPRS
PGS Source
PGS Catalog Publication (PGP) ID PGP000289
Citation (link to publication) Lu X et al. Eur Heart J (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
East Asian: 99.3%
Additional Asian Ancestries: 0.7%
962,970 individuals (100%)
Score Development/Training
East Asian: 100%
4,855 individuals (100%)
PGS Evaluation
East Asian: 100%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST010867
[
  • 29,319 cases
  • , 183,134 controls
]
 East Asian
(Japanese)		 BBJ
19106391, 22531126
[
  • 4,664 cases
  • , 4,533 controls
]
 East Asian
(Chinese)		 Other
Europe PMC: 26690388
[
  • 3,835 cases
  • , 9,375 controls
]
 East Asian
(Chinese)		 Other, PUUMA
GWAS Catalog: GCST005172
Europe PMC: 29263402
 6,942 individuals East Asian SCES, SCHS, SIMES, SP2
GWAS Catalog: GCST005172
Europe PMC: 29263402
 2,603 individuals South East Asian SCES, SCHS, SIMES, SP2
GWAS Catalog: GCST001260
[
  • 806 cases
  • , 1,337 controls
]
 East Asian
(Japanese)		 CAGE
GWAS Catalog: GCST005978
Europe PMC: 29403010
 136,615 individuals East Asian BBJ
GWAS Catalog: GCST007847
Europe PMC: 30718926
 191,764 individuals East Asian BBJ
GWAS Catalog: GCST001351
Europe PMC: 22158537
 15,000 individuals East Asian AGEN
GWAS Catalog: GCST001351
Europe PMC: 22158537
 2,034 individuals South East Asian AGEN
GWAS Catalog: GCST001351
Europe PMC: 22158537
 1,783 individuals Asian unspecified AGEN
GWAS Catalog: GCST004904
 173,430 individuals East Asian
(Japanese)		 BBJ
GWAS Catalog: GCST005838
[
  • 16,256 cases
  • , 27,294 controls
]
 East Asian
(Japanese)		 BBJ
GWAS Catalog: GCST002461
[
  • 9,223 cases
  • , 5,160 controls
]
 East Asian AGEN
Europe PMC: 29083407
 47,532 individuals East Asian NR
—
[
  • 9,223 cases
  • , 5,160 controls
]
 East Asian
(Chinese)		 Other
Europe PMC: 28334899
 69,414 individuals East Asian AGEN
GWAS Catalog: GCST001587
Europe PMC: 22751097
 6,534 individuals East Asian BAS, CAS
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
—
[
  • 2,800 cases
  • , 2,055 controls
]
,
64.7 % Male samples
 East Asian NR — Mean = 54.77 years
Sd = 7.53 years		 — — —

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
PPM012875 PSS009589|
East Asian Ancestry|
41,271 individuals
 PGP000289 |
Lu X et al. Eur Heart J (2022)
 Reported Trait: Incident coronary artery disease HR: 1.44 [1.36, 1.52] C-index: 0.615 [0.598, 0.631] — — —
PPM012876 PSS009589|
East Asian Ancestry|
41,271 individuals
 PGP000289 |
Lu X et al. Eur Heart J (2022)
 Reported Trait: Incident coronary artery disease — — Hazard Ratio (HR, highest vs lowest quintile): 2.91 [2.43, 3.49] — —
PPM012877 PSS009589|
East Asian Ancestry|
41,271 individuals
 PGP000289 |
Lu X et al. Eur Heart J (2022)
 Reported Trait: Incident coronary artery disease (men) — — Hazard Ratio (HR, highest vs lowest quintile): 3.88 [2.94, 5.13] sex and first 4 PCs —
PPM012878 PSS009589|
East Asian Ancestry|
41,271 individuals
 PGP000289 |
Lu X et al. Eur Heart J (2022)
 Reported Trait: Incident coronary artery disease (women) — — Hazard Ratio (HR, highest vs lowest quintile): 2.27 [1.78, 2.9] sex and first 4 PCs —
PPM012879 PSS009589|
East Asian Ancestry|
41,271 individuals
 PGP000289 |
Lu X et al. Eur Heart J (2022)
 Reported Trait: Coronary artery disease — — Hazard Ratio (HR, highest vs lowest quintile): 5.66 [3.98, 8.04] sex, first 4 PCs and CAD family history —
PPM021711 PSS011758|
East Asian Ancestry|
34,111 individuals
 PGP000662 |
Xia X et al. Am J Clin Nutr (2023)
|Ext.		 Reported Trait: Incident CAD HR: 1.37 [1.29, 1.46] — — Age, sex, urbanicity, per-capita household income, educational attainment, family history of CAD, smoking, alcohol consumption, BMI, physical activity, red meat intake, poultry intake, fish intake, hypertension, diabetes, and hypercholesteremia —
PPM021704 PSS011752|
East Asian Ancestry|
39,164 individuals
 PGP000658 |
Hu C et al. Med Sci Sports Exerc (2023)
|Ext.		 Reported Trait: Incident CAD HR: 1.38 [1.3, 1.47] — — Age, sex, cohort source, living geographical zone, urban or rural residents, education attainment, family history of CVD, current smoking status, drinking, healthy diet score, sleep duration, physical activity level, BMI, hypertension, diabetes, and dyslipidemia —

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
PSS011758 — Median = 11.7 years 34,111 individuals,
41.8 % Male samples
 Mean = 52.3 years
Sd = 10.5 years		 East Asian
(Chinese)		 — CIMIC, ChinaMUCA-1998, InterASIA —
PSS009589 — Mean = 13.0 years
[
  • 1,303 cases
  • , 39,968 controls
]
,
42.5 % Male samples
 Mean = 52.3 years
Sd = 10.6 years		 East Asian — CIMIC, ChinaMUCA-1998, InterASIA —
PSS011752 — Median = 11.6 years 39,164 individuals,
42.4 % Male samples
 Mean = 53.9 years
Sd = 10.5 years		 East Asian
(Chinese)		 — CIMIC, ChinaMUCA-1998, InterASIA —