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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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: 55.6%
African: 22.2%
East Asian: 11.1%
South Asian: 11.1%
9 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST003116
Europe PMC: 26343387
141,217 individuals European NR
GWAS Catalog: GCST003116
Europe PMC: 26343387
3,139 individuals African American or Afro-Caribbean NR
GWAS Catalog: GCST003116
Europe PMC: 26343387
4,095 individuals Hispanic or Latin American NR
GWAS Catalog: GCST003116
Europe PMC: 26343387
25,557 individuals South Asian NR
GWAS Catalog: GCST003116
Europe PMC: 26343387
2,268 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) NR
GWAS Catalog: GCST003116
Europe PMC: 26343387
11,323 individuals East Asian NR
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)

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
PSS009521
[
  • 25,706 cases
  • , 232,696 controls
]
European
(Finnish)
FinnGen
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