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
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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
Variants
Original Genome Build hg19
Number of Variants 6,630,150
Development Method
Name LDpred
Parameters ρ = 0.003; LD panel = 503 1000G Europeans
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: 100%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST003116
Europe PMC: 26343387
11,323 individuals East Asian
GWAS Catalog: GCST003116
Europe PMC: 26343387
25,557 individuals South Asian
GWAS Catalog: GCST003116
Europe PMC: 26343387
2,268 individuals Greater Middle Eastern (Middle Eastern, North African or Persian)
GWAS Catalog: GCST003116
Europe PMC: 26343387
4,095 individuals Hispanic or Latin American
GWAS Catalog: GCST003116
Europe PMC: 26343387
141,217 individuals European
GWAS Catalog: GCST003116
Europe PMC: 26343387
3,139 individuals African American or Afro-Caribbean
Score Development/Training
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
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).
[
  • 398 cases
]
,
86.7 % Male samples
Mean = 60.6 years
Iqr = [54.4, 66.1] years
South Asian UKB Used to select optimal LDpred thresholds
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). 6,846 individuals,
52.1 % Male samples
Mean = 52.8 years
Iqr = [46.3, 60.2] years
South Asian UKB 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

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
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