PGS Publication: PGP000090

Publication Information (EuropePMC)
Title Validation of a Genome-Wide Polygenic Score for Coronary Artery Disease in South Asians.
PubMed ID 32762905(Europe PMC)
doi 10.1016/j.jacc.2020.06.024
Publication Date Aug. 1, 2020
Journal J Am Coll Cardiol
Author(s) Wang M, Menon R, Mishra S, Patel AP, Chaffin M, Tanneeru D, Deshmukh M, Mathew O, Apte S, Devanboo CS, Sundaram S, Lakshmipathy P, Murugan S, Sharma KK, Rajendran K, Santhosh S, Thachathodiyl R, Ahamed H, Balegadde AV, Alexander T, Swaminathan K, Gupta R, Mullasari AS, Sigamani A, Kanchi M, Peterson AS, Butterworth AS, Danesh J, Di Angelantonio E, Naheed A, Inouye M, Chowdhury R, Vedam RL, Kathiresan S, Gupta R, Khera AV.
Released in PGS Catalog: Aug. 19, 2020

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution PGS Scoring File (FTP Link)
PGS000296
(GPS_CAD_SA)
PGP000090 |
Wang M et al. J Am Coll Cardiol (2020)
Coronary artery disease coronary artery disease 6,630,150
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000296/ScoringFiles/PGS000296.txt.gz - Check Terms/Licenses

External PGS Evaluated By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution PGS Scoring File (FTP Link)
PGS000013
(GPS_CAD)
PGP000006 |
Khera AV et al. Nat Genet (2018)
Coronary artery disease coronary artery disease 6,630,150
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/PGS000013.txt.gz - Check Terms/Licenses

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)
Evaluated Score 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 PGS000296
(GPS_CAD_SA)
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 PGS000296
(GPS_CAD_SA)
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 PGS000296
(GPS_CAD_SA)
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
PPM000747 PGS000013
(GPS_CAD)
PSS000367|
South Asian Ancestry|
7,244 individuals
PGP000090 |
Wang M et al. J Am Coll Cardiol (2020)
|Ext.
Reported Trait: Coronary artery disease OR: 1.5302 AUROC: 0.8021 age, sex, top 5 genetic PCs
PPM000748 PGS000013
(GPS_CAD)
PSS000365|
South Asian Ancestry|
491 individuals
PGP000090 |
Wang M et al. J Am Coll Cardiol (2020)
|Ext.
Reported Trait: Myocardial infarction (first-ever) OR: 1.4605 AUROC: 0.6482 age, sex, top 5 genetic PCs
PPM000749 PGS000013
(GPS_CAD)
PSS000366|
South Asian Ancestry|
2,963 individuals
PGP000090 |
Wang M et al. J Am Coll Cardiol (2020)
|Ext.
Reported Trait: Coronary artery disease OR: 1.5793 AUROC: 0.7066 age, sex, top 5 genetic PCs
PPM000744 PGS000296
(GPS_CAD_SA)
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
PSS000367 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
PSS000367 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
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