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 C... S, 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.Show more
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

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Polygenic Score ID & Name
PGS Publication ID (PGP)
Reported Trait
Mapped Trait(s) (Ontology)
Number of Variants
Ancestry distribution
GWAS
Dev
Eval
Scoring File (FTP Link)
PGS000296
(GPS_CAD_SA)
PGP000090 |
Wang M et al. J Am Coll Cardiol (2020)
Coronary artery diseasecoronary artery disease6,630,150
G
D
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000296/ScoringFiles/PGS000296.txt.gz - Check Terms/Licenses
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External PGS Evaluated By This Publication

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Polygenic Score ID & Name
PGS Publication ID (PGP)
Reported Trait
Mapped Trait(s) (Ontology)
Number of Variants
Ancestry distribution
GWAS
Dev
Eval
Scoring File (FTP Link)
PGS000013
(GPS_CAD)
PGP000006 |
Khera AV et al. Nat Genet (2018)
Coronary artery diseasecoronary artery disease6,630,150
G
D
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/PGS000013.txt.gz - Check Terms/Licenses
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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.

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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
PPM000743PGS000296
(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—
PPM000744PGS000296
(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 d... isease, current smoking, family history of myocardial infarctionShow more—
PPM000745PGS000296
(GPS_CAD_SA)
PSS000366|
South Asian Ancestry|
2,963 individuals
PGP000090 |
Wang M et al. J Am Coll Cardiol (2020)
Reported Trait: Coronary artery diseaseOR: 1.66 [1.53, 1.81]AUROC: 0.712—age, sex, top 5 genetic PCs—
PPM000746PGS000296
(GPS_CAD_SA)
PSS000366|
South Asian Ancestry|
2,963 individuals
PGP000090 |
Wang M et al. J Am Coll Cardiol (2020)
Reported Trait: Coronary artery diseaseOR: 1.58 [1.42, 1.75]——age, sex, top 5 genetic PCs, diabetes, hypertension, hypercholesterolemia, smoking, body mass index—
PPM000747PGS000013
(GPS_CAD)
PSS000367|
South Asian Ancestry|
7,244 individuals
PGP000090 |
Wang M et al. J Am Coll Cardiol (2020)
|Ext.		Reported Trait: Coronary artery diseaseOR: 1.5302AUROC: 0.8021—age, sex, top 5 genetic PCs—
PPM000748PGS000013
(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: 1.4605AUROC: 0.6482—age, sex, top 5 genetic PCs—
PPM000749PGS000013
(GPS_CAD)
PSS000366|
South Asian Ancestry|
2,963 individuals
PGP000090 |
Wang M et al. J Am Coll Cardiol (2020)
|Ext.		Reported Trait: Coronary artery diseaseOR: 1.5793AUROC: 0.7066—age, sex, top 5 genetic PCs—
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Evaluated Samples

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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
PSS000365Case-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—
PSS000365Case-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—
PSS000366Cases composed of men and women diagnosed with coronary artery disease. Controls were selected from ... consenting men and women without any form of heart disease. Show more—
[
  • 1,800 cases
]
,
90.2 % Male samples
Mean = 54.0 years
IQR = [46.0, 60.0] years		South Asian—MedGenome—
PSS000366Cases composed of men and women diagnosed with coronary artery disease. Controls were selected from ... consenting men and women without any form of heart disease. Show more—1,163 individuals,
76.4 % Male samples
Mean = 55.0 years
IQR = [49.0, 62.0] years		South Asian—MedGenome—
PSS000367Ascertainment of coronary artery disease was based on self-report or hospital admission diagnosis. T... his 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).Show more—
[
  • 398 cases
]
,
86.7 % Male samples
Mean = 60.6 years
IQR = [54.4, 66.1] years		South Asian—UKB—
PSS000367Ascertainment of coronary artery disease was based on self-report or hospital admission diagnosis. T... his 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).Show more—6,846 individuals,
52.1 % Male samples
Mean = 52.8 years
IQR = [46.3, 60.2] years		South Asian—UKB—
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