PGS Publication: PGP000129

Publication Information (EuropePMC)
Title Predictive Accuracy of a Polygenic Risk Score Compared With a Clinical Risk Score for Incident Coronary Heart Disease.
PubMed ID 32068817(Europe PMC)
doi 10.1001/jama.2019.21782
Publication Date Feb. 1, 2020
Journal JAMA
Author(s) Mosley JD, Gupta DK, Tan J, Yao J, Wells QS, Shaffer CM, Kundu S, Robinson-Cohen C, Psaty BM, Rich SS, Post WS, Guo X, Rotter JI, Roden DM, Gerszten RE, Wang TJ.
Released in PGS Catalog: Feb. 3, 2021

Associated Polygenic Score(s)

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Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
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Additional Diverse Ancestries
Not Reported

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
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000013
(GPS_CAD)
 PGP000006 |
Khera AV et al. Nat Genet (2018)
 Coronary artery disease coronary artery disease 6,630,150
https://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
PPM001620 PGS000013
(GPS_CAD)
 PSS000837|
European Ancestry|
4,847 individuals
 PGP000129 |
Mosley JD et al. JAMA (2020)
|Ext.		 Reported Trait: Incident coronary heart disease (10-year risk) — C-index: 0.7 [0.677, 0.721] Δ C-index (PRS+covariates vs. covariates alone): -0.001 [-0.009, 0.006] Pooled cohort risk percentile, age, sex, PCs (1-5) —
PPM001617 PGS000013
(GPS_CAD)
 PSS000839|
European Ancestry|
4,847 individuals
 PGP000129 |
Mosley JD et al. JAMA (2020)
|Ext.		 Reported Trait: Prevalent and incident coronary heart disease OR: 1.89 [1.75, 2.03] — — Age, sex, PCs (1-5) —
PPM001618 PGS000013
(GPS_CAD)
 PSS000837|
European Ancestry|
4,847 individuals
 PGP000129 |
Mosley JD et al. JAMA (2020)
|Ext.		 Reported Trait: Incident coronary heart disease (10-year risk) HR: 1.24 [1.15, 1.34] C-index: 0.669 [0.644, 0.691] — Age, sex, PCs (1-5) —
PPM001619 PGS000013
(GPS_CAD)
 PSS000838|
European Ancestry|
2,390 individuals
 PGP000129 |
Mosley JD et al. JAMA (2020)
|Ext.		 Reported Trait: Incident coronary heart disease (10-year risk) HR: 1.38 [1.21, 1.58] C-index: 0.672 [0.627, 0.705] — Age, sex, PCs (1-5) —
PPM001621 PGS000013
(GPS_CAD)
 PSS000838|
European Ancestry|
2,390 individuals
 PGP000129 |
Mosley JD et al. JAMA (2020)
|Ext.		 Reported Trait: Incident coronary heart disease (10-year risk) — C-index: 0.681 [0.637, 0.715] Δ C-index (PRS+covariates vs. covariates alone): 0.021 [-0.0004, 0.043] Pooled cohort risk percentile, age, sex, PCs (1-5) —
PPM001622 PGS000013
(GPS_CAD)
 PSS000837|
European Ancestry|
4,847 individuals
 PGP000129 |
Mosley JD et al. JAMA (2020)
|Ext.		 Reported Trait: Incident coronary heart disease (10-year risk) — C-index: 0.549 [0.521, 0.571] — PCs (1-5) —
PPM001623 PGS000013
(GPS_CAD)
 PSS000838|
European Ancestry|
2,390 individuals
 PGP000129 |
Mosley JD et al. JAMA (2020)
|Ext.		 Reported Trait: Incident coronary heart disease (10-year risk) — C-index: 0.587 [0.532, 0.623] — PCs (1-5) —

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
PSS000839 Incident CHD cases were defined as having incident myocardial infarction (MI), fatal coronary event, or silent infarction or having undergone a revasclarization procedure. Prevalent CHD cases were participants with a reported history of MI, heart or arterial surgery, coronary artery bypass graft surgery, or angioplasty; or evidence of having had an MI based on electrocardiogram taken at their visit 1 examination. —
[
  • 1,005 cases
  • , 3,842 controls
]
,
43.6 % Male samples
 Mean = 62.9 years European — ARIC —
PSS000837 Incident CHD cases were defined as having incident myocardial infarction (MI), fatal coronary event, or silent infarction or having undergone a revasclarization procedure. Median = 15.5 years
[
  • 696 cases
  • , 4,151 controls
]
,
43.6 % Male samples
 Mean = 62.9 years European — ARIC —
PSS000838 Incident CHD cases were defined as MI, resuscitated cardiac arrest, definite or probable angina if followed by a revascularization, and CHD dead occuring by visit 5. Median = 14.2 years
[
  • 227 cases
  • , 2,163 controls
]
,
47.8 % Male samples
 Mean = 61.8 years European — MESA —