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 S... S, Post WS, Guo X, Rotter JI, Roden DM, Gerszten RE, Wang TJ.Show more
Released in PGS Catalog: Feb. 3, 2021

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

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
PPM001617PGS000013
(GPS_CAD)
PSS000839|
European Ancestry|
4,847 individuals
PGP000129 |
Mosley JD et al. JAMA (2020)
|Ext.		Reported Trait: Prevalent and incident coronary heart diseaseOR: 1.89 [1.75, 2.03]——Age, sex, PCs (1-5)—
PPM001618PGS000013
(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)—
PPM001619PGS000013
(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)—
PPM001620PGS000013
(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)—
PPM001621PGS000013
(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)—
PPM001622PGS000013
(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)—
PPM001623PGS000013
(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)—
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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
PSS000837Incident CHD cases were defined as having incident myocardial infarction (MI), fatal coronary event,...  or silent infarction or having undergone a revasclarization procedure.Show moreMedian = 15.5 years
[
  • 696 cases
  • , 4,151 controls
]
,
43.6 % Male samples
Mean = 62.9 yearsEuropean—ARIC—
PSS000838Incident CHD cases were defined as MI, resuscitated cardiac arrest, definite or probable angina if f... ollowed by a revascularization, and CHD dead occuring by visit 5.Show moreMedian = 14.2 years
[
  • 227 cases
  • , 2,163 controls
]
,
47.8 % Male samples
Mean = 61.8 yearsEuropean—MESA—
PSS000839Incident 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.Show more—
[
  • 1,005 cases
  • , 3,842 controls
]
,
43.6 % Male samples
Mean = 62.9 yearsEuropean—ARIC—
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