PGS Publication: PGP000257

Publication Information (EuropePMC)
Title Polygenic Risk Score to Identify Subclinical Coronary Heart Disease Risk in Young Adults.
PubMed ID 34463132(Europe PMC)
doi 10.1161/circgen.121.003341
Publication Date Aug. 31, 2021
Journal Circ Genom Precis Med
Author(s) Wells QS, Bagheri M, Aday AW, Gupta DK, Shaffer CM, Wei WQ, Sarna Vaitinadin N, Khan SS, Greenland P, Wang TJ, Stein CM, Roden DM, Mosley JD.
Released in PGS Catalog: Nov. 25, 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
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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
PPM009241 PGS000013
(GPS_CAD)
 PSS007665|
European Ancestry|
1,132 individuals
 PGP000257 |
Wells QS et al. Circ Genom Precis Med (2021)
|Ext.		 Reported Trait: Coronary artery calcium score > 20 OR: 1.74 [1.29, 2.36] AUROC: 0.794 [0.728, 0.84] — Age, sex, PCs(1-5) —
PPM009242 PGS000013
(GPS_CAD)
 PSS007665|
European Ancestry|
1,132 individuals
 PGP000257 |
Wells QS et al. Circ Genom Precis Med (2021)
|Ext.		 Reported Trait: Coronary artery calcium score > 20 OR: 1.87 [1.41, 2.5] — — — —
PPM009243 PGS000013
(GPS_CAD)
 PSS007665|
European Ancestry|
1,132 individuals
 PGP000257 |
Wells QS et al. Circ Genom Precis Med (2021)
|Ext.		 Reported Trait: Coronary artery calcium score > 20 — AUROC: 0.864 [0.807, 0.904] C statistic change (vs. no PRS): 0.015 [0.004, 0.028]
Integrated discrimination improvement (vs. no PRS): 0.027 [-0.006, 0.054]		 Age, sex, PCs(1-5), systolic blood pressure, total cholesterol, high density lipoprotein cholesterol, triglycerides, current smoker, waist circumference —
PPM009244 PGS000013
(GPS_CAD)
 PSS007666|
European Ancestry|
663 individuals
 PGP000257 |
Wells QS et al. Circ Genom Precis Med (2021)
|Ext.		 Reported Trait: Coronary artery calcium score > 300 OR: 1.9 [1.42, 2.54] AUROC: 0.804 [0.751, 0.845] — Age, sex, PCs(1-5) —
PPM009245 PGS000013
(GPS_CAD)
 PSS007666|
European Ancestry|
663 individuals
 PGP000257 |
Wells QS et al. Circ Genom Precis Med (2021)
|Ext.		 Reported Trait: Coronary artery calcium score > 300 OR: 2.11 [1.57, 2.83] — — — —
PPM009246 PGS000013
(GPS_CAD)
 PSS007666|
European Ancestry|
663 individuals
 PGP000257 |
Wells QS et al. Circ Genom Precis Med (2021)
|Ext.		 Reported Trait: Coronary artery calcium score > 300 — AUROC: 0.855 [0.805, 0.887] C statistic change (vs. no PRS): 0.02 [0.001, 0.039]
Integrated discrimination improvement (vs. no PRS): 0.039 [0.0005, 0.072]		 Age, sex, PCs(1-5), systolic blood pressure, total cholesterol, high density lipoprotein cholesterol, triglycerides, current smoker, body mass index —

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
PSS007666 Of the 663 individuals, 500 individuals had a coronary artery calcium (CAC) score ≤ 300, whilst the remaining 93 had a CAC score > 300. To calculate CAC scores, participants underwent two computed tomography scans from the root of the aorta to the apex of the heart at year 30. From these, Agatston scores, adjusted using a standard calcium phantom scanned underneath each participant, were computed for the four major arteries. The CAC Agatston score is the average of two scans. —
[
  • 93 cases
  • , 570 controls
]
,
46.5 % Male samples
 Mean = 27.8 years
Sd = 4.7 years		 European — FOS —
PSS007665 Of the 1,132 individuals, 1,070 had a coronary artery calcium (CAC) score ≤ 20, whilst the remaining 62 had a CAC score >20. To calculate CAC scores, participants underwent two computed tomography scans from the root of the aorta to the apex of the heart at year 15. From these, Agatston scores, adjusted using a standard calcium phantom scanned underneath each participant, were computed for the four major arteries. The CAC Agatston score is the average of two scans. —
[
  • 62 cases
  • , 1,070 controls
]
,
48.1 % Male samples
 Mean = 25.6 years
Sd = 3.3 years		 European — CARDIA —