PGS Publication: PGP000152

Publication Information (EuropePMC)
Title Population Bias in Polygenic Risk Prediction Models for Coronary Artery Disease.
PubMed ID 33170024(Europe PMC)
doi 10.1161/circgen.120.002932
Publication Date Nov. 10, 2020
Journal Circ Genom Precis Med
Author(s) Gola D, Erdmann J, Läll K, Mägi R, Müller-Myhsok B, Schunkert H, König IR.
Released in PGS Catalog: March 22, 2021

Associated Polygenic Score(s)

PGS Developed By This Publication

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000747 PRS_EB PGP000152
Gola D et al. Circ Genom Precis Med (2020)
Coronary artery disease coronary artery disease 375,822 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000747/ScoringFiles/PGS000747.txt.gz
PGS000748 PRS_DE PGP000152
Gola D et al. Circ Genom Precis Med (2020)
Coronary artery disease coronary artery disease 3,423,987 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000748/ScoringFiles/PGS000748.txt.gz
PGS000749 PRS_COMBINED PGP000152
Gola D et al. Circ Genom Precis Med (2020)
Coronary artery disease coronary artery disease 1,056,021 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000749/ScoringFiles/PGS000749.txt.gz
PGS000746 PRS_UKB PGP000152
Gola D et al. Circ Genom Precis Med (2020)
Coronary artery disease coronary artery disease 1,940 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000746/ScoringFiles/PGS000746.txt.gz

External PGS Evaluated By This Publication

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000018 metaGRS_CAD PGP000007
Inouye M et al. J Am Coll Cardiol (2018)
Coronary artery disease coronary artery disease 1,745,179 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000018/ScoringFiles/PGS000018.txt.gz
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 ID)
Evaluated Score PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM001839 PGS000747
(PRS_EB)
PSS000931 PGP000152
Gola D et al. Circ Genom Precis Med (2020)
Reported Trait: Coronary artery disease AUROC: 0.6043 [0.6004, 0.6082] Area under the Precision-Recall curve (AUPRC): 0.0712 [0.0703, 0.076]
PPM001841 PGS000748
(PRS_DE)
PSS000930 PGP000152
Gola D et al. Circ Genom Precis Med (2020)
Reported Trait: Coronary artery disease AUROC: 0.6156 [0.5963, 0.6349] Area under the Precision-Recall curve (AUPRC): 0.0506 [0.0504, 0.0508]
PPM001842 PGS000748
(PRS_DE)
PSS000931 PGP000152
Gola D et al. Circ Genom Precis Med (2020)
Reported Trait: Coronary artery disease AUROC: 0.5989 [0.595, 0.6028] Area under the Precision-Recall curve (AUPRC): 0.0696 [0.0694, 0.0698]
PPM001843 PGS000749
(PRS_COMBINED)
PSS000930 PGP000152
Gola D et al. Circ Genom Precis Med (2020)
Reported Trait: Coronary artery disease AUROC: 0.6112 [0.5919, 0.6305] Area under the Precision-Recall curve (AUPRC): 0.048 [0.0473, 0.0487]
PPM001845 PGS000018
(metaGRS_CAD)
PSS000929 PGP000152
Gola D et al. Circ Genom Precis Med (2020)
Ext.
Reported Trait: Coronary artery disease AUROC: 0.5015 [0.483, 0.514] Area under the Precision-Recall curve (AUPRC): 0.5205 [0.5201, 0.521]
PPM001846 PGS000018
(metaGRS_CAD)
PSS000930 PGP000152
Gola D et al. Circ Genom Precis Med (2020)
Ext.
Reported Trait: Coronary artery disease AUROC: 0.6597 [0.6405, 0.6789] Area under the Precision-Recall curve (AUPRC): 0.0673 [0.0668, 0.0679]
PPM001848 PGS000013
(GPS_CAD)
PSS000929 PGP000152
Gola D et al. Circ Genom Precis Med (2020)
Ext.
Reported Trait: Coronary artery disease AUROC: 0.6699 [0.6557, 0.684]
PPM001849 PGS000013
(GPS_CAD)
PSS000930 PGP000152
Gola D et al. Circ Genom Precis Med (2020)
Ext.
Reported Trait: Coronary artery disease AUROC: 0.5617 [0.5402, 0.5833]
PPM001850 PGS000013
(GPS_CAD)
PSS000931 PGP000152
Gola D et al. Circ Genom Precis Med (2020)
Ext.
Reported Trait: Coronary artery disease AUROC: 0.6374 [0.6335, 0.6412] May be an overlap between score development and testing samples
PPM001836 PGS000746
(PRS_UKB)
PSS000931 PGP000152
Gola D et al. Circ Genom Precis Med (2020)
Reported Trait: Coronary artery disease AUROC: 0.6133 [0.6094, 0.6172] Area under the Precision-Recall curve (AUPRC): 0.0752 [0.0745, 0.076]
PPM001837 PGS000747
(PRS_EB)
PSS000929 PGP000152
Gola D et al. Circ Genom Precis Med (2020)
Reported Trait: Coronary artery disease AUROC: 0.5407 [0.5253, 0.5561] Area under the Precision-Recall curve (AUPRC): 0.498 [0.4962, 0.4998]
PPM001838 PGS000747
(PRS_EB)
PSS000930 PGP000152
Gola D et al. Circ Genom Precis Med (2020)
Reported Trait: Coronary artery disease AUROC: 0.6565 [0.6369, 0.676] Area under the Precision-Recall curve (AUPRC): 0.0765 [0.0755, 0.0774]
PPM001840 PGS000748
(PRS_DE)
PSS000929 PGP000152
Gola D et al. Circ Genom Precis Med (2020)
Reported Trait: Coronary artery disease AUROC: 0.6752 [0.6612, 0.6891] Area under the Precision-Recall curve (AUPRC): 0.6891 [0.6887, 0.6895]
PPM001844 PGS000749
(PRS_COMBINED)
PSS000931 PGP000152
Gola D et al. Circ Genom Precis Med (2020)
Reported Trait: Coronary artery disease AUROC: 0.5988 [0.5949, 0.6027] Area under the Precision-Recall curve (AUPRC): 0.0697 [0.0688, 0.0705]
PPM001834 PGS000746
(PRS_UKB)
PSS000929 PGP000152
Gola D et al. Circ Genom Precis Med (2020)
Reported Trait: Coronary artery disease AUROC: 0.5143 [0.4992, 0.5294] Area under the Precision-Recall curve (AUPRC): 0.5607 [0.5593, 0.5621]
PPM001835 PGS000746
(PRS_UKB)
PSS000930 PGP000152
Gola D et al. Circ Genom Precis Med (2020)
Reported Trait: Coronary artery disease AUROC: 0.6049 [0.5857, 0.6241] Area under the Precision-Recall curve (AUPRC): 0.046 [0.0454, 0.0466]
PPM001847 PGS000018
(metaGRS_CAD)
PSS000931 PGP000152
Gola D et al. Circ Genom Precis Med (2020)
Ext.
Reported Trait: Coronary artery disease AUROC: 0.6377 [0.6339, 0.6416] Area under the Precision-Recall curve (AUPRC): 0.0832 [0.083, 0.0835] May be an overlap between score development and testing sample

Evaluated Samples

PGS Sample Set ID
(PSS ID)
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
PSS000929 For GERMIFSI and GERMIFSII, CAD was defined as Myocardinal infarction before the age of 60 and 1 or more 1st- degree relative with CAD. In GERMIFSIII CAD was defined as myocardial infarction between the ages of 26 and 74. In GERMIFSIV, cases were based on a CAD diagnosis before age 65 in men or age 70 in women. In Luric, cases were ascertained as >50% angiographic confirmation of vascular obstruction in 1 or more coronary vessel
[
  • 2,919 cases
  • , 2,662 controls
]
European 6 cohorts
  • GERMIFSI
  • ,GERMIFSII
  • ,GERMIFSIII
  • ,GERMIFSIV
  • ,GERMIFSV
  • ,LURIC
PSS000930 CAD ascertainment was based on myocardial infarction diagnosis or death cause using ICD-10 codes I21.X, I22.X, I23.X, I24.1, or I25.2
[
  • 840 cases
  • , 26,208 controls
]
European EB
PSS000931 CAD ascertainment was based on a composite of myocardial infarction or coronary revascularization. Myocardial infarction was based on ICD-9 codes 410.X, 411.X, 412.X, or 429.79, or ICD-10 codes I21.X, I22.X, I23.X, I24.1, or I25.2. Coronary revascularization was assessed based on 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, K49.0-49.9, K50.2, K75.1-75.4, or K75.8-75.9)
[
  • 21,025 cases
  • , 410,789 controls
]
European UKB