PGS Publication: PGP000166

Publication Information (EuropePMC)
Title Genetic Risk Score to Identify Risk of Venous Thromboembolism in Patients With Cardiometabolic Disease.
PubMed ID 33434447(Europe PMC)
doi 10.1161/circgen.120.003006
Publication Date Jan. 12, 2021
Journal Circ Genom Precis Med
Author(s) Marston NA, Melloni GEM, Gurmu Y, Bonaca MP, Kamanu FK, Roselli C, Lee C, Cavallari I, Giugliano RP, Scirica BM, Bhatt DL, Steg PG, Cohen M, Storey RF, Keech AC, Raz I, Mosenzon O, Braunwald E, Lubitz SA, Ellinor PT, Sabatine MS, Ruff CT.
Released in PGS Catalog: April 28, 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 Scoring File (FTP Link)
PGS000043
(PRS_VTE)
 PGP000030 |
Klarin D et al. Nat Genet (2019)
 Venous thromboembolism venous thromboembolism 297
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000043/ScoringFiles/PGS000043.txt.gz

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
PPM001939 PGS000043
(PRS_VTE)
 PSS000973|
European Ancestry|
29,663 individuals
 PGP000166 |
Marston NA et al. Circ Genom Precis Med (2021)
|Ext.		 Reported Trait: Venous Thromboembolism HR: 1.47 [1.29, 1.68] — Hazard Ratio (HR, top tertile vs bottom tertile): 2.7 [1.8, 4.06] Age, sex, PCs(1-5), obesity(BMI≥30), active smoking, history of heart failure, diabetes status. 273 of original 297 SNPs from Klarin et al (PGS000043) used that reached minimum imputation of 0.58.
PPM001940 PGS000043
(PRS_VTE)
 PSS000973|
European Ancestry|
29,663 individuals
 PGP000166 |
Marston NA et al. Circ Genom Precis Med (2021)
|Ext.		 Reported Trait: Venous Thromboembolism — — Hazard Ratio (HR, middle tertile vs bottom 3.33%): 1.88 [1.23, 2.89] Age, sex, PCs(1-5), obesity(BMI≥30), active smoking, history of heart failure, diabetes status. 273 of original 297 SNPs from Klarin et al (PGS000043) used that reached minimum imputation of 0.58.
PPM001941 PGS000043
(PRS_VTE)
 PSS000973|
European Ancestry|
29,663 individuals
 PGP000166 |
Marston NA et al. Circ Genom Precis Med (2021)
|Ext.		 Reported Trait: Venous Thromboembolism — C-index: 0.67 [0.63, 0.71] — — 273 of original 297 SNPs from Klarin et al (PGS000043) used that reached minimum imputation of 0.58.
PPM001942 PGS000043
(PRS_VTE)
 PSS000973|
European Ancestry|
29,663 individuals
 PGP000166 |
Marston NA et al. Circ Genom Precis Med (2021)
|Ext.		 Reported Trait: Venous Thromboembolism — C-index: 0.67 [0.63, 0.71] — Age, obesity(BMI≥30), active smoking, history of heart failure, diabetes status. 273 of original 297 SNPs from Klarin et al (PGS000043) used that reached minimum imputation of 0.58.
PPM001943 PGS000043
(PRS_VTE)
 PSS000973|
European Ancestry|
29,663 individuals
 PGP000166 |
Marston NA et al. Circ Genom Precis Med (2021)
|Ext.		 Reported Trait: Venous Thromboembolism in individuals without monogenic mutations HR: 1.53 [1.3, 1.82] — Hazard Ratio (HR, top tertile vs. bottom tertile): 2.88 [1.85, 4.49] Age, sex, PCs(1-5), obesity(BMI≥30), active smoking, history of heart failure, diabetes status. 273 of original 297 SNPs from Klarin et al (PGS000043) used that reached minimum imputation of 0.58.
PPM001944 PGS000043
(PRS_VTE)
 PSS000973|
European Ancestry|
29,663 individuals
 PGP000166 |
Marston NA et al. Circ Genom Precis Med (2021)
|Ext.		 Reported Trait: Venous Thromboembolism in individuals without monogenic mutations — — Hazard Ratio (HR, middle tertile vs. bottom tertile): 2.11 [1.34, 3.33] Age, sex, PCs(1-5), obesity(BMI≥30), active smoking, history of heart failure, diabetes status. 273 of original 297 SNPs from Klarin et al (PGS000043) used that reached minimum imputation of 0.58.

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
PSS000973 Cases show venous thromboembolism events, 95 of which were deep vein thrombosis and 79 were pulmonary embolism. 27,189 individuals did not carry a Venous Thromboembolism monogenic mutation. Median = 2.4 years
[
  • 174 cases
  • , 29,489 controls
]
,
74.59 % Male samples
 Mean = 64.23 years European — NR —