Trait: venous thromboembolism

Experimental Factor Ontology (EFO) Information
Identifier EFO_0004286
Description Occlusion of the lumen of a vein by a thrombus that has migrated from a distal site via the blood stream. [NCIT: C99537]
Trait category
Cardiovascular disease
Synonyms 2 synonyms
  • VTE
  • venous thromboembolism
Mapped terms 9 mapped terms
  • ICD10:I74
  • ICD10:I82
  • MESH:D054556
  • MONDO:0005399
  • MeSH:D054556
  • MedDRA:10066899
  • NCIT:C99537
  • NCIt:C99537
  • UMLS:C1861172

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:
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Ancestry legend
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Multi-ancestry (excluding European)
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Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
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
PGS002235
(elasticnet_VTE)
 PGP000267 |
Kolin DA et al. Sci Rep (2021)
 Venous thromboembolism venous thromboembolism 36
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002235/ScoringFiles/PGS002235.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
PPM001639 PGS000043
(PRS_VTE)
 PSS000850|
European Ancestry|
715 individuals
 PGP000133 |
Naito T et al. Gastroenterology (2020)
|Ext.		 Reported Trait: Thromboembolic disease event in individuals with inflammatory bowel disease — — Odds Ratio (OR, top 5% vs. remaining 95%): 2.7 [1.03, 7.09] Age at last visit, PCs(1-2) Included 265/297 variants from the original score
PPM000102 PGS000043
(PRS_VTE)
 PSS000066|
European Ancestry|
55,965 individuals
 PGP000030 |
Klarin D et al. Nat Genet (2019)
 Reported Trait: Venous thromboembolism — — OR (top 5% of individuals with the highest PRS_VTE relative to the rest of the population): 2.89 [2.52, 3.3] age, sex, 5 PCs of ancestry —
PPM000103 PGS000043
(PRS_VTE)
 PSS000067|
European Ancestry|
10,975 individuals
 PGP000030 |
Klarin D et al. Nat Genet (2019)
 Reported Trait: Venous thromboembolism — — HR (top 5% of individuals with the highest PRS_VTE relative to the rest of the population): 2.51 [1.97, 3.19] age, 10 PCs of ancestry, hormone therapy intervention status —
PPM001640 PGS000043
(PRS_VTE)
 PSS000850|
European Ancestry|
715 individuals
 PGP000133 |
Naito T et al. Gastroenterology (2020)
|Ext.		 Reported Trait: Thromboembolic disease event in individuals with inflammatory bowel disease — — Odds Ratio (OR, top 5% vs. remaining 95%): 3.13 [1.37, 7.18] Disease duration, age at disease onset, PCs(1-2) Included 265/297 variants from the original score
PPM001641 PGS000043
(PRS_VTE)
 PSS000850|
European Ancestry|
715 individuals
 PGP000133 |
Naito T et al. Gastroenterology (2020)
|Ext.		 Reported Trait: Thromboembolic disease event in in individuals of inflammatory bowel disease that are carriers of at least 1 thrombophillia pathogenic variant — — Odds Ratio (OR, top 5% vs. remaining 95%): 8.56 [1.76, 41.57] Age at last visit, PCs(1-2) Included 265/297 variants from the original score
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.
PPM012709 PGS002235
(elasticnet_VTE)
 PSS009500|
European Ancestry|
269,164 individuals
 PGP000267 |
Kolin DA et al. Sci Rep (2021)
 Reported Trait: Incident venous thromboembolism — — Odds Ratio (OR, top 1% vs bottom 99%): 5.37 [5.34, 5.4] — —
PPM012710 PGS002235
(elasticnet_VTE)
 PSS009500|
European Ancestry|
269,164 individuals
 PGP000267 |
Kolin DA et al. Sci Rep (2021)
 Reported Trait: Incident venous thromboembolism — — Subhazard ratio (SHR, top 20.2% vs bottom 79.8%): 3.02 [2.63, 3.47] — —
PPM012711 PGS002235
(elasticnet_VTE)
 PSS009500|
European Ancestry|
269,164 individuals
 PGP000267 |
Kolin DA et al. Sci Rep (2021)
 Reported Trait: Incident venous thromboembolism — — Subhazard ratio (SHR, top 20.2% vs bottom 79.8%): 7.51 [6.28, 8.98] — —

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
PSS009500 — —
[
  • 2,295 cases
  • , 266,869 controls
]
 — European
(British)		 — UKB —
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 —
PSS000850 All individuals had inflammatory bowel disease, defined on the basis of clinical symptoms as well as standard endoscopic, radiographic and histologic findings. Cases are individuals with a thromboembolic disease (TED) event. Disease activity at the time of TED for Chron's disease was measured by the Harvey-Bradshaw Index and colonoscopy report at the time of clotting event (when available). Patients were considered to have active disease if they had Harvey-Bradshaw Index scores !5 and/or endoscopy showed active disease, Disease activity at the time of TED for Ulcerative Colitis was evaluated by the full Mayo score. A full Mayo score >2 was considered as active disease. —
[
  • 63 cases
  • , 652 controls
]
,
53.3 % Male samples
 — European — CSMC —
PSS000066 VTE was defined in the MVP cohort using the following diagnosis codes for: - Deep Venous Thrombosis ICD-10 codes: {I80.1, I80.2, I82.22, I82.4, I82.5} and ICD-9 codes: {451.11, 451.19, 453.2, 453.4} - Pulmonary Embolism ICD-10 codes: {I26.0, I26.9} and ICD-9 code {415.1} —
[
  • 2,100 cases
  • , 53,865 controls
]
 — European — MVP MVP Cohort = 3.0
PSS000067 — —
[
  • 690 cases
  • , 10,285 controls
]
,
0.0 % Male samples
 Mean = 65.0 years European — WHI, WHI-GARNET, WHI-HT, WHI-LLS, WHI-MS —