| 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 | venous thromboembolism |
| Mapped term(s) |
8 mapped terms
|
| Polygenic Score ID & Name | PGS Publication ID (PGP) | Reported Trait | Mapped Trait(s) (Ontology) | Number of Variants | Ancestry distribution | PGS Scoring File (FTP Link) |
|---|---|---|---|---|---|---|
| PGS000043 (PRS_VTE) |
PGP000030 | Klarin D et al. Nat Genet (2019) |
Venous thromboembolism | venous thromboembolism | 297 | - |
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000043/ScoringFiles/PGS000043.txt.gz |
|
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. |
|
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 |
|---|---|---|---|---|---|---|---|---|
| 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. | — | [ ,
53.3 % Male samples |
— | European | — | CSMC | — |
| 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 | [ ,
74.59 % Male samples |
Mean = 64.23 years | European | — | — | |
| 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} | — | [
|
— | European | — | MVP | MVP Cohort = 3.0 |
| PSS000067 | — | — | [ ,
0.0 % Male samples |
Mean = 65.0 years | European | — | WHI, WHI-GARNET, WHI-HT, WHI-LLS, WHI-MS | — |