Polygenic Score (PGS) ID: PGS000043

Predicted Trait
Reported Trait Venous thromboembolism
Mapped Trait(s) venous thromboembolism (EFO_0004286)
Released in PGS Catalog: Dec. 18, 2019
Download Score FTP directory
Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name PRS_VTE
Development Method
Name Pruning + Clumping
Parameters P < 1×10^−5; R^2 > 0.2
Variants
Original Genome Build GRCh37
Number of Variants 297
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000030
Citation (link to publication) Klarin D et al. Nat Genet (2019)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 88.7%
African: 7.9%
Hispanic or Latin American: 3.4%
650,119 individuals (100%)
PGS Evaluation
European: 80%
Multi-ancestry (including European): 20%
  • African
  • European
  • Hispanic or Latin American
  • Additional Asian Ancestries
5 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST009097
Europe PMC: 31676865
 51,661 individuals African American or Afro-Caribbean MVP, UKB
GWAS Catalog: GCST009097
Europe PMC: 31676865
 21,868 individuals Hispanic or Latin American MVP, UKB
GWAS Catalog: GCST009097
Europe PMC: 31676865
 576,590 individuals European MVP, UKB

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) 		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 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 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 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 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 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 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 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 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 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 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 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.
PPM014990 PSS009948|
Multi-ancestry (including European)|
615,967 individuals
 PGP000369 |
Jaworek T et al. Neurology (2022)
|Ext.		 Reported Trait: Early onset stroke OR: 1.13 [1.1, 1.16] — — 10 principal components for ancestry and sex —
PPM014991 PSS009948|
Multi-ancestry (including European)|
615,967 individuals
 PGP000369 |
Jaworek T et al. Neurology (2022)
|Ext.		 Reported Trait: Late onset stroke OR: 1.04 [1.01, 1.08] — — 10 principal components for ancestry and sex —

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 —
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 —
PSS009948 — —
[
  • 16,730 cases
  • , 599,237 controls
]
 — African unspecified, European, Hispanic or Latin American, African American or Afro-Caribbean, Asian unspecified Africa, European, Hispanics, Afro-Carribean, Pan-Asian BBJ, EPIC_CAD, GMC, RACE, UKB HELSINKI
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 —