Polygenic Score (PGS) ID: PGS000043

Predicted Trait
Reported Trait Venous thromboembolism
Mapped Trait(s) venous thromboembolism (EFO_0004286)
Released in PGS: Dec. 18, 2019

Score Details

Score Construction
PGS Name PRS_VTE
Variants
Original Genome Build GRCh37
Number of Variants 297
Development Method
Name Pruning + Clumping
Parameters P < 1×10^−5; R^2 > 0.2
PGS Source
PGS Catalog Publication (PGP) ID PGP000030
Citation (link to publication) Klarin D et al. Nat Genet (2019)

Contributing Samples

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

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)
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
PPM000103 PSS000067 PGP000030
Klarin D et al. (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
PPM000102 PSS000066 PGP000030
Klarin D et al. (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

Evaluated Samples

PGS Sample Set ID
(PSS ID)
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
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