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(Variants and weights)

Polygenic Score (PGS) ID: PGS000043

Predicted Trait

Reported Trait: Venous thromboembolism
Mapped Trait(s) (Experimental Factor Ontology (EFO) IDs): venous thromboembolism

Score Details

Name: PRS_VTE

Original Genome Build: GRCh37
Number of Variants: 297

PGS Development Method: Pruning + Clumping
PGS Development Details/Relevant Parameters: P < 1×10^−5; R^2 > 0.2

Citation: Klarin D et al. Nat Genet (2019) | PGS Catalog Publication ID: PGP000030

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST009097
PubMed: 31676865
51,661 individuals African American or Afro-Caribbean
GWAS Catalog: GCST009097
PubMed: 31676865
21,868 individuals Hispanic or Latin American
GWAS Catalog: GCST009097
PubMed: 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 (PPM) ID PGS Catalog Sample Set (PSS) ID Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000102 PSS000066 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
PPM000103 PSS000067 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

Evaluated Samples

PGS Catalog Sample Set (PSS) ID Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers 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} 55,965 individuals
[ 2,100 cases, 53,865 controls]
European MVP MVP Cohort = 3.0
PSS000067 10,975 individuals
[ 690 cases, 10,285 controls]
0.00 %% Male samples
European WHI, WHI-GARNET, WHI-HT, WHI-LLS, WHI-MS