PGS Publication: PGP000030

Publication Information (EuropePMC)
Title Genome-wide association analysis of venous thromboembolism identifies new risk loci and genetic overlap with arterial vascular disease.
PubMed ID 31676865(Europe PMC)
doi 10.1038/s41588-019-0519-3
Publication Date Nov. 1, 2019
Journal Nat Genet
Author(s) Klarin D, Busenkell E, Judy R, Lynch J, Levin M, Haessler J, Aragam K, Chaffin M, Haas M, Lindström S, Assimes TL, Huang J, Min Lee K, Shao Q, Huffman JE, Kabrhel C, Huang Y, Sun YV, Vujkovic M, Saleheen D, Miller DR, Reaven P, DuVall S, Boden WE, Pyarajan S, Reiner AP, Trégouët DA, Henke P, Kooperberg C, Gaziano JM, Concato J, Rader DJ, Cho K, Chang KM, Wilson PWF, Smith NL, O'Donnell CJ, Tsao PS, Kathiresan S, Obi A, Damrauer SM, Natarajan P, INVENT Consortium, Veterans Affairs’ Million Veteran Program.
Released in PGS: Dec. 18, 2019

Associated Polygenic Score(s)

PGS Developed By This Publication

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants 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 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)
Evaluated Score 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
PPM000102 PGS000043 (PRS_VTE) 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
PPM000103 PGS000043 (PRS_VTE) 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

Evaluated Samples

PGS Sample Set ID
(PSS ID)
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
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