Polygenic Score (PGS) ID: PGS003332

Predicted Trait
Reported Trait Venous thromboembolism
Mapped Trait(s) venous thromboembolism (EFO_0004286)
Released in PGS Catalog: Jan. 24, 2023
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Score Details

Score Construction
PGS Name PRS_VTE_EUR_GHOUSE
Development Method
Name PRS-CS
Parameters auto
Variants
Original Genome Build hg19
Number of Variants 1,092,045
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000398
Citation (link to publication) Ghouse J et al. Nat Genet (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
1,064,421 individuals (100%)
PGS Evaluation
Multi-ancestry (including European): 66.7%
  • European
  • African
  • Additional Asian Ancestries
  • Not Reported
European: 33.3%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
—
[
  • 57,467 cases
  • , 1,006,954 controls
]
 European
(Icelandic, American, Danish and Finnish)		 CHB, DBDS, FinnGen, IHCS, deCODE

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
PPM016143 PSS010047|
European Ancestry|
436,440 individuals
 PGP000398 |
Ghouse J et al. Nat Genet (2023)
 Reported Trait: Prevalent VTE OR: 1.51 AUROC: 0.664 [0.659, 0.669] — age, sex, 4 PCs —
PPM020880 PSS011439|
Multi-ancestry (including European)|
70,406 individuals
 PGP000597 |
Shi Z et al. Thromb Res (2023)
|Ext.		 Reported Trait: Incident cancer-associated thrombosis — — Hazard ratio (HR, top PRS decile vs rest): 1.75 [1.62, 1.88] Age, gender, BMI and 10 PCs —
PPM022174 PSS011827|
Multi-ancestry (including European)|
8,210 individuals
 PGP000681 |
Rifkin AS et al. World J Gastroenterol (2023)
|Ext.		 Reported Trait: Incident venous thromboembolism in individuals with inflammatory bowel disease — AUROC: 0.68 [0.65, 0.71] Hazard ratio (HR, PGS in top 10% vs middle 80%): 1.98 [1.52, 2.57] Sex, body mass index, 10 PCs 1,515 SNPs from F2 and F5 genes excluded

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
PSS011827 — —
[
  • 366 cases
  • , 7,435 controls
]
 — European — UKB —
PSS011827 — —
[
  • 12 cases
  • , 397 controls
]
 — Not reported — UKB —
PSS010047 — —
[
  • 23,723 cases
  • , 412,717 controls
]
 — European — UKB —
PSS011439 — — 68,709 individuals,
52.59 % Male samples
 Mean = 60.42 years
Ci = [60.37, 60.48] years		 European — UKB —
PSS011439 — — 105 individuals,
52.38 % Male samples
 Mean = 55.61 years
Ci = [54.11, 57.11] years		 African unspecified — UKB —
PSS011439 — — 730 individuals,
49.18 % Male samples
 Mean = 57.46 years
Ci = [56.89, 58.03] years		 Asian unspecified — UKB —
PSS011439 — — 862 individuals,
51.86 % Male samples
 Mean = 57.82 years
Ci = [57.28, 58.36] years		 Not reported — UKB —