Polygenic Score (PGS) ID: PGS001796

Predicted Trait
Reported Trait Venous thromboembolism
Mapped Trait(s) venous thromboembolism (EFO_0004286)
Released in PGS Catalog: Sept. 8, 2022
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Score Details

Score Construction
PGS Name 1kgeur_gbmi_leaveUKBBout_VTE_pst_eff_a1_b0.5_phiauto
Development Method
Name PRS-CS-auto
Parameters effective sample size and other defualt parameters
Variants
Original Genome Build GRCh37
Number of Variants 910,337
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000262
Citation (link to publication) Wang Y et al. medRxiv (2021) Preprint
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 79%
East Asian: 12.4%
African: 4.1%
Additional Asian Ancestries: 2.4%
Additional Diverse Ancestries: 2.2%
628,261 individuals (100%)
PGS Evaluation
African: 50%
European: 50%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
[
  • 1,337 cases
  • , 24,548 controls
]
African unspecified BioMe, BioVU, MGI, UCLA
[
  • 1,037 cases
  • , 12,479 controls
]
Native American BioMe, UCLA
[
  • 193 cases
  • , 77,462 controls
]
East Asian CKB, UCLA
[
  • 17,403 cases
  • , 478,925 controls
]
European 6 cohorts
  • BioMe
  • ,BioVU
  • ,EB
  • ,FinnGen
  • ,MGI
  • ,UCLA
[
  • 84 cases
  • , 14,793 controls
]
Asian unspecified G&H

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
PPM009310 PSS007700|
African Ancestry|
6,137 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Venous thromboembolism AUROC: 0.672 Nagelkerke's R2 (covariates regressed out): 0.00488 sex,age,age2,age*sex,age^2*sex, 20PCs
PPM009300 PSS007719|
European Ancestry|
356,269 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Venous thromboembolism AUROC: 0.675 Nagelkerke's R2 (covariates regressed out): 0.02221 sex,age,age2,age*sex,age^2*sex, 20PCs

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
PSS007719
[
  • 6,549 cases
  • , 349,719 controls
]
European UKB
PSS007700
[
  • 120 cases
  • , 6,016 controls
]
African unspecified Africa or admixed-ancestry diaspora UKB