Polygenic Score (PGS) ID: PGS002235

Predicted Trait
Reported Trait Venous thromboembolism
Mapped Trait(s) venous thromboembolism (EFO_0004286)
Released in PGS Catalog: Dec. 10, 2021
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Score Details

Score Construction
PGS Name elasticnet_VTE
Development Method
Name Elastic net logistic regression of genome-wide significant SNPs
Parameters NR
Variants
Original Genome Build NR
Number of Variants 36
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000267
Citation (link to publication) Kolin DA et al. Sci Rep (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 92.4%
African: 5.1%
Hispanic or Latin American: 2.1%
Multi-ancestry (including European): 0.4%
  • European
  • Additional Diverse Ancestries
1,020,612 individuals (100%)
Score Development/Training
European: 100%
126,247 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST001557
Europe PMC: 22672568
 2,962 individuals European, Other NR
GWAS Catalog: GCST002808
Europe PMC: 25772935
 60,139 individuals European 11 cohorts
  • ARIC
  • ,CHS
  • ,EOVT
  • ,GIFT
  • ,HPFS
  • ,HVH
  • ,MARTHA
  • ,Mayo_VTE
  • ,NHS
  • ,NHS2
  • ,WGHS
GWAS Catalog: GCST003390
Europe PMC: 26908601
 258,962 individuals European 23andMe
GWAS Catalog: GCST001253
Europe PMC: 21980494
 2,652 individuals European 3C, MARTHA
GWAS Catalog: GCST002012
Europe PMC: 23650146
 44,499 individuals European ARIC, CHS, HVH, RS, WGHS
GWAS Catalog: GCST009097
Europe PMC: 31676865
 576,590 individuals European MVP, UKB
GWAS Catalog: GCST009097
Europe PMC: 31676865
 51,661 individuals African American or Afro-Caribbean MVP, UKB
GWAS Catalog: GCST009097
Europe PMC: 31676865
 21,868 individuals Hispanic or Latin American MVP, UKB
[
  • 447 cases
  • , 832 controls
]
,
48.94 % Male samples
 European, NR NR
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
—
[
  • 1,131 cases
  • , 125,116 controls
]
,
47.3 % Male samples
 European
(British)		 UKB — — — — —

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
PPM012709 PSS009500|
European Ancestry|
269,164 individuals
 PGP000267 |
Kolin DA et al. Sci Rep (2021)
 Reported Trait: Incident venous thromboembolism — — Odds Ratio (OR, top 1% vs bottom 99%): 5.37 [5.34, 5.4] — —
PPM012710 PSS009500|
European Ancestry|
269,164 individuals
 PGP000267 |
Kolin DA et al. Sci Rep (2021)
 Reported Trait: Incident venous thromboembolism — — Subhazard ratio (SHR, top 20.2% vs bottom 79.8%): 3.02 [2.63, 3.47] — —
PPM012711 PSS009500|
European Ancestry|
269,164 individuals
 PGP000267 |
Kolin DA et al. Sci Rep (2021)
 Reported Trait: Incident venous thromboembolism — — Subhazard ratio (SHR, top 20.2% vs bottom 79.8%): 7.51 [6.28, 8.98] — —

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
PSS009500 — —
[
  • 2,295 cases
  • , 266,869 controls
]
 — European
(British)		 — UKB —