Polygenic Score (PGS) ID: PGS001264

Predicted Trait
Reported Trait Deep vein thrombosis
Mapped Trait(s) deep vein thrombosis (EFO_0003907)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC166
Released in PGS Catalog: Oct. 21, 2021
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name GBE_HC166
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 839
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
269,704 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 Sample Sets

Development Samples

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
—
[
  • 5,629 cases
  • , 264,075 controls
]
 European UKB — — — white British ancestry —

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
PPM008825 PSS004317|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: DVT — AUROC: 0.59693 [0.54555, 0.64831] R²: 0.01434
Incremental AUROC (full-covars): -0.01669
PGS R2 (no covariates): 1e-05
PGS AUROC (no covariates): 0.48616 [0.43296, 0.53936]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008826 PSS004318|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: DVT — AUROC: 0.61394 [0.40098, 0.8269] R²: 0.02433
Incremental AUROC (full-covars): -0.05665
PGS R2 (no covariates): 0.02803
PGS AUROC (no covariates): 0.34405 [0.14931, 0.5388]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008827 PSS004319|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: DVT — AUROC: 0.66169 [0.63804, 0.68534] R²: 0.03622
Incremental AUROC (full-covars): 0.02668
PGS R2 (no covariates): 0.01176
PGS AUROC (no covariates): 0.58323 [0.55692, 0.60955]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008828 PSS004320|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: DVT — AUROC: 0.64561 [0.58823, 0.703] R²: 0.02969
Incremental AUROC (full-covars): 0.00326
PGS R2 (no covariates): 0.00504
PGS AUROC (no covariates): 0.56273 [0.50177, 0.62369]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008829 PSS004321|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: DVT — AUROC: 0.63698 [0.62257, 0.65138] R²: 0.02749
Incremental AUROC (full-covars): 0.0419
PGS R2 (no covariates): 0.01535
PGS AUROC (no covariates): 0.5923 [0.57682, 0.60778]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

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
PSS004317 — —
[
  • 114 cases
  • , 6,383 controls
]
 — African unspecified — UKB —
PSS004318 — —
[
  • 7 cases
  • , 1,697 controls
]
 — East Asian — UKB —
PSS004319 — —
[
  • 483 cases
  • , 24,422 controls
]
 — European non-white British ancestry UKB —
PSS004320 — —
[
  • 94 cases
  • , 7,737 controls
]
 — South Asian — UKB —
PSS004321 — —
[
  • 1,430 cases
  • , 65,995 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)