Polygenic Score (PGS) ID: PGS001266

Predicted Trait
Reported Trait Deep vein thrombosis (diagnosed by doctor)
Mapped Trait(s) deep vein thrombosis (EFO_0003907)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC1006152
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_BIN_FC1006152
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,773
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%
190,625 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
—
[
  • 5,810 cases
  • , 184,815 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
PPM008835 PSS003780|
African Ancestry|
4,351 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: DVT diagnosed by doctor — AUROC: 0.60583 [0.55495, 0.65672] R²: 0.01929
Incremental AUROC (full-covars): -0.01777
PGS R2 (no covariates): 8e-05
PGS AUROC (no covariates): 0.50292 [0.45113, 0.55471]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008836 PSS003781|
East Asian Ancestry|
949 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: DVT diagnosed by doctor — AUROC: 0.63783 [0.4637, 0.81195] R²: 0.03121
Incremental AUROC (full-covars): -0.05863
PGS R2 (no covariates): 0.02253
PGS AUROC (no covariates): 0.35887 [0.15439, 0.56334]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008837 PSS003782|
European Ancestry|
17,524 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: DVT diagnosed by doctor — AUROC: 0.64909 [0.62535, 0.67282] R²: 0.03386
Incremental AUROC (full-covars): 0.02852
PGS R2 (no covariates): 0.01323
PGS AUROC (no covariates): 0.58862 [0.56306, 0.61418]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008838 PSS003783|
South Asian Ancestry|
5,450 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: DVT diagnosed by doctor — AUROC: 0.62654 [0.57175, 0.68132] R²: 0.02365
Incremental AUROC (full-covars): 0.00654
PGS R2 (no covariates): 0.00539
PGS AUROC (no covariates): 0.56216 [0.50579, 0.61854]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008839 PSS003784|
European Ancestry|
47,689 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: DVT diagnosed by doctor — AUROC: 0.63094 [0.61664, 0.64525] R²: 0.02868
Incremental AUROC (full-covars): 0.04553
PGS R2 (no covariates): 0.0177
PGS AUROC (no covariates): 0.59437 [0.5792, 0.60954]		 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
PSS003780 — —
[
  • 121 cases
  • , 4,230 controls
]
 — African unspecified — UKB —
PSS003781 — —
[
  • 9 cases
  • , 940 controls
]
 — East Asian — UKB —
PSS003782 — —
[
  • 508 cases
  • , 17,016 controls
]
 — European non-white British ancestry UKB —
PSS003783 — —
[
  • 106 cases
  • , 5,344 controls
]
 — South Asian — UKB —
PSS003784 — —
[
  • 1,476 cases
  • , 46,213 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)