Polygenic Score (PGS) ID: PGS001265

Predicted Trait
Reported Trait Deep vein thrombosis (leg)
Mapped Trait(s) deep vein thrombosis (EFO_0003907)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC6006152
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_FC6006152
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,530
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%
269,382 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
  • , 263,572 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
PPM008830 PSS003994|
African Ancestry|
6,348 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot in the leg (DVT) — AUROC: 0.57103 [0.5199, 0.62216] R²: 0.01008
Incremental AUROC (full-covars): -0.02728
PGS R2 (no covariates): 0.0
PGS AUROC (no covariates): 0.49766 [0.44543, 0.54989]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008831 PSS003995|
East Asian Ancestry|
1,640 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot in the leg (DVT) — AUROC: 0.63771 [0.46295, 0.81247] R²: 0.02767
Incremental AUROC (full-covars): -0.06036
PGS R2 (no covariates): 0.02301
PGS AUROC (no covariates): 0.36208 [0.17892, 0.54524]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008832 PSS003996|
European Ancestry|
24,838 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot in the leg (DVT) — AUROC: 0.65672 [0.63317, 0.68026] R²: 0.03399
Incremental AUROC (full-covars): 0.02882
PGS R2 (no covariates): 0.01234
PGS AUROC (no covariates): 0.58768 [0.56206, 0.61329]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008833 PSS003997|
South Asian Ancestry|
7,556 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot in the leg (DVT) — AUROC: 0.62462 [0.57005, 0.67919] R²: 0.02045
Incremental AUROC (full-covars): 0.0075
PGS R2 (no covariates): 0.00479
PGS AUROC (no covariates): 0.56322 [0.5071, 0.61933]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008834 PSS003998|
European Ancestry|
67,349 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot in the leg (DVT) — AUROC: 0.63743 [0.62331, 0.65154] R²: 0.02831
Incremental AUROC (full-covars): 0.04083
PGS R2 (no covariates): 0.01552
PGS AUROC (no covariates): 0.59171 [0.57659, 0.60683]		 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
PSS003996 — —
[
  • 508 cases
  • , 24,330 controls
]
 — European non-white British ancestry UKB —
PSS003997 — —
[
  • 106 cases
  • , 7,450 controls
]
 — South Asian — UKB —
PSS003998 — —
[
  • 1,476 cases
  • , 65,873 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS003994 — —
[
  • 121 cases
  • , 6,227 controls
]
 — African unspecified — UKB —
PSS003995 — —
[
  • 9 cases
  • , 1,631 controls
]
 — East Asian — UKB —