Polygenic Score (PGS) ID: PGS000931

Predicted Trait
Reported Trait Blood clot or deep vein thrombosis (diagnosed by doctor)
Mapped Trait(s)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC11006152
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_FC11006152
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 534
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%
192,089 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
—
[
  • 7,351 cases
  • , 184,738 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
PPM007482 PSS003790|
African Ancestry|
4,390 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot or DVT diagnosed by doctor — AUROC: 0.61925 [0.57619, 0.6623] R²: 0.02193
Incremental AUROC (full-covars): -0.00229
PGS R2 (no covariates): 0.00035
PGS AUROC (no covariates): 0.50724 [0.46275, 0.55173]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007483 PSS003791|
East Asian Ancestry|
952 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot or DVT diagnosed by doctor — AUROC: 0.68652 [0.54244, 0.83061] R²: 0.05141
Incremental AUROC (full-covars): 0.00532
PGS R2 (no covariates): 0.00103
PGS AUROC (no covariates): 0.5328 [0.37688, 0.68873]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007484 PSS003792|
European Ancestry|
17,648 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot or DVT diagnosed by doctor — AUROC: 0.64786 [0.62647, 0.66925] R²: 0.03411
Incremental AUROC (full-covars): 0.03737
PGS R2 (no covariates): 0.01507
PGS AUROC (no covariates): 0.59359 [0.57084, 0.61634]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007485 PSS003793|
South Asian Ancestry|
5,480 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot or DVT diagnosed by doctor — AUROC: 0.63964 [0.59263, 0.68666] R²: 0.02677
Incremental AUROC (full-covars): 0.01249
PGS R2 (no covariates): 0.00502
PGS AUROC (no covariates): 0.55473 [0.50496, 0.60449]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007486 PSS003794|
European Ancestry|
48,060 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot or DVT diagnosed by doctor — AUROC: 0.62837 [0.61546, 0.64128] R²: 0.02953
Incremental AUROC (full-covars): 0.0429
PGS R2 (no covariates): 0.01795
PGS AUROC (no covariates): 0.59176 [0.57816, 0.60536]		 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
PSS003790 — —
[
  • 160 cases
  • , 4,230 controls
]
 — African unspecified — UKB —
PSS003791 — —
[
  • 12 cases
  • , 940 controls
]
 — East Asian — UKB —
PSS003792 — —
[
  • 640 cases
  • , 17,008 controls
]
 — European non-white British ancestry UKB —
PSS003793 — —
[
  • 136 cases
  • , 5,344 controls
]
 — South Asian — UKB —
PSS003794 — —
[
  • 1,859 cases
  • , 46,201 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)