Polygenic Score (PGS) ID: PGS001278

Predicted Trait
Reported Trait previously: Blood clot in the leg (DVT) or lung
Mapped Trait(s)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC12006152
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_FC12006152
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 551
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
—
[
  • 7,351 cases
  • , 262,031 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
PPM008888 PSS003795|
African Ancestry|
6,348 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot in the leg (DVT) or lung — AUROC: 0.59279 [0.55016, 0.63542] R²: 0.01242
Incremental AUROC (full-covars): -0.00635
PGS R2 (no covariates): 0.00013
PGS AUROC (no covariates): 0.5015 [0.45729, 0.5457]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008889 PSS003796|
East Asian Ancestry|
1,640 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot in the leg (DVT) or lung — AUROC: 0.66743 [0.52454, 0.81033] R²: 0.03638
Incremental AUROC (full-covars): 0.00793
PGS R2 (no covariates): 7e-05
PGS AUROC (no covariates): 0.50497 [0.35161, 0.65832]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008890 PSS003797|
European Ancestry|
24,838 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot in the leg (DVT) or lung — AUROC: 0.65354 [0.63231, 0.67477] R²: 0.03366
Incremental AUROC (full-covars): 0.03495
PGS R2 (no covariates): 0.01331
PGS AUROC (no covariates): 0.59164 [0.56886, 0.61442]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008891 PSS003798|
South Asian Ancestry|
7,556 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot in the leg (DVT) or lung — AUROC: 0.63523 [0.58822, 0.68224] R²: 0.02321
Incremental AUROC (full-covars): 0.01038
PGS R2 (no covariates): 0.00457
PGS AUROC (no covariates): 0.55523 [0.50541, 0.60504]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008892 PSS003799|
European Ancestry|
67,349 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot in the leg (DVT) or lung — AUROC: 0.63525 [0.6226, 0.64791] R²: 0.02918
Incremental AUROC (full-covars): 0.03836
PGS R2 (no covariates): 0.01554
PGS AUROC (no covariates): 0.58956 [0.57602, 0.6031]		 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
PSS003795 — —
[
  • 160 cases
  • , 6,188 controls
]
 — African unspecified — UKB —
PSS003796 — —
[
  • 12 cases
  • , 1,628 controls
]
 — East Asian — UKB —
PSS003797 — —
[
  • 640 cases
  • , 24,198 controls
]
 — European non-white British ancestry UKB —
PSS003798 — —
[
  • 136 cases
  • , 7,420 controls
]
 — South Asian — UKB —
PSS003799 — —
[
  • 1,859 cases
  • , 65,490 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)