Polygenic Score (PGS) ID: PGS000930

Predicted Trait
Reported Trait Blood clot (diagnosed by doctor)
Mapped Trait(s) thrombotic disease (MONDO_0000831)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC3006152
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_FC3006152
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 118
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%
187,324 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
—
[
  • 2,361 cases
  • , 184,963 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
PPM007477 PSS003914|
African Ancestry|
4,286 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot diagnosed by doctor — AUROC: 0.64618 [0.56748, 0.72489] R²: 0.02826
Incremental AUROC (full-covars): 0.00845
PGS R2 (no covariates): 0.00198
PGS AUROC (no covariates): 0.53535 [0.45318, 0.61752]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007478 PSS003915|
East Asian Ancestry|
945 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot diagnosed by doctor — AUROC: 0.83468 [0.6451, 1.0] R²: 0.18847
Incremental AUROC (full-covars): -0.00149
PGS R2 (no covariates): 0.00357
PGS AUROC (no covariates): 0.56702 [0.36049, 0.77355]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007479 PSS003916|
European Ancestry|
17,235 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot diagnosed by doctor — AUROC: 0.62906 [0.59189, 0.66622] R²: 0.02094
Incremental AUROC (full-covars): 0.04321
PGS R2 (no covariates): 0.01048
PGS AUROC (no covariates): 0.59654 [0.5564, 0.63667]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007480 PSS003917|
South Asian Ancestry|
5,381 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot diagnosed by doctor — AUROC: 0.71068 [0.63185, 0.78951] R²: 0.04649
Incremental AUROC (full-covars): 0.02778
PGS R2 (no covariates): 0.00789
PGS AUROC (no covariates): 0.59225 [0.49685, 0.68766]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007481 PSS003918|
European Ancestry|
46,847 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot diagnosed by doctor — AUROC: 0.6205 [0.59778, 0.64322] R²: 0.01789
Incremental AUROC (full-covars): 0.05259
PGS R2 (no covariates): 0.01324
PGS AUROC (no covariates): 0.60274 [0.57915, 0.62633]		 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
PSS003914 — —
[
  • 54 cases
  • , 4,232 controls
]
 — African unspecified — UKB —
PSS003915 — —
[
  • 5 cases
  • , 940 controls
]
 — East Asian — UKB —
PSS003916 — —
[
  • 211 cases
  • , 17,024 controls
]
 — European non-white British ancestry UKB —
PSS003917 — —
[
  • 36 cases
  • , 5,345 controls
]
 — South Asian — UKB —
PSS003918 — —
[
  • 584 cases
  • , 46,263 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)