Polygenic Score (PGS) ID: PGS001279

Predicted Trait
Reported Trait previously: Blood clot in the lung
Mapped Trait(s)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC8006152
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_FC8006152
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 94
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
—
[
  • 2,361 cases
  • , 267,021 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
PPM008893 PSS004014|
African Ancestry|
6,348 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot in the lung — AUROC: 0.63917 [0.56071, 0.71763] R²: 0.02075
Incremental AUROC (full-covars): 0.01133
PGS R2 (no covariates): 0.00182
PGS AUROC (no covariates): 0.53508 [0.45261, 0.61756]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008894 PSS004015|
East Asian Ancestry|
1,640 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot in the lung — AUROC: 0.82557 [0.62097, 1.0] R²: 0.16736
Incremental AUROC (full-covars): -0.00024
PGS R2 (no covariates): 0.00388
PGS AUROC (no covariates): 0.57456 [0.37482, 0.77429]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008895 PSS004016|
European Ancestry|
24,838 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot in the lung — AUROC: 0.62994 [0.59262, 0.66726] R²: 0.01985
Incremental AUROC (full-covars): 0.03629
PGS R2 (no covariates): 0.00848
PGS AUROC (no covariates): 0.59191 [0.55186, 0.63196]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008896 PSS004017|
South Asian Ancestry|
7,556 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot in the lung — AUROC: 0.71053 [0.63261, 0.78846] PGS R2 (no covariates): 0.00898
R²: 0.04621
Incremental AUROC (full-covars): 0.02759
PGS AUROC (no covariates): 0.60144 [0.50751, 0.69537]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008897 PSS004018|
European Ancestry|
67,349 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot in the lung — AUROC: 0.62416 [0.60164, 0.64668] R²: 0.01763
Incremental AUROC (full-covars): 0.04457
PGS R2 (no covariates): 0.01146
PGS AUROC (no covariates): 0.60034 [0.57683, 0.62385]		 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
PSS004014 — —
[
  • 54 cases
  • , 6,294 controls
]
 — African unspecified — UKB —
PSS004015 — —
[
  • 5 cases
  • , 1,635 controls
]
 — East Asian — UKB —
PSS004016 — —
[
  • 211 cases
  • , 24,627 controls
]
 — European non-white British ancestry UKB —
PSS004017 — —
[
  • 36 cases
  • , 7,520 controls
]
 — South Asian — UKB —
PSS004018 — —
[
  • 584 cases
  • , 66,765 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)