Polygenic Score (PGS) ID: PGS001280

Predicted Trait
Reported Trait PE (time-to-event)
Mapped Trait(s) pulmonary embolism (EFO_0003827)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC943
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_HC943
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 88
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%
269,704 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
—
[
  • 4,746 cases
  • , 264,958 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
PPM008898 PSS004731|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE PE — AUROC: 0.64593 [0.59381, 0.69806] R²: 0.02844
Incremental AUROC (full-covars): 0.007
PGS R2 (no covariates): 0.00302
PGS AUROC (no covariates): 0.54566 [0.48787, 0.60344]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008899 PSS004732|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE PE — AUROC: 0.80741 [0.66178, 0.95305] R²: 0.12326
Incremental AUROC (full-covars): -0.00228
PGS R2 (no covariates): 2e-05
PGS AUROC (no covariates): 0.51798 [0.36629, 0.66968]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008900 PSS004733|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE PE — AUROC: 0.67617 [0.64866, 0.70368] R²: 0.04057
Incremental AUROC (full-covars): 0.02926
PGS R2 (no covariates): 0.01403
PGS AUROC (no covariates): 0.60765 [0.57812, 0.63719]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008901 PSS004734|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE PE — AUROC: 0.68371 [0.61554, 0.75187] R²: 0.03438
Incremental AUROC (full-covars): 0.03127
PGS R2 (no covariates): 0.01152
PGS AUROC (no covariates): 0.6164 [0.54879, 0.684]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008902 PSS004735|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE PE — AUROC: 0.65102 [0.6355, 0.66654] R²: 0.03061
Incremental AUROC (full-covars): 0.03417
PGS R2 (no covariates): 0.01357
PGS AUROC (no covariates): 0.59996 [0.58313, 0.61679]		 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
PSS004732 — —
[
  • 8 cases
  • , 1,696 controls
]
 — East Asian — UKB —
PSS004733 — —
[
  • 363 cases
  • , 24,542 controls
]
 — European non-white British ancestry UKB —
PSS004734 — —
[
  • 53 cases
  • , 7,778 controls
]
 — South Asian — UKB —
PSS004735 — —
[
  • 1,155 cases
  • , 66,270 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS004731 — —
[
  • 96 cases
  • , 6,401 controls
]
 — African unspecified — UKB —