Polygenic Score (PGS) ID: PGS001277

Predicted Trait
Reported Trait PE +/- DVT
Mapped Trait(s)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC203
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_HC203
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 96
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
—
[
  • 4,663 cases
  • , 265,041 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
PPM008883 PSS004344|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: PE +/- DVT — AUROC: 0.65081 [0.59936, 0.70226] R²: 0.03099
Incremental AUROC (full-covars): 0.01
PGS R2 (no covariates): 0.00418
PGS AUROC (no covariates): 0.55179 [0.49456, 0.60901]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008884 PSS004345|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: PE +/- DVT — AUROC: 0.8083 [0.66236, 0.95424] R²: 0.12334
Incremental AUROC (full-covars): -0.0014
PGS R2 (no covariates): 0.0
PGS AUROC (no covariates): 0.51341 [0.35575, 0.67107]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008885 PSS004346|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: PE +/- DVT — AUROC: 0.67497 [0.64702, 0.70293] R²: 0.03998
Incremental AUROC (full-covars): 0.03149
PGS R2 (no covariates): 0.01508
PGS AUROC (no covariates): 0.61144 [0.58149, 0.6414]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008886 PSS004347|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: PE +/- DVT — AUROC: 0.69135 [0.62082, 0.76187] R²: 0.03814
Incremental AUROC (full-covars): 0.03509
PGS R2 (no covariates): 0.01582
PGS AUROC (no covariates): 0.63463 [0.5672, 0.70206]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008887 PSS004348|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: PE +/- DVT — AUROC: 0.64659 [0.63085, 0.66233] R²: 0.02867
Incremental AUROC (full-covars): 0.03414
PGS R2 (no covariates): 0.0129
PGS AUROC (no covariates): 0.59812 [0.58116, 0.61507]		 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
PSS004348 — —
[
  • 1,130 cases
  • , 66,295 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS004344 — —
[
  • 99 cases
  • , 6,398 controls
]
 — African unspecified — UKB —
PSS004345 — —
[
  • 8 cases
  • , 1,696 controls
]
 — East Asian — UKB —
PSS004346 — —
[
  • 358 cases
  • , 24,547 controls
]
 — European non-white British ancestry UKB —
PSS004347 — —
[
  • 53 cases
  • , 7,778 controls
]
 — South Asian — UKB —