Polygenic Score (PGS) ID: PGS001033

Predicted Trait
Reported Trait Other coagulation defects (time-to-event)
Mapped Trait(s) blood coagulation disease (EFO_0009314)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC624
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_HC624
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1
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
—
[
  • 1,180 cases
  • , 268,524 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
PPM007928 PSS004546|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other coagulation defects — AUROC: 0.68816 [0.60114, 0.77518] R²: 0.03983
Incremental AUROC (full-covars): -0.00134
PGS R2 (no covariates): 0.00067
PGS AUROC (no covariates): 0.49799 [0.49722, 0.49876]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007929 PSS004547|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other coagulation defects — AUROC: 0.8546 [0.65205, 1.0] R²: 0.119
Incremental AUROC (full-covars): 0.0
PGS R2 (no covariates): 8e-05
PGS AUROC (no covariates): 0.49971 [0.49913, 0.50028]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007930 PSS004548|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other coagulation defects — AUROC: 0.64742 [0.59655, 0.69828] R²: 0.03199
Incremental AUROC (full-covars): 0.06677
PGS R2 (no covariates): 0.0303
PGS AUROC (no covariates): 0.58367 [0.54735, 0.61999]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007931 PSS004549|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other coagulation defects — AUROC: 0.66881 [0.55798, 0.77963] R²: 0.02584
Incremental AUROC (full-covars): 0.02341
PGS R2 (no covariates): 0.00994
PGS AUROC (no covariates): 0.54143 [0.46669, 0.61618]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007932 PSS004550|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other coagulation defects — AUROC: 0.65623 [0.61832, 0.69414] R²: 0.05179
Incremental AUROC (full-covars): 0.12049
PGS R2 (no covariates): 0.05781
PGS AUROC (no covariates): 0.63402 [0.60616, 0.66189]		 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
PSS004546 — —
[
  • 35 cases
  • , 6,462 controls
]
 — African unspecified — UKB —
PSS004547 — —
[
  • 3 cases
  • , 1,701 controls
]
 — East Asian — UKB —
PSS004548 — —
[
  • 123 cases
  • , 24,782 controls
]
 — European non-white British ancestry UKB —
PSS004549 — —
[
  • 18 cases
  • , 7,813 controls
]
 — South Asian — UKB —
PSS004550 — —
[
  • 268 cases
  • , 67,157 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)