Polygenic Score (PGS) ID: PGS000961

Predicted Trait
Reported Trait Phlebitis and thrombophlebitis (time-to-event)
Mapped Trait(s)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC987
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_HC987
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,143
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
—
[
  • 9,249 cases
  • , 260,455 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
PPM007629 PSS004756|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE phlebitis and thrombophlebitis — AUROC: 0.63235 [0.59259, 0.67211] R²: 0.02507
Incremental AUROC (full-covars): 0.00771
PGS R2 (no covariates): 0.00171
PGS AUROC (no covariates): 0.53507 [0.4917, 0.57844]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007630 PSS004757|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE phlebitis and thrombophlebitis — AUROC: 0.66631 [0.52571, 0.80691] R²: 0.04004
Incremental AUROC (full-covars): -0.006
PGS R2 (no covariates): 4e-05
PGS AUROC (no covariates): 0.50807 [0.37643, 0.63972]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007631 PSS004758|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE phlebitis and thrombophlebitis — AUROC: 0.66949 [0.64981, 0.68916] R²: 0.04365
Incremental AUROC (full-covars): 0.03126
PGS R2 (no covariates): 0.01428
PGS AUROC (no covariates): 0.59647 [0.57489, 0.61804]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007632 PSS004759|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE phlebitis and thrombophlebitis — AUROC: 0.63064 [0.58623, 0.67504] R²: 0.02362
Incremental AUROC (full-covars): 0.00728
PGS R2 (no covariates): 0.0042
PGS AUROC (no covariates): 0.55251 [0.5057, 0.59933]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007633 PSS004760|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE phlebitis and thrombophlebitis — AUROC: 0.64191 [0.63056, 0.65326] R²: 0.03444
Incremental AUROC (full-covars): 0.03745
PGS R2 (no covariates): 0.01698
PGS AUROC (no covariates): 0.58931 [0.57719, 0.60143]		 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
PSS004756 — —
[
  • 173 cases
  • , 6,324 controls
]
 — African unspecified — UKB —
PSS004757 — —
[
  • 15 cases
  • , 1,689 controls
]
 — East Asian — UKB —
PSS004758 — —
[
  • 710 cases
  • , 24,195 controls
]
 — European non-white British ancestry UKB —
PSS004759 — —
[
  • 145 cases
  • , 7,686 controls
]
 — South Asian — UKB —
PSS004760 — —
[
  • 2,312 cases
  • , 65,113 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)