Polygenic Score (PGS) ID: PGS000938

Predicted Trait
Reported Trait Varicose veins of lower extremities (time-to-event)
Mapped Trait(s) Varicose veins (HP_0002619)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC990
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_HC990
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 2,563
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
—
[
  • 12,137 cases
  • , 257,567 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
PPM007517 PSS004761|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE varicose veins of lower extremities — AUROC: 0.62136 [0.57332, 0.6694] R²: 0.02314
Incremental AUROC (full-covars): -0.00473
PGS R2 (no covariates): 0.00107
PGS AUROC (no covariates): 0.52967 [0.4753, 0.58404]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007518 PSS004762|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE varicose veins of lower extremities — AUROC: 0.6963 [0.60332, 0.78927] R²: 0.06309
Incremental AUROC (full-covars): 0.06018
PGS R2 (no covariates): 0.03496
PGS AUROC (no covariates): 0.64663 [0.54765, 0.7456]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007519 PSS004763|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE varicose veins of lower extremities — AUROC: 0.65961 [0.6439, 0.67533] R²: 0.04514
Incremental AUROC (full-covars): 0.02733
PGS R2 (no covariates): 0.01623
PGS AUROC (no covariates): 0.59749 [0.58043, 0.61455]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007520 PSS004764|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE varicose veins of lower extremities — AUROC: 0.67693 [0.64508, 0.70878] R²: 0.04959
Incremental AUROC (full-covars): 0.02832
PGS R2 (no covariates): 0.01507
PGS AUROC (no covariates): 0.59602 [0.56097, 0.63107]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007521 PSS004765|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE varicose veins of lower extremities — AUROC: 0.64564 [0.63595, 0.65534] R²: 0.03681
Incremental AUROC (full-covars): 0.05082
PGS R2 (no covariates): 0.02091
PGS AUROC (no covariates): 0.61143 [0.60132, 0.62154]		 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
PSS004764 — —
[
  • 253 cases
  • , 7,578 controls
]
 — South Asian — UKB —
PSS004765 — —
[
  • 3,056 cases
  • , 64,369 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS004761 — —
[
  • 122 cases
  • , 6,375 controls
]
 — African unspecified — UKB —
PSS004762 — —
[
  • 31 cases
  • , 1,673 controls
]
 — East Asian — UKB —
PSS004763 — —
[
  • 1,101 cases
  • , 23,804 controls
]
 — European non-white British ancestry UKB —