Polygenic Score (PGS) ID: PGS000937

Predicted Trait
Reported Trait Varicose veins
Mapped Trait(s) Varicose veins (HP_0002619)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC401
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_HC401
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 2,603
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
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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
—
[
  • 9,036 cases
  • , 260,668 controls
]
EuropeanUKB———white British ancestry—
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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.

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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
PPM007512PSS004476|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Varicose veins—AUROC: 0.59208 [0.53676, 0.64739]PGS R2 (no covariates): 0.0
R²: 0.01447
Incremental AUROC (full-covars): -0.02413
PGS AUROC (no covariates): 0.49013 [0.43623, 0.54403]		age, sex, UKB array type, Genotype PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM007513PSS004477|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Varicose veins—AUROC: 0.71088 [0.62204, 0.79971]R²: 0.07134
Incremental AUROC (full-covars): 0.04391
PGS R2 (no covariates): 0.01451
PGS AUROC (no covariates): 0.60481 [0.48689, 0.72274]		age, sex, UKB array type, Genotype PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM007514PSS004478|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Varicose veins—AUROC: 0.65191 [0.63315, 0.67067]R²: 0.0371
Incremental AUROC (full-covars): 0.03634
PGS R2 (no covariates): 0.01715
PGS AUROC (no covariates): 0.60589 [0.58649, 0.62529]		age, sex, UKB array type, Genotype PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM007515PSS004479|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Varicose veins—AUROC: 0.67258 [0.63464, 0.71052]R²: 0.04734
Incremental AUROC (full-covars): 0.02962
PGS R2 (no covariates): 0.01842
PGS AUROC (no covariates): 0.60625 [0.56528, 0.64722]		age, sex, UKB array type, Genotype PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM007516PSS004480|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Varicose veins—AUROC: 0.63516 [0.62363, 0.64669]R²: 0.02861
Incremental AUROC (full-covars): 0.05484
PGS R2 (no covariates): 0.01871
PGS AUROC (no covariates): 0.60775 [0.59597, 0.61953]		age, sex, UKB array type, Genotype PCsFull Model & PGS R2 is estimated using Nagelkerke's method
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Evaluated Samples

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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
PSS004476——
[
  • 107 cases
  • , 6,390 controls
]
—African unspecified—UKB—
PSS004477——
[
  • 25 cases
  • , 1,679 controls
]
—East Asian—UKB—
PSS004478——
[
  • 819 cases
  • , 24,086 controls
]
—Europeannon-white British ancestryUKB—
PSS004479——
[
  • 172 cases
  • , 7,659 controls
]
—South Asian—UKB—
PSS004480——
[
  • 2,219 cases
  • , 65,206 controls
]
—Europeanwhite British ancestryUKBTesting cohort (heldout set)
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