Polygenic Score (PGS) ID: PGS001536

Predicted Trait
Reported Trait Vitiligo (time-to-event)
Mapped Trait(s) Vitiligo (EFO_0004208)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1188
Released in PGS Catalog: Nov. 25, 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_HC1188
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 77
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
—
[
  • 582 cases
  • , 269,122 controls
]
 European UKB — — — white British ancestry Training + validation cohort (train_val)

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
PPM005215 PSS004173|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE vitiligo — AUROC: 0.63509 [0.52563, 0.74454] R²: 0.01654
Incremental AUROC (full-covars): -0.00281
PGS R2 (no covariates): 0.0
PGS AUROC (no covariates): 0.51169 [0.39527, 0.62811]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005216 PSS004174|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE vitiligo — AUROC: 0.82774 [0.75298, 0.90249] R²: 0.08055
Incremental AUROC (full-covars): 0.01924
PGS R2 (no covariates): 0.00431
PGS AUROC (no covariates): 0.57823 [0.37976, 0.7767]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005217 PSS004175|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE vitiligo — AUROC: 0.6991 [0.61917, 0.77902] R²: 0.03993
Incremental AUROC (full-covars): 0.01341
PGS R2 (no covariates): 0.00254
PGS AUROC (no covariates): 0.55625 [0.47549, 0.63701]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005218 PSS004176|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE vitiligo — AUROC: 0.64566 [0.58746, 0.70386] R²: 0.02575
Incremental AUROC (full-covars): 0.0309
PGS R2 (no covariates): 0.01048
PGS AUROC (no covariates): 0.60302 [0.5391, 0.66694]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005219 PSS004177|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE vitiligo — AUROC: 0.63449 [0.58754, 0.68144] R²: 0.01686
Incremental AUROC (full-covars): 0.08163
PGS R2 (no covariates): 0.01621
PGS AUROC (no covariates): 0.64193 [0.59907, 0.68478]		 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
PSS004173 — —
[
  • 17 cases
  • , 6,480 controls
]
 — African unspecified — UKB —
PSS004174 — —
[
  • 6 cases
  • , 1,698 controls
]
 — East Asian — UKB —
PSS004175 — —
[
  • 45 cases
  • , 24,860 controls
]
 — European non-white British ancestry UKB —
PSS004176 — —
[
  • 71 cases
  • , 7,760 controls
]
 — South Asian — UKB —
PSS004177 — —
[
  • 131 cases
  • , 67,294 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)