Polygenic Score (PGS) ID: PGS000982

Predicted Trait
Reported Trait Use of sun / ultraviolet protection (never / rarely)
Mapped Trait(s) sun exposure measurement (EFO_0010729)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC10002267
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_BIN_FC10002267
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,141
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%
269,577 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
—
[
  • 23,211 cases
  • , 246,366 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
PPM007693 PSS003716|
African Ancestry|
6,273 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Use of sun/uv protection (Never/rarely) — AUROC: 0.64715 [0.63358, 0.66073] R²: 0.08512
Incremental AUROC (full-covars): -0.00513
PGS R2 (no covariates): 0.00843
PGS AUROC (no covariates): 0.53885 [0.52453, 0.55317]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007694 PSS003717|
East Asian Ancestry|
1,652 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Use of sun/uv protection (Never/rarely) — AUROC: 0.65071 [0.62093, 0.68049] R²: 0.08666
Incremental AUROC (full-covars): 0.00648
PGS R2 (no covariates): 0.00172
PGS AUROC (no covariates): 0.52165 [0.49059, 0.5527]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007695 PSS003718|
European Ancestry|
24,868 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Use of sun/uv protection (Never/rarely) — AUROC: 0.69857 [0.68892, 0.70822] R²: 0.09864
Incremental AUROC (full-covars): 0.00464
PGS R2 (no covariates): 0.01659
PGS AUROC (no covariates): 0.5824 [0.57161, 0.5932]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007696 PSS003719|
South Asian Ancestry|
7,396 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Use of sun/uv protection (Never/rarely) — AUROC: 0.61231 [0.59955, 0.62507] R²: 0.05067
Incremental AUROC (full-covars): -0.00303
PGS R2 (no covariates): 0.00035
PGS AUROC (no covariates): 0.51061 [0.49745, 0.52377]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007697 PSS003720|
European Ancestry|
67,387 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Use of sun/uv protection (Never/rarely) — AUROC: 0.6934 [0.68657, 0.70024] R²: 0.08321
Incremental AUROC (full-covars): 0.01615
PGS R2 (no covariates): 0.00982
PGS AUROC (no covariates): 0.56628 [0.55865, 0.5739]		 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
PSS003716 — —
[
  • 3,409 cases
  • , 2,864 controls
]
 — African unspecified — UKB —
PSS003717 — —
[
  • 469 cases
  • , 1,183 controls
]
 — East Asian — UKB —
PSS003718 — —
[
  • 2,951 cases
  • , 21,917 controls
]
 — European non-white British ancestry UKB —
PSS003719 — —
[
  • 3,696 cases
  • , 3,700 controls
]
 — South Asian — UKB —
PSS003720 — —
[
  • 5,808 cases
  • , 61,579 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)