Polygenic Score (PGS) ID: PGS001041

Predicted Trait
Reported Trait Skin cancer
Mapped Trait(s) skin carcinoma (EFO_0009259)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/cancer1003
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_cancer1003
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,298
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
—
[
  • 18,507 cases
  • , 251,197 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
PPM007963 PSS007621|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Skin cancer — AUROC: 0.78777 [0.7126, 0.86293] R²: 0.06151
Incremental AUROC (full-covars): 0.00386
PGS R2 (no covariates): 0.00103
PGS AUROC (no covariates): 0.5229 [0.37426, 0.67153]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007964 PSS007622|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Skin cancer — AUROC: 0.83061 [0.75233, 0.9089] R²: 0.10839
Incremental AUROC (full-covars): 0.0017
PGS R2 (no covariates): 0.00376
PGS AUROC (no covariates): 0.56985 [0.36492, 0.77477]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007965 PSS007623|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Skin cancer — AUROC: 0.71667 [0.70431, 0.72902] R²: 0.09613
Incremental AUROC (full-covars): 0.03439
PGS R2 (no covariates): 0.04566
PGS AUROC (no covariates): 0.65086 [0.63722, 0.6645]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007966 PSS007624|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Skin cancer — AUROC: 0.76232 [0.67332, 0.85131] R²: 0.07091
Incremental AUROC (full-covars): -0.01012
PGS R2 (no covariates): 6e-05
PGS AUROC (no covariates): 0.49291 [0.37897, 0.60686]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007967 PSS007625|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Skin cancer — AUROC: 0.6935 [0.68584, 0.70116] R²: 0.07834
Incremental AUROC (full-covars): 0.04393
PGS R2 (no covariates): 0.03573
PGS AUROC (no covariates): 0.63289 [0.62459, 0.64118]		 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
PSS007621 — —
[
  • 12 cases
  • , 6,485 controls
]
 — African unspecified — UKB —
PSS007622 — —
[
  • 9 cases
  • , 1,695 controls
]
 — East Asian — UKB —
PSS007623 — —
[
  • 1,649 cases
  • , 23,256 controls
]
 — European non-white British ancestry UKB —
PSS007624 — —
[
  • 20 cases
  • , 7,811 controls
]
 — South Asian — UKB —
PSS007625 — —
[
  • 4,637 cases
  • , 62,788 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)