Polygenic Score (PGS) ID: PGS001244

Predicted Trait
Reported Trait Ease of skin tanning (get mildly or occasionally tanned)
Mapped Trait(s) suntan (EFO_0004279)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC30001727
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_FC30001727
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 958
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%
264,822 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
—
[
  • 58,817 cases
  • , 206,005 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
PPM008729 PSS003879|
African Ancestry|
4,524 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ease of skin tanning (Get mildly or occasionally tanned) — AUROC: 0.52345 [0.50398, 0.54292] R²: 0.00289
Incremental AUROC (full-covars): -0.04291
PGS R2 (no covariates): 0.00485
PGS AUROC (no covariates): 0.46513 [0.44563, 0.48463]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008730 PSS003880|
East Asian Ancestry|
1,541 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ease of skin tanning (Get mildly or occasionally tanned) — AUROC: 0.54571 [0.50672, 0.5847] PGS R2 (no covariates): 0.00029
R²: 0.01015
Incremental AUROC (full-covars): -0.01074
PGS AUROC (no covariates): 0.50235 [0.46279, 0.54191]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008731 PSS003881|
European Ancestry|
24,421 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ease of skin tanning (Get mildly or occasionally tanned) — AUROC: 0.64487 [0.63683, 0.65291] R²: 0.06277
Incremental AUROC (full-covars): 0.03781
PGS R2 (no covariates): 0.05363
PGS AUROC (no covariates): 0.63901 [0.631, 0.64703]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008732 PSS003882|
South Asian Ancestry|
6,616 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ease of skin tanning (Get mildly or occasionally tanned) — AUROC: 0.5248 [0.50879, 0.54081] R²: 0.00212
Incremental AUROC (full-covars): -0.01511
PGS R2 (no covariates): 0.00013
PGS AUROC (no covariates): 0.50088 [0.48459, 0.51717]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008733 PSS003883|
European Ancestry|
66,187 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ease of skin tanning (Get mildly or occasionally tanned) — AUROC: 0.63688 [0.63202, 0.64174] R²: 0.05636
Incremental AUROC (full-covars): 0.0631
PGS R2 (no covariates): 0.04114
PGS AUROC (no covariates): 0.61836 [0.61342, 0.62331]		 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
PSS003879 — —
[
  • 1,037 cases
  • , 3,487 controls
]
 — African unspecified — UKB —
PSS003880 — —
[
  • 251 cases
  • , 1,290 controls
]
 — East Asian — UKB —
PSS003881 — —
[
  • 5,255 cases
  • , 19,166 controls
]
 — European non-white British ancestry UKB —
PSS003882 — —
[
  • 1,622 cases
  • , 4,994 controls
]
 — South Asian — UKB —
PSS003883 — —
[
  • 14,769 cases
  • , 51,418 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)