Polygenic Score (PGS) ID: PGS001247

Predicted Trait
Reported Trait Ease of skin tanning (never tan, only burn)
Mapped Trait(s) suntan (EFO_0004279)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC40001727
Released in PGS Catalog: Oct. 21, 2021
Download Score FTP directory
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Score Details

Score Construction
PGS Name GBE_BIN_FC40001727
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 3,159
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. medRxiv (2021) Preprint
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
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
[
  • 47,412 cases
  • , 217,410 controls
]
European white British ancestry UKB

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
PPM008744 PSS003924|
African Ancestry|
4,524 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Ease of skin tanning (Never tan, only burn) AUROC: 0.72336 [0.70495, 0.74178] : 0.1468
Incremental AUROC (full-covars): -0.02841
PGS R2 (no covariates): 0.03694
PGS AUROC (no covariates): 0.40146 [0.38146, 0.42147]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008745 PSS003925|
East Asian Ancestry|
1,541 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Ease of skin tanning (Never tan, only burn) AUROC: 0.60911 [0.55312, 0.6651] : 0.06219
Incremental AUROC (full-covars): -0.04068
PGS R2 (no covariates): 0.00142
PGS AUROC (no covariates): 0.46835 [0.41763, 0.51907]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008746 PSS003926|
European Ancestry|
24,421 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Ease of skin tanning (Never tan, only burn) AUROC: 0.7732 [0.76576, 0.78064] : 0.23458
Incremental AUROC (full-covars): 0.08314
PGS R2 (no covariates): 0.24179
PGS AUROC (no covariates): 0.77686 [0.76951, 0.78422]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008747 PSS003927|
South Asian Ancestry|
6,616 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Ease of skin tanning (Never tan, only burn) AUROC: 0.54182 [0.51791, 0.56574] : 0.00258
Incremental AUROC (full-covars): -0.04265
PGS R2 (no covariates): 0.00055
PGS AUROC (no covariates): 0.48795 [0.46261, 0.51329]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008748 PSS003928|
European Ancestry|
66,187 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Ease of skin tanning (Never tan, only burn) AUROC: 0.74303 [0.7382, 0.74787] : 0.18357
Incremental AUROC (full-covars): 0.17233
PGS R2 (no covariates): 0.18165
PGS AUROC (no covariates): 0.74085 [0.73597, 0.74572]
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
PSS003924
[
  • 798 cases
  • , 3,726 controls
]
African unspecified UKB
PSS003925
[
  • 128 cases
  • , 1,413 controls
]
East Asian UKB
PSS003926
[
  • 4,667 cases
  • , 19,754 controls
]
European non-white British ancestry UKB
PSS003927
[
  • 552 cases
  • , 6,064 controls
]
South Asian UKB
PSS003928
[
  • 11,988 cases
  • , 54,199 controls
]
European white British ancestry UKB Testing cohort (heldout set)