Polygenic Score (PGS) ID: PGS001245

Predicted Trait
Reported Trait Ease of skin tanning (get moderately tanned)
Mapped Trait(s) suntan (EFO_0004279)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC20001727
Released in PGS Catalog: Oct. 21, 2021
Download Score FTP directory
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_FC20001727
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 2,693
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
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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
—
[
  • 110,214 cases
  • , 154,608 controls
]
EuropeanUKB———white British ancestry—
Showing 1 to 1 of 1 rows

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.

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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
PPM008734PSS003820|
African Ancestry|
4,524 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Ease of skin tanning (Get moderately tanned)—AUROC: 0.56845 [0.54941, 0.58748]R²: 0.0181
Incremental AUROC (full-covars): -0.00634
PGS R2 (no covariates): 0.00058
PGS AUROC (no covariates): 0.4935 [0.47406, 0.51294]		age, sex, UKB array type, Genotype PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM008735PSS003821|
East Asian Ancestry|
1,541 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Ease of skin tanning (Get moderately tanned)—AUROC: 0.56854 [0.53942, 0.59766]R²: 0.0235
Incremental AUROC (full-covars): -0.00697
PGS R2 (no covariates): 3e-05
PGS AUROC (no covariates): 0.50505 [0.47505, 0.53504]		age, sex, UKB array type, Genotype PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM008736PSS003822|
European Ancestry|
24,421 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Ease of skin tanning (Get moderately tanned)—AUROC: 0.60803 [0.60093, 0.61513]R²: 0.0505
Incremental AUROC (full-covars): 0.02684
PGS R2 (no covariates): 0.04554
PGS AUROC (no covariates): 0.59926 [0.59214, 0.60639]		age, sex, UKB array type, Genotype PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM008737PSS003823|
South Asian Ancestry|
6,616 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Ease of skin tanning (Get moderately tanned)—AUROC: 0.53215 [0.51774, 0.54657]R²: 0.00473
Incremental AUROC (full-covars): -0.01571
PGS R2 (no covariates): 0.00011
PGS AUROC (no covariates): 0.4952 [0.4807, 0.5097]		age, sex, UKB array type, Genotype PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM008738PSS003824|
European Ancestry|
66,187 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Ease of skin tanning (Get moderately tanned)—AUROC: 0.59038 [0.58606, 0.5947]R²: 0.03719
Incremental AUROC (full-covars): 0.0541
PGS R2 (no covariates): 0.03521
PGS AUROC (no covariates): 0.58661 [0.58228, 0.59094]		age, sex, UKB array type, Genotype PCsFull Model & PGS R2 is estimated using Nagelkerke's method
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Evaluated Samples

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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
PSS003820——
[
  • 1,138 cases
  • , 3,386 controls
]
—African unspecified—UKB—
PSS003821——
[
  • 580 cases
  • , 961 controls
]
—East Asian—UKB—
PSS003822——
[
  • 9,176 cases
  • , 15,245 controls
]
—Europeannon-white British ancestryUKB—
PSS003823——
[
  • 2,395 cases
  • , 4,221 controls
]
—South Asian—UKB—
PSS003824——
[
  • 27,274 cases
  • , 38,913 controls
]
—Europeanwhite British ancestryUKBTesting cohort (heldout set)
Showing 1 to 5 of 5 rows
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