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
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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. 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
[
  • 110,214 cases
  • , 154,608 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
PPM008734 PSS003820|
African Ancestry|
4,524 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Ease of skin tanning (Get moderately tanned) AUROC: 0.56845 [0.54941, 0.58748] : 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 PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008735 PSS003821|
East Asian Ancestry|
1,541 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Ease of skin tanning (Get moderately tanned) AUROC: 0.56854 [0.53942, 0.59766] : 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 PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008736 PSS003822|
European Ancestry|
24,421 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Ease of skin tanning (Get moderately tanned) AUROC: 0.60803 [0.60093, 0.61513] : 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 PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008737 PSS003823|
South Asian Ancestry|
6,616 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Ease of skin tanning (Get moderately tanned) AUROC: 0.53215 [0.51774, 0.54657] : 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 PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008738 PSS003824|
European Ancestry|
66,187 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Ease of skin tanning (Get moderately tanned) AUROC: 0.59038 [0.58606, 0.5947] : 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 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
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
]
European non-white British ancestry UKB
PSS003823
[
  • 2,395 cases
  • , 4,221 controls
]
South Asian UKB
PSS003824
[
  • 27,274 cases
  • , 38,913 controls
]
European white British ancestry UKB Testing cohort (heldout set)