Polygenic Score (PGS) ID: PGS001246

Predicted Trait
Reported Trait Ease of skin tanning (get very tanned)
Mapped Trait(s) suntan (EFO_0004279)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC10001727
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_FC10001727
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 4,130
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
[
  • 54,310 cases
  • , 210,512 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
PPM008739 PSS003706|
African Ancestry|
4,524 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Ease of skin tanning (Get very tanned) AUROC: 0.55472 [0.5369, 0.57253] : 0.00767
Incremental AUROC (full-covars): -0.09744
PGS R2 (no covariates): 0.02303
PGS AUROC (no covariates): 0.42303 [0.40544, 0.44063]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008740 PSS003707|
East Asian Ancestry|
1,541 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Ease of skin tanning (Get very tanned) AUROC: 0.57445 [0.54548, 0.60341] : 0.0252
Incremental AUROC (full-covars): 0.0116
PGS R2 (no covariates): 0.00504
PGS AUROC (no covariates): 0.53511 [0.50559, 0.56464]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008741 PSS003708|
European Ancestry|
24,421 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Ease of skin tanning (Get very tanned) AUROC: 0.74853 [0.74163, 0.75543] : 0.19694
Incremental AUROC (full-covars): 0.07826
PGS R2 (no covariates): 0.20123
PGS AUROC (no covariates): 0.75019 [0.74322, 0.75717]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008742 PSS003709|
South Asian Ancestry|
6,616 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Ease of skin tanning (Get very tanned) AUROC: 0.53071 [0.51584, 0.54558] : 0.00488
Incremental AUROC (full-covars): -0.02206
PGS R2 (no covariates): 0.00175
PGS AUROC (no covariates): 0.51457 [0.4998, 0.52934]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008743 PSS003710|
European Ancestry|
66,187 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Ease of skin tanning (Get very tanned) AUROC: 0.73548 [0.73096, 0.74] : 0.17513
Incremental AUROC (full-covars): 0.13981
PGS R2 (no covariates): 0.14977
PGS AUROC (no covariates): 0.71732 [0.71263, 0.72202]
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
PSS003708
[
  • 5,648 cases
  • , 18,773 controls
]
European non-white British ancestry UKB
PSS003709
[
  • 2,117 cases
  • , 4,499 controls
]
South Asian UKB
PSS003710
[
  • 13,602 cases
  • , 52,585 controls
]
European white British ancestry UKB Testing cohort (heldout set)
PSS003706
[
  • 1,589 cases
  • , 2,935 controls
]
African unspecified UKB
PSS003707
[
  • 605 cases
  • , 936 controls
]
East Asian UKB