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 |
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. 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 |
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 |
---|---|---|---|---|---|---|---|---|
— | [
|
European | UKB | — | — | — | white British ancestry | — |
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. PLoS Genet (2022) |
Reported Trait: Ease of skin tanning (Never tan, only burn) | — | AUROC: 0.72336 [0.70495, 0.74178] | R²: 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. PLoS Genet (2022) |
Reported Trait: Ease of skin tanning (Never tan, only burn) | — | AUROC: 0.60911 [0.55312, 0.6651] | R²: 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. PLoS Genet (2022) |
Reported Trait: Ease of skin tanning (Never tan, only burn) | — | AUROC: 0.7732 [0.76576, 0.78064] | R²: 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. PLoS Genet (2022) |
Reported Trait: Ease of skin tanning (Never tan, only burn) | — | AUROC: 0.54182 [0.51791, 0.56574] | R²: 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. PLoS Genet (2022) |
Reported Trait: Ease of skin tanning (Never tan, only burn) | — | AUROC: 0.74303 [0.7382, 0.74787] | R²: 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 |
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 | — | — | [
|
— | African unspecified | — | UKB | — |
PSS003925 | — | — | [
|
— | East Asian | — | UKB | — |
PSS003926 | — | — | [
|
— | European | non-white British ancestry | UKB | — |
PSS003927 | — | — | [
|
— | South Asian | — | UKB | — |
PSS003928 | — | — | [
|
— | European | white British ancestry | UKB | Testing cohort (heldout set) |