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 |
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 |
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 |
---|---|---|---|---|---|---|---|---|
PPM008734 | PSS003820| 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 PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM008735 | PSS003821| 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 PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM008736 | PSS003822| 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 PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM008737 | PSS003823| 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 PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM008738 | PSS003824| 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 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 |
---|---|---|---|---|---|---|---|---|
PSS003820 | — | — | [
|
— | African unspecified | — | UKB | — |
PSS003821 | — | — | [
|
— | East Asian | — | UKB | — |
PSS003822 | — | — | [
|
— | European | non-white British ancestry | UKB | — |
PSS003823 | — | — | [
|
— | South Asian | — | UKB | — |
PSS003824 | — | — | [
|
— | European | white British ancestry | UKB | Testing cohort (heldout set) |