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 |
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. 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 |
---|---|---|---|---|---|---|---|---|
PPM008739 | PSS003706| African Ancestry| 4,524 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Ease of skin tanning (Get very tanned) | — | AUROC: 0.55472 [0.5369, 0.57253] | R²: 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. PLoS Genet (2022) |
Reported Trait: Ease of skin tanning (Get very tanned) | — | AUROC: 0.57445 [0.54548, 0.60341] | R²: 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. PLoS Genet (2022) |
Reported Trait: Ease of skin tanning (Get very tanned) | — | AUROC: 0.74853 [0.74163, 0.75543] | R²: 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. PLoS Genet (2022) |
Reported Trait: Ease of skin tanning (Get very tanned) | — | AUROC: 0.53071 [0.51584, 0.54558] | R²: 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. PLoS Genet (2022) |
Reported Trait: Ease of skin tanning (Get very tanned) | — | AUROC: 0.73548 [0.73096, 0.74] | R²: 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 |
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 | — | — | [
|
— | European | non-white British ancestry | UKB | — |
PSS003709 | — | — | [
|
— | South Asian | — | UKB | — |
PSS003710 | — | — | [
|
— | European | white British ancestry | UKB | Testing cohort (heldout set) |
PSS003706 | — | — | [
|
— | African unspecified | — | UKB | — |
PSS003707 | — | — | [
|
— | East Asian | — | UKB | — |