Predicted Trait | |
Reported Trait | Cereal consumption (biscuit cereal) |
Mapped Trait(s) | diet measurement (EFO_0008111) |
Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC20001468 |
Score Construction | |
PGS Name | GBE_BIN_FC20001468 |
Development Method | |
Name | snpnet |
Parameters | NR |
Variants | |
Original Genome Build | GRCh37 |
Number of Variants | 146 |
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% 227,069 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 |
---|---|---|---|---|---|---|---|---|
PPM008048 | PSS003810| African Ancestry| 4,766 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Cereal type: Biscuit cereal (e.g. Weetabix) | — | AUROC: 0.53868 [0.51659, 0.56077] | PGS R2 (no covariates): 0.00013 R²: 0.00503 Incremental AUROC (full-covars): 0.00148 PGS AUROC (no covariates): 0.50487 [0.48225, 0.52748] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM008049 | PSS003811| East Asian Ancestry| 988 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Cereal type: Biscuit cereal (e.g. Weetabix) | — | AUROC: 0.56685 [0.51503, 0.61867] | R²: 0.02055 Incremental AUROC (full-covars): 0.00316 PGS R2 (no covariates): 0.00024 PGS AUROC (no covariates): 0.50224 [0.44501, 0.55946] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM008050 | PSS003812| European Ancestry| 18,951 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Cereal type: Biscuit cereal (e.g. Weetabix) | — | AUROC: 0.58711 [0.57552, 0.5987] | R²: 0.01991 Incremental AUROC (full-covars): 0.00031 PGS R2 (no covariates): 4e-05 PGS AUROC (no covariates): 0.50281 [0.49093, 0.51469] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM008051 | PSS003813| South Asian Ancestry| 5,759 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Cereal type: Biscuit cereal (e.g. Weetabix) | — | AUROC: 0.56331 [0.54576, 0.58087] | R²: 0.01354 Incremental AUROC (full-covars): -0.00093 PGS R2 (no covariates): 2e-05 PGS AUROC (no covariates): 0.49754 [0.47927, 0.5158] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM008052 | PSS003814| European Ancestry| 56,841 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Cereal type: Biscuit cereal (e.g. Weetabix) | — | AUROC: 0.55057 [0.54462, 0.55652] | R²: 0.00808 Incremental AUROC (full-covars): 0.00209 PGS R2 (no covariates): 0.00069 PGS AUROC (no covariates): 0.51496 [0.50892, 0.521] |
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 |
---|---|---|---|---|---|---|---|---|
PSS003810 | — | — | [
|
— | African unspecified | — | UKB | — |
PSS003811 | — | — | [
|
— | East Asian | — | UKB | — |
PSS003812 | — | — | [
|
— | European | non-white British ancestry | UKB | — |
PSS003813 | — | — | [
|
— | South Asian | — | UKB | — |
PSS003814 | — | — | [
|
— | European | white British ancestry | UKB | Testing cohort (heldout set) |