Predicted Trait | |
Reported Trait | Cereal consumption (other) |
Mapped Trait(s) | diet measurement (EFO_0008111) |
Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC50001468 |
Score Construction | |
PGS Name | GBE_BIN_FC50001468 |
Development Method | |
Name | snpnet |
Parameters | NR |
Variants | |
Original Genome Build | GRCh37 |
Number of Variants | 1,286 |
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 |
---|---|---|---|---|---|---|---|---|
PPM008053 | PSS003959| African Ancestry| 4,766 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Cereal type: Other (e.g. Cornflakes, Frosties) | — | AUROC: 0.61741 [0.59849, 0.63633] | R²: 0.04438 Incremental AUROC (full-covars): -0.00159 PGS R2 (no covariates): 0.0 PGS AUROC (no covariates): 0.49817 [0.47857, 0.51776] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM008054 | PSS003960| East Asian Ancestry| 988 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Cereal type: Other (e.g. Cornflakes, Frosties) | — | AUROC: 0.64303 [0.60109, 0.68497] | R²: 0.07487 Incremental AUROC (full-covars): -0.00286 PGS R2 (no covariates): 0.00017 PGS AUROC (no covariates): 0.5106 [0.46867, 0.55253] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM008055 | PSS003961| European Ancestry| 18,951 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Cereal type: Other (e.g. Cornflakes, Frosties) | — | AUROC: 0.60408 [0.59345, 0.6147] | R²: 0.03191 Incremental AUROC (full-covars): 0.00341 PGS R2 (no covariates): 0.00282 PGS AUROC (no covariates): 0.53042 [0.51944, 0.54141] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM008056 | PSS003962| South Asian Ancestry| 5,759 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Cereal type: Other (e.g. Cornflakes, Frosties) | — | AUROC: 0.59996 [0.58323, 0.61669] | R²: 0.03365 Incremental AUROC (full-covars): 0.00229 PGS R2 (no covariates): 0.0016 PGS AUROC (no covariates): 0.52513 [0.50821, 0.54206] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM008057 | PSS003963| European Ancestry| 56,841 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Cereal type: Other (e.g. Cornflakes, Frosties) | — | AUROC: 0.58769 [0.58186, 0.59353] | R²: 0.02328 Incremental AUROC (full-covars): 0.00502 PGS R2 (no covariates): 0.00268 PGS AUROC (no covariates): 0.52828 [0.52234, 0.53422] |
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 |
---|---|---|---|---|---|---|---|---|
PSS003959 | — | — | [
|
— | African unspecified | — | UKB | — |
PSS003960 | — | — | [
|
— | East Asian | — | UKB | — |
PSS003961 | — | — | [
|
— | European | non-white British ancestry | UKB | — |
PSS003962 | — | — | [
|
— | South Asian | — | UKB | — |
PSS003963 | — | — | [
|
— | European | white British ancestry | UKB | Testing cohort (heldout set) |