| Predicted Trait | |
| Reported Trait | Beef intake |
| Mapped Trait(s) | diet measurement (EFO_0008111) |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/QT_FC1001369 |
| Score Construction | |
| PGS Name | GBE_QT_FC1001369 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 991 |
| 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% 268,862 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
|
|---|---|---|---|---|---|---|---|---|
| — | 268,862 individuals | 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 |
|---|---|---|---|---|---|---|---|---|
| PPM008038 | PSS007556| African Ancestry| 6,271 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Beef intake | — | — | R²: 0.09702 [0.08335, 0.11069] Incremental R2 (full-covars): -0.00013 PGS R2 (no covariates): 0.00023 [-0.00051, 0.00097] | age, sex, UKB array type, Genotype PCs | — |
| PPM008039 | PSS007557| East Asian Ancestry| 1,641 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Beef intake | — | — | R²: 0.05046 [0.03024, 0.07067] Incremental R2 (full-covars): -0.00046 PGS R2 (no covariates): 0.00038 [-0.00147, 0.00224] | age, sex, UKB array type, Genotype PCs | — |
| PPM008040 | PSS007558| European Ancestry| 24,795 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Beef intake | — | — | R²: 0.03152 [0.02725, 0.03579] Incremental R2 (full-covars): 0.0011 PGS R2 (no covariates): 0.00146 [0.00051, 0.00241] | age, sex, UKB array type, Genotype PCs | — |
| PPM008041 | PSS007559| South Asian Ancestry| 7,508 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Beef intake | — | — | R²: 0.0873 [0.07536, 0.09924] Incremental R2 (full-covars): -0.0011 PGS R2 (no covariates): 0.00018 [-0.00042, 0.00078] | age, sex, UKB array type, Genotype PCs | — |
| PPM008042 | PSS007560| European Ancestry| 67,208 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Beef intake | — | — | R²: 0.02397 [0.02169, 0.02626] Incremental R2 (full-covars): 0.00158 PGS R2 (no covariates): 0.00171 [0.00109, 0.00234] | age, sex, UKB array type, Genotype PCs | — |
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
|
|---|---|---|---|---|---|---|---|---|
| PSS007556 | — | — | 6,271 individuals | — | African unspecified | — | UKB | — |
| PSS007557 | — | — | 1,641 individuals | — | East Asian | — | UKB | — |
| PSS007558 | — | — | 24,795 individuals | — | European | non-white British ancestry | UKB | — |
| PSS007559 | — | — | 7,508 individuals | — | South Asian | — | UKB | — |
| PSS007560 | — | — | 67,208 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |