| Predicted Trait | |
| Reported Trait | Basophil percentage |
| Mapped Trait(s) | basophil percentage of leukocytes (EFO_0007992) |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI30220 |
| Score Construction | |
| PGS Name | GBE_INI30220 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 3,205 |
| 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% 261,893 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
|
|---|---|---|---|---|---|---|---|---|
| — | 261,893 individuals | European | UKB | — | — | — | white British ancestry | Training + validation cohort (train_val) |
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 |
|---|---|---|---|---|---|---|---|---|
| PPM007055 | PSS007011| African Ancestry| 6,120 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Basophill % | — | — | R²: 0.00639 [0.00253, 0.01025] Incremental R2 (full-covars): 0.00238 PGS R2 (no covariates): 0.00249 [0.00007, 0.00491] | age, sex, UKB array type, Genotype PCs | — |
| PPM007056 | PSS007012| East Asian Ancestry| 1,654 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Basophill % | — | — | R²: 0.01523 [0.00371, 0.02675] Incremental R2 (full-covars): 0.00867 PGS R2 (no covariates): 0.00896 [0.00007, 0.01786] | age, sex, UKB array type, Genotype PCs | — |
| PPM007057 | PSS007013| European Ancestry| 24,130 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Basophill % | — | — | R²: 0.01922 [0.01584, 0.0226] Incremental R2 (full-covars): 0.01406 PGS R2 (no covariates): 0.0152 [0.01219, 0.01822] | age, sex, UKB array type, Genotype PCs | — |
| PPM007058 | PSS007014| South Asian Ancestry| 7,491 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Basophill % | — | — | R²: 0.01668 [0.01106, 0.0223] Incremental R2 (full-covars): 0.01178 PGS R2 (no covariates): 0.01253 [0.00763, 0.01742] | age, sex, UKB array type, Genotype PCs | — |
| PPM007059 | PSS007015| European Ancestry| 65,520 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Basophill % | — | — | R²: 0.01674 [0.01482, 0.01866] Incremental R2 (full-covars): 0.01485 PGS R2 (no covariates): 0.01504 [0.01321, 0.01686] | 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
|
|---|---|---|---|---|---|---|---|---|
| PSS007011 | — | — | 6,120 individuals | — | African unspecified | — | UKB | — |
| PSS007012 | — | — | 1,654 individuals | — | East Asian | — | UKB | — |
| PSS007013 | — | — | 24,130 individuals | — | European | non-white British ancestry | UKB | — |
| PSS007014 | — | — | 7,491 individuals | — | South Asian | — | UKB | — |
| PSS007015 | — | — | 65,520 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |