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 |
---|---|---|---|---|---|---|---|---|
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 | — |
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 | — |
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) |