| Predicted Trait | |
| Reported Trait | Immature reticulocyte fraction |
| Mapped Trait(s) | reticulocyte amount (OBA_0002272) |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI30280 |
| Score Construction | |
| PGS Name | GBE_INI30280 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 10,871 |
| 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% 258,164 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
|
|---|---|---|---|---|---|---|---|---|
| — | 258,164 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 |
|---|---|---|---|---|---|---|---|---|
| PPM007065 | PSS007031| African Ancestry| 5,973 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Immature reticulocyte fraction | — | — | R²: 0.03195 [0.02354, 0.04036] Incremental R2 (full-covars): 0.01989 PGS R2 (no covariates): 0.01953 [0.01287, 0.02619] | age, sex, UKB array type, Genotype PCs | — |
| PPM007066 | PSS007032| East Asian Ancestry| 1,623 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Immature reticulocyte fraction | — | — | R²: 0.04983 [0.02973, 0.06992] Incremental R2 (full-covars): 0.02998 PGS R2 (no covariates): 0.03394 [0.01708, 0.05081] | age, sex, UKB array type, Genotype PCs | — |
| PPM007067 | PSS007033| European Ancestry| 23,680 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Immature reticulocyte fraction | — | — | R²: 0.10073 [0.09364, 0.10782] Incremental R2 (full-covars): 0.08989 PGS R2 (no covariates): 0.09045 [0.08366, 0.09725] | age, sex, UKB array type, Genotype PCs | — |
| PPM007068 | PSS007034| South Asian Ancestry| 7,321 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Immature reticulocyte fraction | — | — | R²: 0.07122 [0.06025, 0.0822] Incremental R2 (full-covars): 0.05964 PGS R2 (no covariates): 0.06252 [0.05214, 0.0729] | age, sex, UKB array type, Genotype PCs | — |
| PPM007069 | PSS007035| European Ancestry| 64,524 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Immature reticulocyte fraction | — | — | R²: 0.09976 [0.09547, 0.10405] Incremental R2 (full-covars): 0.0902 PGS R2 (no covariates): 0.09063 [0.0865, 0.09477] | 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
|
|---|---|---|---|---|---|---|---|---|
| PSS007031 | — | — | 5,973 individuals | — | African unspecified | — | UKB | — |
| PSS007032 | — | — | 1,623 individuals | — | East Asian | — | UKB | — |
| PSS007033 | — | — | 23,680 individuals | — | European | non-white British ancestry | UKB | — |
| PSS007034 | — | — | 7,321 individuals | — | South Asian | — | UKB | — |
| PSS007035 | — | — | 64,524 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |