| Predicted Trait | |
| Reported Trait | Median T2star in caudate (L) |
| Mapped Trait(s) | neuroimaging measurement (EFO_0004346) |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25028 |
| Score Construction | |
| PGS Name | GBE_INI25028 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 1,009 |
| 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% 20,228 individuals (100%) |
| PGS Evaluation | European: 40% African: 20% East Asian: 20% South Asian: 20% 5 Sample Sets |
Study Identifiers
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Sample Numbers
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Sample Ancestry
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Cohort(s)
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Phenotype Definitions & Methods
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Age of Study Participants
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Participant Follow-up Time
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Additional Ancestry Description
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Additional Sample/Cohort Information
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|---|---|---|---|---|---|---|---|---|
| — | 20,228 individuals | European | UKB | — | — | — | white British ancestry | Training + validation cohort (train_val) |
PGS Performance Metric ID (PPM) |
PGS Sample Set ID (PSS) |
Performance Source
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Trait
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PGS Effect Sizes (per SD change) |
Classification Metrics
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Other Metrics
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Covariates Included in the Model
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PGS Performance: Other Relevant Information |
|---|---|---|---|---|---|---|---|---|
| PPM005465 | PSS005301| African Ancestry| 177 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Median T2star in caudate (L) | — | — | R²: 0.18535 [0.1683, 0.2024] Incremental R2 (full-covars): -0.00024 PGS R2 (no covariates): 0.00163 [-0.00033, 0.00359] | age, sex, UKB array type, Genotype PCs | — |
| PPM005466 | PSS005302| East Asian Ancestry| 103 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Median T2star in caudate (L) | — | — | R²: 0.12277 [0.09364, 0.1519] Incremental R2 (full-covars): 0.0064 PGS R2 (no covariates): 0.01704 [0.00488, 0.0292] | age, sex, UKB array type, Genotype PCs | — |
| PPM005467 | PSS005303| European Ancestry| 1,543 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Median T2star in caudate (L) | — | — | R²: 0.0983 [0.09127, 0.10532] Incremental R2 (full-covars): 0.0566 PGS R2 (no covariates): 0.06093 [0.05518, 0.06669] | age, sex, UKB array type, Genotype PCs | — |
| PPM005468 | PSS005304| South Asian Ancestry| 293 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Median T2star in caudate (L) | — | — | R²: 0.13605 [0.12194, 0.15016] Incremental R2 (full-covars): 0.03811 PGS R2 (no covariates): 0.03132 [0.02373, 0.03891] | age, sex, UKB array type, Genotype PCs | — |
| PPM005469 | PSS005305| European Ancestry| 4,942 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Median T2star in caudate (L) | — | — | R²: 0.09505 [0.09083, 0.09926] Incremental R2 (full-covars): 0.06213 PGS R2 (no covariates): 0.06423 [0.06065, 0.06781] | 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
|
|---|---|---|---|---|---|---|---|---|
| PSS005301 | — | — | 177 individuals | — | African unspecified | — | UKB | — |
| PSS005302 | — | — | 103 individuals | — | East Asian | — | UKB | — |
| PSS005303 | — | — | 1,543 individuals | — | European | non-white British ancestry | UKB | — |
| PSS005304 | — | — | 293 individuals | — | South Asian | — | UKB | — |
| PSS005305 | — | — | 4,942 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |