| Predicted Trait | |
| Reported Trait | Volume of thalamus (R) |
| Mapped Trait(s) | |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25012 |
| Score Construction | |
| PGS Name | GBE_INI25012 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 1,792 |
| 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% 22,312 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
|
Cohort(s)
|
Phenotype Definitions & Methods
|
Age of Study Participants
|
Participant Follow-up Time
|
Additional Ancestry Description
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Additional Sample/Cohort Information
|
|---|---|---|---|---|---|---|---|---|
| — | 22,312 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 |
|---|---|---|---|---|---|---|---|---|
| PPM005405 | PSS005241| African Ancestry| 200 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Vol. of thalamus (R) | — | — | R²: 0.29788 [0.27926, 0.31651] Incremental R2 (full-covars): -0.0213 PGS R2 (no covariates): 0.00832 [0.00392, 0.01271] | age, sex, UKB array type, Genotype PCs | — |
| PPM005406 | PSS005242| East Asian Ancestry| 113 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Vol. of thalamus (R) | — | — | R²: 0.28598 [0.24979, 0.32216] Incremental R2 (full-covars): 0.00325 PGS R2 (no covariates): 0.01445 [0.00322, 0.02567] | age, sex, UKB array type, Genotype PCs | — |
| PPM005407 | PSS005243| European Ancestry| 1,739 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Vol. of thalamus (R) | — | — | R²: 0.36351 [0.35397, 0.37304] Incremental R2 (full-covars): 0.01877 PGS R2 (no covariates): 0.02416 [0.02039, 0.02793] | age, sex, UKB array type, Genotype PCs | — |
| PPM005408 | PSS005244| South Asian Ancestry| 328 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Vol. of thalamus (R) | — | — | R²: 0.40018 [0.38338, 0.41698] Incremental R2 (full-covars): 0.00859 PGS R2 (no covariates): 0.00576 [0.00242, 0.0091] | age, sex, UKB array type, Genotype PCs | — |
| PPM005409 | PSS005245| European Ancestry| 5,443 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Vol. of thalamus (R) | — | — | R²: 0.30158 [0.29579, 0.30737] Incremental R2 (full-covars): 0.02093 PGS R2 (no covariates): 0.02391 [0.02163, 0.02619] | 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
|
|---|---|---|---|---|---|---|---|---|
| PSS005241 | — | — | 200 individuals | — | African unspecified | — | UKB | — |
| PSS005242 | — | — | 113 individuals | — | East Asian | — | UKB | — |
| PSS005243 | — | — | 1,739 individuals | — | European | non-white British ancestry | UKB | — |
| PSS005244 | — | — | 328 individuals | — | South Asian | — | UKB | — |
| PSS005245 | — | — | 5,443 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |