| Predicted Trait | |
| Reported Trait | Mean FA in posterior thalamic radiation on FA skeleton (R) |
| Mapped Trait(s) | |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25084 |
| Score Construction | |
| PGS Name | GBE_INI25084 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 1,877 |
| 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% 21,081 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 |
|---|---|---|---|---|---|---|---|---|
| — | 21,081 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 |
|---|---|---|---|---|---|---|---|---|
| PPM005585 | PSS005421| African Ancestry| 182 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in posterior thalamic radiation on FA skeleton (R) | — | — | R²: 0.1424 [0.12667, 0.15813] Incremental R2 (full-covars): -0.03601 PGS R2 (no covariates): 0.01206 [0.00679, 0.01734] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005586 | PSS005422| East Asian Ancestry| 106 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in posterior thalamic radiation on FA skeleton (R) | — | — | R²: 0.17421 [0.14154, 0.20687] Incremental R2 (full-covars): 0.01178 PGS R2 (no covariates): 0.02938 [0.01361, 0.04514] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005587 | PSS005423| European Ancestry| 1,651 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in posterior thalamic radiation on FA skeleton (R) | — | — | R²: 0.17318 [0.16463, 0.18172] Incremental R2 (full-covars): 0.00646 PGS R2 (no covariates): 0.01072 [0.00818, 0.01327] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005588 | PSS005424| South Asian Ancestry| 299 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in posterior thalamic radiation on FA skeleton (R) | — | — | R²: 0.08193 [0.07029, 0.09356] Incremental R2 (full-covars): -0.01513 PGS R2 (no covariates): 0.00106 [-0.00038, 0.0025] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005589 | PSS005425| European Ancestry| 5,120 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in posterior thalamic radiation on FA skeleton (R) | — | — | R²: 0.12387 [0.11921, 0.12852] Incremental R2 (full-covars): 0.01624 PGS R2 (no covariates): 0.01489 [0.01308, 0.01671] |
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 |
|---|---|---|---|---|---|---|---|---|
| PSS005421 | — | — | 182 individuals | — | African unspecified | — | UKB | — |
| PSS005422 | — | — | 106 individuals | — | East Asian | — | UKB | — |
| PSS005423 | — | — | 1,651 individuals | — | European | non-white British ancestry | UKB | — |
| PSS005424 | — | — | 299 individuals | — | South Asian | — | UKB | — |
| PSS005425 | — | — | 5,120 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |