| Predicted Trait | |
| Reported Trait | Mean FA in posterior thalamic radiation on FA skeleton (L) |
| Mapped Trait(s) | |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25085 |
| Score Construction | |
| PGS Name | GBE_INI25085 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 1,654 |
| 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 |
|---|---|---|---|---|---|---|---|---|
| PPM005590 | PSS005426| African Ancestry| 182 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in posterior thalamic radiation on FA skeleton (L) | — | — | R²: 0.10053 [0.08667, 0.11439] Incremental R2 (full-covars): -0.0155 PGS R2 (no covariates): 4e-05 [-0.00028, 0.00036] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005591 | PSS005427| East Asian Ancestry| 106 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in posterior thalamic radiation on FA skeleton (L) | — | — | R²: 0.15309 [0.12169, 0.18449] Incremental R2 (full-covars): 0.03689 PGS R2 (no covariates): 0.0449 [0.02572, 0.06408] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005592 | PSS005428| European Ancestry| 1,651 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in posterior thalamic radiation on FA skeleton (L) | — | — | R²: 0.16189 [0.15352, 0.17027] Incremental R2 (full-covars): 0.00494 PGS R2 (no covariates): 0.00914 [0.00679, 0.01149] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005593 | PSS005429| South Asian Ancestry| 299 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in posterior thalamic radiation on FA skeleton (L) | — | — | R²: 0.11566 [0.10234, 0.12898] Incremental R2 (full-covars): -0.00523 PGS R2 (no covariates): 0.00567 [0.00235, 0.00898] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005594 | PSS005430| European Ancestry| 5,120 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in posterior thalamic radiation on FA skeleton (L) | — | — | R²: 0.12456 [0.1199, 0.12923] Incremental R2 (full-covars): 0.01782 PGS R2 (no covariates): 0.01718 [0.01523, 0.01912] |
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 |
|---|---|---|---|---|---|---|---|---|
| PSS005426 | — | — | 182 individuals | — | African unspecified | — | UKB | — |
| PSS005427 | — | — | 106 individuals | — | East Asian | — | UKB | — |
| PSS005428 | — | — | 1,651 individuals | — | European | non-white British ancestry | UKB | — |
| PSS005429 | — | — | 299 individuals | — | South Asian | — | UKB | — |
| PSS005430 | — | — | 5,120 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |