| Predicted Trait | |
| Reported Trait | Mean FA in superior longitudinal fasciculus on FA skeleton (R) |
| Mapped Trait(s) | |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25096 |
| Score Construction | |
| PGS Name | GBE_INI25096 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 1,463 |
| 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 |
|---|---|---|---|---|---|---|---|---|
| PPM005635 | PSS005471| African Ancestry| 182 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in superior longitudinal fasciculus on FA skeleton (R) | — | — | R²: 0.0751 [0.06278, 0.08742] Incremental R2 (full-covars): -0.03155 PGS R2 (no covariates): 0.01242 [0.00707, 0.01776] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005636 | PSS005472| East Asian Ancestry| 106 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in superior longitudinal fasciculus on FA skeleton (R) | — | — | R²: 0.11887 [0.09008, 0.14765] Incremental R2 (full-covars): 0.01456 PGS R2 (no covariates): 0.02009 [0.00693, 0.03325] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005637 | PSS005473| European Ancestry| 1,651 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in superior longitudinal fasciculus on FA skeleton (R) | — | — | R²: 0.08203 [0.07551, 0.08856] Incremental R2 (full-covars): 0.01197 PGS R2 (no covariates): 0.01503 [0.01203, 0.01803] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005638 | PSS005474| South Asian Ancestry| 299 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in superior longitudinal fasciculus on FA skeleton (R) | — | — | R²: 0.06608 [0.05545, 0.07671] Incremental R2 (full-covars): -0.00695 PGS R2 (no covariates): 0.00652 [0.00297, 0.01007] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005639 | PSS005475| European Ancestry| 5,120 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in superior longitudinal fasciculus on FA skeleton (R) | — | — | R²: 0.0524 [0.04912, 0.05567] Incremental R2 (full-covars): 0.0172 PGS R2 (no covariates): 0.01711 [0.01517, 0.01905] |
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 |
|---|---|---|---|---|---|---|---|---|
| PSS005471 | — | — | 182 individuals | — | African unspecified | — | UKB | — |
| PSS005472 | — | — | 106 individuals | — | East Asian | — | UKB | — |
| PSS005473 | — | — | 1,651 individuals | — | European | non-white British ancestry | UKB | — |
| PSS005474 | — | — | 299 individuals | — | South Asian | — | UKB | — |
| PSS005475 | — | — | 5,120 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |