| Predicted Trait | |
| Reported Trait | Mean ICVF in superior fronto-occipital fasciculus on FA skeleton (L) |
| Mapped Trait(s) | |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25387 |
| Score Construction | |
| PGS Name | GBE_INI25387 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 402 |
| 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% 21,080 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 |
|---|---|---|---|---|---|---|---|---|
| — | 21,080 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 |
|---|---|---|---|---|---|---|---|---|
| PPM005865 | PSS005701| African Ancestry| 182 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in superior fronto-occipital fasciculus on FA skeleton (L) | — | — | R²: 0.29905 [0.28042, 0.31769] Incremental R2 (full-covars): -0.01079 PGS R2 (no covariates): 0.00141 [-0.00041, 0.00324] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005866 | PSS005702| East Asian Ancestry| 106 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in superior fronto-occipital fasciculus on FA skeleton (L) | — | — | R²: 0.23959 [0.20431, 0.27486] Incremental R2 (full-covars): 0.01737 PGS R2 (no covariates): 0.01934 [0.00641, 0.03226] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005867 | PSS005703| European Ancestry| 1,651 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in superior fronto-occipital fasciculus on FA skeleton (L) | — | — | R²: 0.26457 [0.25517, 0.27396] Incremental R2 (full-covars): 0.01053 PGS R2 (no covariates): 0.00657 [0.00457, 0.00857] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005868 | PSS005704| South Asian Ancestry| 299 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in superior fronto-occipital fasciculus on FA skeleton (L) | — | — | R²: 0.21751 [0.20135, 0.23367] Incremental R2 (full-covars): -0.00421 PGS R2 (no covariates): 0.00322 [0.00072, 0.00573] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005869 | PSS005705| European Ancestry| 5,120 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in superior fronto-occipital fasciculus on FA skeleton (L) | — | — | R²: 0.20822 [0.20277, 0.21368] Incremental R2 (full-covars): 0.00598 PGS R2 (no covariates): 0.00596 [0.0048, 0.00712] |
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 |
|---|---|---|---|---|---|---|---|---|
| PSS005701 | — | — | 182 individuals | — | African unspecified | — | UKB | — |
| PSS005702 | — | — | 106 individuals | — | East Asian | — | UKB | — |
| PSS005703 | — | — | 1,651 individuals | — | European | non-white British ancestry | UKB | — |
| PSS005704 | — | — | 299 individuals | — | South Asian | — | UKB | — |
| PSS005705 | — | — | 5,120 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |