| Predicted Trait | |
| Reported Trait | Mean ICVF in superior longitudinal fasciculus on FA skeleton (L) |
| Mapped Trait(s) | |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25385 |
| Score Construction | |
| PGS Name | GBE_INI25385 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 1,974 |
| 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 |
|---|---|---|---|---|---|---|---|---|
| PPM005855 | PSS005691| African Ancestry| 182 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in superior longitudinal fasciculus on FA skeleton (L) | — | — | R²: 0.10983 [0.09549, 0.12417] Incremental R2 (full-covars): 0.00225 PGS R2 (no covariates): 0.00525 [0.00174, 0.00875] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005856 | PSS005692| East Asian Ancestry| 106 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in superior longitudinal fasciculus on FA skeleton (L) | — | — | R²: 0.16573 [0.13355, 0.19792] Incremental R2 (full-covars): 0.0478 PGS R2 (no covariates): 0.06379 [0.04139, 0.0862] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005857 | PSS005693| European Ancestry| 1,651 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in superior longitudinal fasciculus on FA skeleton (L) | — | — | R²: 0.16717 [0.15871, 0.17562] Incremental R2 (full-covars): 0.05272 PGS R2 (no covariates): 0.05041 [0.04511, 0.0557] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005858 | PSS005694| South Asian Ancestry| 299 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in superior longitudinal fasciculus on FA skeleton (L) | — | — | R²: 0.09514 [0.08279, 0.1075] Incremental R2 (full-covars): 0.03963 PGS R2 (no covariates): 0.04338 [0.03456, 0.0522] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005859 | PSS005695| European Ancestry| 5,120 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in superior longitudinal fasciculus on FA skeleton (L) | — | — | R²: 0.13229 [0.12753, 0.13705] Incremental R2 (full-covars): 0.05913 PGS R2 (no covariates): 0.05935 [0.05589, 0.0628] |
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 |
|---|---|---|---|---|---|---|---|---|
| PSS005692 | — | — | 106 individuals | — | East Asian | — | UKB | — |
| PSS005693 | — | — | 1,651 individuals | — | European | non-white British ancestry | UKB | — |
| PSS005694 | — | — | 299 individuals | — | South Asian | — | UKB | — |
| PSS005695 | — | — | 5,120 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |
| PSS005691 | — | — | 182 individuals | — | African unspecified | — | UKB | — |