| Predicted Trait | |
| Reported Trait | Mean ICVF in superior longitudinal fasciculus on FA skeleton (R) |
| Mapped Trait(s) | |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25384 |
| Score Construction | |
| PGS Name | GBE_INI25384 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 1,750 |
| 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 |
|---|---|---|---|---|---|---|---|---|
| PPM005850 | PSS005686| African Ancestry| 182 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in superior longitudinal fasciculus on FA skeleton (R) | — | — | R²: 0.11009 [0.09574, 0.12444] Incremental R2 (full-covars): -0.01244 PGS R2 (no covariates): 0.00024 [-0.00051, 0.00099] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005851 | PSS005687| East Asian Ancestry| 106 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in superior longitudinal fasciculus on FA skeleton (R) | — | — | R²: 0.14796 [0.1169, 0.17902] Incremental R2 (full-covars): 0.04141 PGS R2 (no covariates): 0.06303 [0.04074, 0.08532] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005852 | PSS005688| European Ancestry| 1,651 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in superior longitudinal fasciculus on FA skeleton (R) | — | — | R²: 0.14625 [0.13814, 0.15436] Incremental R2 (full-covars): 0.05156 PGS R2 (no covariates): 0.05133 [0.04599, 0.05667] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005853 | PSS005689| South Asian Ancestry| 299 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in superior longitudinal fasciculus on FA skeleton (R) | — | — | R²: 0.07664 [0.06532, 0.08795] Incremental R2 (full-covars): 0.02934 PGS R2 (no covariates): 0.03361 [0.02576, 0.04145] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005854 | PSS005690| European Ancestry| 5,120 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in superior longitudinal fasciculus on FA skeleton (R) | — | — | R²: 0.10139 [0.09707, 0.10571] Incremental R2 (full-covars): 0.05428 PGS R2 (no covariates): 0.05507 [0.05173, 0.05842] |
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 |
|---|---|---|---|---|---|---|---|---|
| PSS005686 | — | — | 182 individuals | — | African unspecified | — | UKB | — |
| PSS005687 | — | — | 106 individuals | — | East Asian | — | UKB | — |
| PSS005688 | — | — | 1,651 individuals | — | European | non-white British ancestry | UKB | — |
| PSS005689 | — | — | 299 individuals | — | South Asian | — | UKB | — |
| PSS005690 | — | — | 5,120 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |