| Predicted Trait | |
| Reported Trait | Mean ICVF in anterior limb of internal capsule on FA skeleton (L) |
| Mapped Trait(s) | |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25361 |
| Score Construction | |
| PGS Name | GBE_INI25361 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 870 |
| 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 |
|---|---|---|---|---|---|---|---|---|
| PPM005735 | PSS005571| African Ancestry| 182 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in anterior limb of internal capsule on FA skeleton (L) | — | — | R²: 0.11773 [0.10302, 0.13244] Incremental R2 (full-covars): -0.01067 PGS R2 (no covariates): 8e-05 [-0.00036, 0.00053] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005736 | PSS005572| East Asian Ancestry| 106 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in anterior limb of internal capsule on FA skeleton (L) | — | — | R²: 0.20113 [0.16718, 0.23508] Incremental R2 (full-covars): 0.02464 PGS R2 (no covariates): 0.03755 [0.01987, 0.05522] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005737 | PSS005573| European Ancestry| 1,651 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in anterior limb of internal capsule on FA skeleton (L) | — | — | R²: 0.19495 [0.18612, 0.20377] Incremental R2 (full-covars): 0.03378 PGS R2 (no covariates): 0.03764 [0.033, 0.04228] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005738 | PSS005574| South Asian Ancestry| 299 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in anterior limb of internal capsule on FA skeleton (L) | — | — | R²: 0.08108 [0.06949, 0.09266] Incremental R2 (full-covars): 0.01498 PGS R2 (no covariates): 0.02425 [0.01752, 0.03098] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005739 | PSS005575| European Ancestry| 5,120 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in anterior limb of internal capsule on FA skeleton (L) | — | — | R²: 0.11362 [0.10911, 0.11813] Incremental R2 (full-covars): 0.02678 PGS R2 (no covariates): 0.02712 [0.0247, 0.02954] |
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 |
|---|---|---|---|---|---|---|---|---|
| PSS005571 | — | — | 182 individuals | — | African unspecified | — | UKB | — |
| PSS005572 | — | — | 106 individuals | — | East Asian | — | UKB | — |
| PSS005573 | — | — | 1,651 individuals | — | European | non-white British ancestry | UKB | — |
| PSS005574 | — | — | 299 individuals | — | South Asian | — | UKB | — |
| PSS005575 | — | — | 5,120 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |