| Predicted Trait | |
| Reported Trait | Mean ICVF in posterior limb of internal capsule on FA skeleton (R) |
| Mapped Trait(s) | |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25362 |
| Score Construction | |
| PGS Name | GBE_INI25362 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 1,957 |
| 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 |
|---|---|---|---|---|---|---|---|---|
| PPM005740 | PSS005576| African Ancestry| 182 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in posterior limb of internal capsule on FA skeleton (R) | — | — | R²: 0.1618 [0.14542, 0.17819] Incremental R2 (full-covars): 0.0105 PGS R2 (no covariates): 0.00746 [0.00329, 0.01163] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005741 | PSS005577| East Asian Ancestry| 106 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in posterior limb of internal capsule on FA skeleton (R) | — | — | R²: 0.04877 [0.02887, 0.06868] Incremental R2 (full-covars): -0.01018 PGS R2 (no covariates): 0.00147 [-0.00216, 0.00509] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005742 | PSS005578| European Ancestry| 1,651 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in posterior limb of internal capsule on FA skeleton (R) | — | — | R²: 0.12234 [0.11471, 0.12996] Incremental R2 (full-covars): 0.04641 PGS R2 (no covariates): 0.04549 [0.04044, 0.05055] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005743 | PSS005579| South Asian Ancestry| 299 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in posterior limb of internal capsule on FA skeleton (R) | — | — | R²: 0.0448 [0.03584, 0.05375] Incremental R2 (full-covars): 0.0214 PGS R2 (no covariates): 0.0251 [0.01826, 0.03194] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005744 | PSS005580| European Ancestry| 5,120 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in posterior limb of internal capsule on FA skeleton (R) | — | — | R²: 0.0829 [0.07891, 0.08688] Incremental R2 (full-covars): 0.04026 PGS R2 (no covariates): 0.04105 [0.03812, 0.04399] |
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 |
|---|---|---|---|---|---|---|---|---|
| PSS005576 | — | — | 182 individuals | — | African unspecified | — | UKB | — |
| PSS005577 | — | — | 106 individuals | — | East Asian | — | UKB | — |
| PSS005578 | — | — | 1,651 individuals | — | European | non-white British ancestry | UKB | — |
| PSS005579 | — | — | 299 individuals | — | South Asian | — | UKB | — |
| PSS005580 | — | — | 5,120 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |