| Predicted Trait | |
| Reported Trait | Mean FA in posterior limb of internal capsule on FA skeleton (R) |
| Mapped Trait(s) | |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25074 |
| Score Construction | |
| PGS Name | GBE_INI25074 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 2,080 |
| 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% 21,081 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 |
|---|---|---|---|---|---|---|---|---|
| — | 21,081 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 |
|---|---|---|---|---|---|---|---|---|
| PPM005555 | PSS005391| African Ancestry| 182 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in posterior limb of internal capsule on FA skeleton (R) | — | — | R²: 0.10126 [0.08735, 0.11516] Incremental R2 (full-covars): 0.00693 PGS R2 (no covariates): 0.00898 [0.00442, 0.01355] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005556 | PSS005392| East Asian Ancestry| 106 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in posterior limb of internal capsule on FA skeleton (R) | — | — | R²: 0.11266 [0.08444, 0.14088] Incremental R2 (full-covars): 0.02462 PGS R2 (no covariates): 0.03487 [0.01779, 0.05194] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005557 | PSS005393| European Ancestry| 1,651 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in posterior limb of internal capsule on FA skeleton (R) | — | — | R²: 0.06571 [0.05977, 0.07166] Incremental R2 (full-covars): 0.02939 PGS R2 (no covariates): 0.03223 [0.02791, 0.03654] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005558 | PSS005394| South Asian Ancestry| 299 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in posterior limb of internal capsule on FA skeleton (R) | — | — | R²: 0.05258 [0.04296, 0.0622] Incremental R2 (full-covars): 0.02787 PGS R2 (no covariates): 0.03215 [0.02447, 0.03984] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005559 | PSS005395| European Ancestry| 5,120 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in posterior limb of internal capsule on FA skeleton (R) | — | — | R²: 0.03187 [0.02927, 0.03448] Incremental R2 (full-covars): 0.01857 PGS R2 (no covariates): 0.01919 [0.01714, 0.02124] |
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 |
|---|---|---|---|---|---|---|---|---|
| PSS005391 | — | — | 182 individuals | — | African unspecified | — | UKB | — |
| PSS005392 | — | — | 106 individuals | — | East Asian | — | UKB | — |
| PSS005393 | — | — | 1,651 individuals | — | European | non-white British ancestry | UKB | — |
| PSS005394 | — | — | 299 individuals | — | South Asian | — | UKB | — |
| PSS005395 | — | — | 5,120 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |