| Predicted Trait | |
| Reported Trait | Mean FA in anterior limb of internal capsule on FA skeleton (L) |
| Mapped Trait(s) | |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25073 |
| Score Construction | |
| PGS Name | GBE_INI25073 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 731 |
| 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 |
|---|---|---|---|---|---|---|---|---|
| PPM005550 | PSS005386| African Ancestry| 182 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in anterior limb of internal capsule on FA skeleton (L) | — | — | R²: 0.13016 [0.1149, 0.14541] Incremental R2 (full-covars): -0.01152 PGS R2 (no covariates): 0.00308 [0.00039, 0.00577] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005551 | PSS005387| East Asian Ancestry| 106 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in anterior limb of internal capsule on FA skeleton (L) | — | — | R²: 0.1652 [0.13305, 0.19736] Incremental R2 (full-covars): 0.00101 PGS R2 (no covariates): 0.00369 [-0.00205, 0.00942] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005552 | PSS005388| European Ancestry| 1,651 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in anterior limb of internal capsule on FA skeleton (L) | — | — | R²: 0.08964 [0.08287, 0.09641] Incremental R2 (full-covars): 0.00698 PGS R2 (no covariates): 0.00749 [0.00536, 0.00962] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005553 | PSS005389| South Asian Ancestry| 299 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in anterior limb of internal capsule on FA skeleton (L) | — | — | R²: 0.07308 [0.06198, 0.08417] Incremental R2 (full-covars): 0.00925 PGS R2 (no covariates): 0.01038 [0.00592, 0.01485] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005554 | PSS005390| European Ancestry| 5,120 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in anterior limb of internal capsule on FA skeleton (L) | — | — | R²: 0.07044 [0.06672, 0.07417] Incremental R2 (full-covars): 0.01315 PGS R2 (no covariates): 0.01414 [0.01237, 0.01591] |
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 |
|---|---|---|---|---|---|---|---|---|
| PSS005386 | — | — | 182 individuals | — | African unspecified | — | UKB | — |
| PSS005387 | — | — | 106 individuals | — | East Asian | — | UKB | — |
| PSS005388 | — | — | 1,651 individuals | — | European | non-white British ancestry | UKB | — |
| PSS005389 | — | — | 299 individuals | — | South Asian | — | UKB | — |
| PSS005390 | — | — | 5,120 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |