| Predicted Trait | |
| Reported Trait | Mean FA in anterior limb of internal capsule on FA skeleton (R) |
| Mapped Trait(s) | |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25072 |
| Score Construction | |
| PGS Name | GBE_INI25072 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 1,280 |
| 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 |
|---|---|---|---|---|---|---|---|---|
| PPM005545 | PSS005381| 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 (R) | — | — | R²: 0.12742 [0.11228, 0.14255] Incremental R2 (full-covars): -0.01571 PGS R2 (no covariates): 0.00174 [-0.00028, 0.00377] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005546 | PSS005382| 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 (R) | — | — | R²: 0.12824 [0.09865, 0.15782] Incremental R2 (full-covars): 0.02196 PGS R2 (no covariates): 0.02948 [0.01369, 0.04528] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005547 | PSS005383| 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 (R) | — | — | R²: 0.0813 [0.07479, 0.0878] Incremental R2 (full-covars): 0.01187 PGS R2 (no covariates): 0.01431 [0.01138, 0.01723] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005548 | PSS005384| 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 (R) | — | — | R²: 0.04851 [0.03923, 0.05778] Incremental R2 (full-covars): 0.0044 PGS R2 (no covariates): 0.00984 [0.00549, 0.01418] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005549 | PSS005385| 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 (R) | — | — | R²: 0.06616 [0.06253, 0.06979] Incremental R2 (full-covars): 0.01169 PGS R2 (no covariates): 0.01223 [0.01058, 0.01388] |
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 |
|---|---|---|---|---|---|---|---|---|
| PSS005381 | — | — | 182 individuals | — | African unspecified | — | UKB | — |
| PSS005382 | — | — | 106 individuals | — | East Asian | — | UKB | — |
| PSS005383 | — | — | 1,651 individuals | — | European | non-white British ancestry | UKB | — |
| PSS005384 | — | — | 299 individuals | — | South Asian | — | UKB | — |
| PSS005385 | — | — | 5,120 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |