| Predicted Trait | |
| Reported Trait | Mean ICVF in anterior limb of internal capsule on FA skeleton (R) |
| Mapped Trait(s) | |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25360 |
| Score Construction | |
| PGS Name | GBE_INI25360 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 1,308 |
| 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 |
|---|---|---|---|---|---|---|---|---|
| PPM005730 | PSS005566| 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 (R) | — | — | R²: 0.1017 [0.08778, 0.11563] Incremental R2 (full-covars): -0.01301 PGS R2 (no covariates): 0.0 [-0.0001, 0.00011] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005731 | PSS005567| 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 (R) | — | — | R²: 0.22948 [0.19451, 0.26446] Incremental R2 (full-covars): 0.01029 PGS R2 (no covariates): 0.01904 [0.00621, 0.03187] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005732 | PSS005568| 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 (R) | — | — | R²: 0.20176 [0.19286, 0.21067] Incremental R2 (full-covars): 0.03564 PGS R2 (no covariates): 0.03538 [0.03087, 0.03989] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005733 | PSS005569| 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 (R) | — | — | R²: 0.09545 [0.08307, 0.10782] Incremental R2 (full-covars): 0.01386 PGS R2 (no covariates): 0.02196 [0.01554, 0.02837] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005734 | PSS005570| 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 (R) | — | — | R²: 0.13007 [0.12533, 0.13481] Incremental R2 (full-covars): 0.03186 PGS R2 (no covariates): 0.03283 [0.03019, 0.03548] |
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 |
|---|---|---|---|---|---|---|---|---|
| PSS005566 | — | — | 182 individuals | — | African unspecified | — | UKB | — |
| PSS005567 | — | — | 106 individuals | — | East Asian | — | UKB | — |
| PSS005568 | — | — | 1,651 individuals | — | European | non-white British ancestry | UKB | — |
| PSS005569 | — | — | 299 individuals | — | South Asian | — | UKB | — |
| PSS005570 | — | — | 5,120 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |