| Predicted Trait | |
| Reported Trait | Mean ICVF in posterior limb of internal capsule on FA skeleton (L) |
| Mapped Trait(s) | |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25363 |
| Score Construction | |
| PGS Name | GBE_INI25363 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 2,010 |
| 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 |
|---|---|---|---|---|---|---|---|---|
| PPM005745 | PSS005581| 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 (L) | — | — | R²: 0.13952 [0.1239, 0.15514] Incremental R2 (full-covars): 0.00594 PGS R2 (no covariates): 0.01188 [0.00665, 0.01712] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005746 | PSS005582| 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 (L) | — | — | R²: 0.15006 [0.11886, 0.18127] Incremental R2 (full-covars): -0.00402 PGS R2 (no covariates): 0.01069 [0.001, 0.02039] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005747 | PSS005583| 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 (L) | — | — | R²: 0.13201 [0.12417, 0.13984] Incremental R2 (full-covars): 0.04679 PGS R2 (no covariates): 0.04419 [0.0392, 0.04918] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005748 | PSS005584| 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 (L) | — | — | R²: 0.05612 [0.04622, 0.06602] Incremental R2 (full-covars): 0.02903 PGS R2 (no covariates): 0.03003 [0.02259, 0.03748] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005749 | PSS005585| 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 (L) | — | — | R²: 0.08175 [0.07779, 0.08572] Incremental R2 (full-covars): 0.03973 PGS R2 (no covariates): 0.04017 [0.03727, 0.04307] |
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 |
|---|---|---|---|---|---|---|---|---|
| PSS005581 | — | — | 182 individuals | — | African unspecified | — | UKB | — |
| PSS005582 | — | — | 106 individuals | — | East Asian | — | UKB | — |
| PSS005583 | — | — | 1,651 individuals | — | European | non-white British ancestry | UKB | — |
| PSS005584 | — | — | 299 individuals | — | South Asian | — | UKB | — |
| PSS005585 | — | — | 5,120 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |