| Predicted Trait | |
| Reported Trait | Mean ICVF in fornix cres+stria terminalis on FA skeleton (L) |
| Mapped Trait(s) | |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25383 |
| Score Construction | |
| PGS Name | GBE_INI25383 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 1,353 |
| 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 |
|---|---|---|---|---|---|---|---|---|
| PPM005845 | PSS005681| African Ancestry| 182 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in fornix cres+stria terminalis on FA skeleton (L) | — | — | R²: 0.08027 [0.0676, 0.09294] Incremental R2 (full-covars): -0.01769 PGS R2 (no covariates): 1e-05 [-0.00016, 0.00019] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005846 | PSS005682| East Asian Ancestry| 106 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in fornix cres+stria terminalis on FA skeleton (L) | — | — | R²: 0.1358 [0.10562, 0.16598] Incremental R2 (full-covars): 0.0417 PGS R2 (no covariates): 0.04443 [0.02534, 0.06351] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005847 | PSS005683| European Ancestry| 1,651 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in fornix cres+stria terminalis on FA skeleton (L) | — | — | R²: 0.10954 [0.10222, 0.11686] Incremental R2 (full-covars): 0.0356 PGS R2 (no covariates): 0.03492 [0.03045, 0.0394] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005848 | PSS005684| South Asian Ancestry| 299 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in fornix cres+stria terminalis on FA skeleton (L) | — | — | R²: 0.0442 [0.03531, 0.0531] Incremental R2 (full-covars): -0.00785 PGS R2 (no covariates): 0.0017 [-0.00012, 0.00352] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005849 | PSS005685| European Ancestry| 5,120 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in fornix cres+stria terminalis on FA skeleton (L) | — | — | R²: 0.05083 [0.0476, 0.05407] Incremental R2 (full-covars): 0.02417 PGS R2 (no covariates): 0.02416 [0.02187, 0.02645] |
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 |
|---|---|---|---|---|---|---|---|---|
| PSS005681 | — | — | 182 individuals | — | African unspecified | — | UKB | — |
| PSS005682 | — | — | 106 individuals | — | East Asian | — | UKB | — |
| PSS005683 | — | — | 1,651 individuals | — | European | non-white British ancestry | UKB | — |
| PSS005684 | — | — | 299 individuals | — | South Asian | — | UKB | — |
| PSS005685 | — | — | 5,120 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |