| Predicted Trait | |
| Reported Trait | Mean ICVF in fornix cres+stria terminalis on FA skeleton (R) |
| Mapped Trait(s) | |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25382 |
| Score Construction | |
| PGS Name | GBE_INI25382 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 2,387 |
| 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 |
|---|---|---|---|---|---|---|---|---|
| PPM005840 | PSS005676| African Ancestry| 182 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in fornix cres+stria terminalis on FA skeleton (R) | — | — | R²: 0.08795 [0.0748, 0.1011] Incremental R2 (full-covars): -0.02955 PGS R2 (no covariates): 0.00072 [-0.00058, 0.00203] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005841 | PSS005677| 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 (R) | — | — | R²: 0.08695 [0.06144, 0.11246] Incremental R2 (full-covars): -0.01282 PGS R2 (no covariates): 0.00268 [-0.00221, 0.00757] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005842 | PSS005678| 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 (R) | — | — | R²: 0.08053 [0.07405, 0.08701] Incremental R2 (full-covars): 0.03184 PGS R2 (no covariates): 0.03068 [0.02646, 0.0349] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005843 | PSS005679| 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 (R) | — | — | R²: 0.03258 [0.02484, 0.04031] Incremental R2 (full-covars): -0.0099 PGS R2 (no covariates): 0.00394 [0.00117, 0.00671] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005844 | PSS005680| 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 (R) | — | — | R²: 0.04456 [0.04151, 0.0476] Incremental R2 (full-covars): 0.02451 PGS R2 (no covariates): 0.02485 [0.02253, 0.02717] |
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 |
|---|---|---|---|---|---|---|---|---|
| PSS005676 | — | — | 182 individuals | — | African unspecified | — | UKB | — |
| PSS005677 | — | — | 106 individuals | — | East Asian | — | UKB | — |
| PSS005678 | — | — | 1,651 individuals | — | European | non-white British ancestry | UKB | — |
| PSS005679 | — | — | 299 individuals | — | South Asian | — | UKB | — |
| PSS005680 | — | — | 5,120 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |