| Predicted Trait | |
| Reported Trait | Mean FA in fornix cres+stria terminalis on FA skeleton (R) |
| Mapped Trait(s) | |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25094 |
| Score Construction | |
| PGS Name | GBE_INI25094 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 1,174 |
| 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 |
|---|---|---|---|---|---|---|---|---|
| PPM005630 | PSS005466| African Ancestry| 182 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in fornix cres+stria terminalis on FA skeleton (R) | — | — | R²: 0.24117 [0.22306, 0.25929] Incremental R2 (full-covars): -0.00159 PGS R2 (no covariates): 0.0008 [-0.00057, 0.00218] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005631 | PSS005467| East Asian Ancestry| 106 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in fornix cres+stria terminalis on FA skeleton (R) | — | — | R²: 0.25447 [0.21883, 0.29011] Incremental R2 (full-covars): -0.01862 PGS R2 (no covariates): 0.00173 [-0.00221, 0.00567] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005632 | PSS005468| European Ancestry| 1,651 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in fornix cres+stria terminalis on FA skeleton (R) | — | — | R²: 0.24781 [0.23851, 0.25711] Incremental R2 (full-covars): 0.00784 PGS R2 (no covariates): 0.00998 [0.00752, 0.01243] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005633 | PSS005469| South Asian Ancestry| 299 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in fornix cres+stria terminalis on FA skeleton (R) | — | — | R²: 0.28903 [0.27211, 0.30595] Incremental R2 (full-covars): 0.0043 PGS R2 (no covariates): 0.00438 [0.00146, 0.0073] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005634 | PSS005470| European Ancestry| 5,120 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in fornix cres+stria terminalis on FA skeleton (R) | — | — | R²: 0.21353 [0.20805, 0.21902] Incremental R2 (full-covars): 0.00284 PGS R2 (no covariates): 0.00511 [0.00403, 0.00618] |
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 |
|---|---|---|---|---|---|---|---|---|
| PSS005468 | — | — | 1,651 individuals | — | European | non-white British ancestry | UKB | — |
| PSS005469 | — | — | 299 individuals | — | South Asian | — | UKB | — |
| PSS005470 | — | — | 5,120 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |
| PSS005466 | — | — | 182 individuals | — | African unspecified | — | UKB | — |
| PSS005467 | — | — | 106 individuals | — | East Asian | — | UKB | — |