| Predicted Trait | |
| Reported Trait | Mean FA in retrolenticular part of internal capsule on FA skeleton (L) |
| Mapped Trait(s) | |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25077 |
| Score Construction | |
| PGS Name | GBE_INI25077 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 1,164 |
| 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 |
|---|---|---|---|---|---|---|---|---|
| PPM005570 | PSS005406| African Ancestry| 182 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in retrolenticular part of internal capsule on FA skeleton (L) | — | — | R²: 0.0844 [0.07147, 0.09733] Incremental R2 (full-covars): -0.00421 PGS R2 (no covariates): 0.00041 [-0.00057, 0.0014] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005571 | PSS005407| East Asian Ancestry| 106 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in retrolenticular part of internal capsule on FA skeleton (L) | — | — | R²: 0.06938 [0.04615, 0.09261] Incremental R2 (full-covars): 0.01178 PGS R2 (no covariates): 0.01605 [0.00424, 0.02786] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005572 | PSS005408| European Ancestry| 1,651 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in retrolenticular part of internal capsule on FA skeleton (L) | — | — | R²: 0.07286 [0.06665, 0.07908] Incremental R2 (full-covars): 0.02661 PGS R2 (no covariates): 0.02982 [0.02566, 0.03399] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005573 | PSS005409| South Asian Ancestry| 299 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in retrolenticular part of internal capsule on FA skeleton (L) | — | — | R²: 0.02856 [0.02129, 0.03583] Incremental R2 (full-covars): 0.00134 PGS R2 (no covariates): 0.0072 [0.00347, 0.01093] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005574 | PSS005410| European Ancestry| 5,120 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in retrolenticular part of internal capsule on FA skeleton (L) | — | — | R²: 0.02818 [0.02572, 0.03064] Incremental R2 (full-covars): 0.00902 PGS R2 (no covariates): 0.00964 [0.00817, 0.01111] |
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 |
|---|---|---|---|---|---|---|---|---|
| PSS005406 | — | — | 182 individuals | — | African unspecified | — | UKB | — |
| PSS005407 | — | — | 106 individuals | — | East Asian | — | UKB | — |
| PSS005408 | — | — | 1,651 individuals | — | European | non-white British ancestry | UKB | — |
| PSS005409 | — | — | 299 individuals | — | South Asian | — | UKB | — |
| PSS005410 | — | — | 5,120 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |