| Predicted Trait | |
| Reported Trait | Mean ICVF in retrolenticular part of internal capsule on FA skeleton (R) |
| Mapped Trait(s) | |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25364 |
| Score Construction | |
| PGS Name | GBE_INI25364 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 2,113 |
| 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 |
|---|---|---|---|---|---|---|---|---|
| PPM005750 | PSS005586| African Ancestry| 182 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in retrolenticular part of internal capsule on FA skeleton (R) | — | — | R²: 0.14562 [0.12977, 0.16146] Incremental R2 (full-covars): 0.0059 PGS R2 (no covariates): 0.00703 [0.00298, 0.01108] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005751 | PSS005587| East Asian Ancestry| 106 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in retrolenticular part of internal capsule on FA skeleton (R) | — | — | R²: 0.05415 [0.03329, 0.07501] Incremental R2 (full-covars): 0.01161 PGS R2 (no covariates): 0.01682 [0.00474, 0.02891] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005752 | PSS005588| European Ancestry| 1,651 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in retrolenticular part of internal capsule on FA skeleton (R) | — | — | R²: 0.11752 [0.11001, 0.12504] Incremental R2 (full-covars): 0.06154 PGS R2 (no covariates): 0.05763 [0.05201, 0.06325] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005753 | PSS005589| South Asian Ancestry| 299 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in retrolenticular part of internal capsule on FA skeleton (R) | — | — | R²: 0.06233 [0.05197, 0.0727] Incremental R2 (full-covars): 0.01734 PGS R2 (no covariates): 0.02365 [0.017, 0.03029] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005754 | PSS005590| European Ancestry| 5,120 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in retrolenticular part of internal capsule on FA skeleton (R) | — | — | R²: 0.07454 [0.07073, 0.07836] Incremental R2 (full-covars): 0.04209 PGS R2 (no covariates): 0.04237 [0.03939, 0.04534] |
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 |
|---|---|---|---|---|---|---|---|---|
| PSS005586 | — | — | 182 individuals | — | African unspecified | — | UKB | — |
| PSS005587 | — | — | 106 individuals | — | East Asian | — | UKB | — |
| PSS005588 | — | — | 1,651 individuals | — | European | non-white British ancestry | UKB | — |
| PSS005589 | — | — | 299 individuals | — | South Asian | — | UKB | — |
| PSS005590 | — | — | 5,120 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |