| Predicted Trait | |
| Reported Trait | Mean FA in posterior limb of internal capsule on FA skeleton (L) |
| Mapped Trait(s) | |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25075 |
| Score Construction | |
| PGS Name | GBE_INI25075 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 1,796 |
| 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 |
|---|---|---|---|---|---|---|---|---|
| PPM005560 | PSS005396| African Ancestry| 182 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in posterior limb of internal capsule on FA skeleton (L) | — | — | R²: 0.06415 [0.05263, 0.07567] Incremental R2 (full-covars): -0.01617 PGS R2 (no covariates): 0.00068 [-0.00059, 0.00195] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005561 | PSS005397| East Asian Ancestry| 106 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in posterior limb of internal capsule on FA skeleton (L) | — | — | R²: 0.18498 [0.15176, 0.2182] Incremental R2 (full-covars): 0.00291 PGS R2 (no covariates): 0.00227 [-0.00223, 0.00677] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005562 | PSS005398| European Ancestry| 1,651 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in posterior limb of internal capsule on FA skeleton (L) | — | — | R²: 0.05203 [0.04666, 0.0574] Incremental R2 (full-covars): 0.02276 PGS R2 (no covariates): 0.02486 [0.02104, 0.02868] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005563 | PSS005399| South Asian Ancestry| 299 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in posterior limb of internal capsule on FA skeleton (L) | — | — | R²: 0.05662 [0.04669, 0.06656] Incremental R2 (full-covars): 0.01575 PGS R2 (no covariates): 0.01628 [0.01072, 0.02184] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005564 | PSS005400| European Ancestry| 5,120 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean FA in posterior limb of internal capsule on FA skeleton (L) | — | — | R²: 0.02731 [0.02488, 0.02973] Incremental R2 (full-covars): 0.01782 PGS R2 (no covariates): 0.01857 [0.01655, 0.02059] |
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 |
|---|---|---|---|---|---|---|---|---|
| PSS005396 | — | — | 182 individuals | — | African unspecified | — | UKB | — |
| PSS005397 | — | — | 106 individuals | — | East Asian | — | UKB | — |
| PSS005398 | — | — | 1,651 individuals | — | European | non-white British ancestry | UKB | — |
| PSS005399 | — | — | 299 individuals | — | South Asian | — | UKB | — |
| PSS005400 | — | — | 5,120 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |