| Predicted Trait | |
| Reported Trait | Mean ICVF in uncinate fasciculus on FA skeleton (R) |
| Mapped Trait(s) | |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25388 |
| Score Construction | |
| PGS Name | GBE_INI25388 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 641 |
| 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 |
|---|---|---|---|---|---|---|---|---|
| PPM005870 | PSS005706| African Ancestry| 182 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in uncinate fasciculus on FA skeleton (R) | — | — | R²: 0.08273 [0.06991, 0.09556] Incremental R2 (full-covars): -0.00301 PGS R2 (no covariates): 6e-05 [-0.00033, 0.00045] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005871 | PSS005707| East Asian Ancestry| 106 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in uncinate fasciculus on FA skeleton (R) | — | — | R²: 0.12122 [0.09223, 0.15022] Incremental R2 (full-covars): 0.03539 PGS R2 (no covariates): 0.0515 [0.03111, 0.0719] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005872 | PSS005708| European Ancestry| 1,651 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in uncinate fasciculus on FA skeleton (R) | — | — | R²: 0.09693 [0.08995, 0.10391] Incremental R2 (full-covars): 0.02174 PGS R2 (no covariates): 0.01857 [0.01524, 0.02189] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005873 | PSS005709| South Asian Ancestry| 299 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in uncinate fasciculus on FA skeleton (R) | — | — | R²: 0.04851 [0.03924, 0.05779] Incremental R2 (full-covars): 0.00598 PGS R2 (no covariates): 0.01025 [0.00582, 0.01469] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005874 | PSS005710| European Ancestry| 5,120 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in uncinate fasciculus on FA skeleton (R) | — | — | R²: 0.06938 [0.06568, 0.07308] Incremental R2 (full-covars): 0.01641 PGS R2 (no covariates): 0.01696 [0.01503, 0.01889] |
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 |
|---|---|---|---|---|---|---|---|---|
| PSS005706 | — | — | 182 individuals | — | African unspecified | — | UKB | — |
| PSS005707 | — | — | 106 individuals | — | East Asian | — | UKB | — |
| PSS005708 | — | — | 1,651 individuals | — | European | non-white British ancestry | UKB | — |
| PSS005709 | — | — | 299 individuals | — | South Asian | — | UKB | — |
| PSS005710 | — | — | 5,120 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |