| Predicted Trait | |
| Reported Trait | Mean ICVF in cingulum cingulate gyrus on FA skeleton (R) |
| Mapped Trait(s) | |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25378 |
| Score Construction | |
| PGS Name | GBE_INI25378 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 3,061 |
| 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 |
|---|---|---|---|---|---|---|---|---|
| PPM005820 | PSS005656| African Ancestry| 182 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in cingulum cingulate gyrus on FA skeleton (R) | — | — | R²: 0.12722 [0.11209, 0.14235] Incremental R2 (full-covars): -0.03034 PGS R2 (no covariates): 0.00098 [-0.00054, 0.0025] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005821 | PSS005657| East Asian Ancestry| 106 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in cingulum cingulate gyrus on FA skeleton (R) | — | — | R²: 0.12758 [0.09805, 0.15711] Incremental R2 (full-covars): 0.00778 PGS R2 (no covariates): 0.01134 [0.00136, 0.02132] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005822 | PSS005658| European Ancestry| 1,651 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in cingulum cingulate gyrus on FA skeleton (R) | — | — | R²: 0.18682 [0.17809, 0.19555] Incremental R2 (full-covars): 0.0501 PGS R2 (no covariates): 0.05161 [0.04626, 0.05696] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005823 | PSS005659| South Asian Ancestry| 299 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in cingulum cingulate gyrus on FA skeleton (R) | — | — | R²: 0.09386 [0.08157, 0.10615] Incremental R2 (full-covars): 0.0171 PGS R2 (no covariates): 0.02922 [0.02188, 0.03657] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005824 | PSS005660| European Ancestry| 5,120 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in cingulum cingulate gyrus on FA skeleton (R) | — | — | R²: 0.14294 [0.13805, 0.14783] Incremental R2 (full-covars): 0.05321 PGS R2 (no covariates): 0.05064 [0.04742, 0.05387] |
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 |
|---|---|---|---|---|---|---|---|---|
| PSS005660 | — | — | 5,120 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |
| PSS005656 | — | — | 182 individuals | — | African unspecified | — | UKB | — |
| PSS005657 | — | — | 106 individuals | — | East Asian | — | UKB | — |
| PSS005658 | — | — | 1,651 individuals | — | European | non-white British ancestry | UKB | — |
| PSS005659 | — | — | 299 individuals | — | South Asian | — | UKB | — |