| Predicted Trait | |
| Reported Trait | Mean ICVF in cingulum cingulate gyrus on FA skeleton (L) |
| Mapped Trait(s) | |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25379 |
| Score Construction | |
| PGS Name | GBE_INI25379 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 1,929 |
| 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 |
|---|---|---|---|---|---|---|---|---|
| PPM005825 | PSS005661| African Ancestry| 182 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in cingulum cingulate gyrus on FA skeleton (L) | — | — | R²: 0.18879 [0.17165, 0.20592] Incremental R2 (full-covars): -0.00476 PGS R2 (no covariates): 0.01188 [0.00665, 0.01712] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005826 | PSS005662| East Asian Ancestry| 106 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in cingulum cingulate gyrus on FA skeleton (L) | — | — | R²: 0.18335 [0.15021, 0.21648] Incremental R2 (full-covars): 0.08378 PGS R2 (no covariates): 0.08328 [0.05821, 0.10835] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005827 | PSS005663| European Ancestry| 1,651 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in cingulum cingulate gyrus on FA skeleton (L) | — | — | R²: 0.17097 [0.16246, 0.17949] Incremental R2 (full-covars): 0.04303 PGS R2 (no covariates): 0.04148 [0.03663, 0.04633] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005828 | PSS005664| South Asian Ancestry| 299 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in cingulum cingulate gyrus on FA skeleton (L) | — | — | R²: 0.11754 [0.10414, 0.13094] Incremental R2 (full-covars): 0.02763 PGS R2 (no covariates): 0.044 [0.03512, 0.05287] |
age, sex, UKB array type, Genotype PCs | — |
| PPM005829 | PSS005665| European Ancestry| 5,120 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in cingulum cingulate gyrus on FA skeleton (L) | — | — | R²: 0.14046 [0.13559, 0.14532] Incremental R2 (full-covars): 0.04996 PGS R2 (no covariates): 0.04859 [0.04542, 0.05175] |
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 |
|---|---|---|---|---|---|---|---|---|
| PSS005661 | — | — | 182 individuals | — | African unspecified | — | UKB | — |
| PSS005662 | — | — | 106 individuals | — | East Asian | — | UKB | — |
| PSS005663 | — | — | 1,651 individuals | — | European | non-white British ancestry | UKB | — |
| PSS005664 | — | — | 299 individuals | — | South Asian | — | UKB | — |
| PSS005665 | — | — | 5,120 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |