| Predicted Trait | |
| Reported Trait | Volume of grey matter in Amygdala (L) |
| Mapped Trait(s) | |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25888 |
| Score Construction | |
| PGS Name | GBE_INI25888 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 115 |
| 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% 22,320 individuals (100%) |
| PGS Evaluation | European: 40% African: 20% East Asian: 20% South Asian: 20% 5 Sample Sets |
Study Identifiers
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Sample Numbers
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Sample Ancestry
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Cohort(s)
|
Phenotype Definitions & Methods
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Age of Study Participants
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Participant Follow-up Time
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Additional Ancestry Description
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Additional Sample/Cohort Information
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|---|---|---|---|---|---|---|---|---|
| — | 22,320 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
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Other Metrics
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Covariates Included in the Model
|
PGS Performance: Other Relevant Information |
|---|---|---|---|---|---|---|---|---|
| PPM006880 | PSS006726| African Ancestry| 200 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Vol. of grey matter in Amygdala (L) | — | — | R²: 0.23372 [0.21572, 0.25173] Incremental R2 (full-covars): -0.00429 PGS R2 (no covariates): 0.00136 [-0.00043, 0.00315] | age, sex, UKB array type, Genotype PCs | — |
| PPM006881 | PSS006727| East Asian Ancestry| 113 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Vol. of grey matter in Amygdala (L) | — | — | R²: 0.23906 [0.2038, 0.27431] Incremental R2 (full-covars): -0.0066 PGS R2 (no covariates): 0.00025 [-0.00124, 0.00174] | age, sex, UKB array type, Genotype PCs | — |
| PPM006882 | PSS006728| European Ancestry| 1,739 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Vol. of grey matter in Amygdala (L) | — | — | R²: 0.26999 [0.26057, 0.27941] Incremental R2 (full-covars): 0.00564 PGS R2 (no covariates): 0.00876 [0.00645, 0.01106] | age, sex, UKB array type, Genotype PCs | — |
| PPM006883 | PSS006729| South Asian Ancestry| 329 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Vol. of grey matter in Amygdala (L) | — | — | R²: 0.32251 [0.30548, 0.33955] Incremental R2 (full-covars): 0.00363 PGS R2 (no covariates): 0.00861 [0.00453, 0.01268] | age, sex, UKB array type, Genotype PCs | — |
| PPM006884 | PSS006730| European Ancestry| 5,443 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Vol. of grey matter in Amygdala (L) | — | — | R²: 0.21374 [0.20825, 0.21922] Incremental R2 (full-covars): 0.00458 PGS R2 (no covariates): 0.00876 [0.00736, 0.01016] | 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
|
|---|---|---|---|---|---|---|---|---|
| PSS006726 | — | — | 200 individuals | — | African unspecified | — | UKB | — |
| PSS006727 | — | — | 113 individuals | — | East Asian | — | UKB | — |
| PSS006728 | — | — | 1,739 individuals | — | European | non-white British ancestry | UKB | — |
| PSS006729 | — | — | 329 individuals | — | South Asian | — | UKB | — |
| PSS006730 | — | — | 5,443 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |