| Predicted Trait | |
| Reported Trait | WA L3 in tract anterior thalamic radiation (L) |
| Mapped Trait(s) | |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25625 |
| Score Construction | |
| PGS Name | GBE_INI25625 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 200 |
| 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
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Sample Numbers
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Sample Ancestry
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Cohort(s)
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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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|---|---|---|---|---|---|---|---|---|
| — | 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
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Trait
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PGS Effect Sizes (per SD change) |
Classification Metrics
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Other Metrics
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Covariates Included in the Model
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PGS Performance: Other Relevant Information |
|---|---|---|---|---|---|---|---|---|
| PPM006285 | PSS006121| African Ancestry| 182 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: WA L3 in tract anterior thalamic radiation (L) | — | — | R²: 0.2431 [0.22496, 0.26124] Incremental R2 (full-covars): 0.00365 PGS R2 (no covariates): 0.00462 [0.00133, 0.00791] | age, sex, UKB array type, Genotype PCs | — |
| PPM006286 | PSS006122| East Asian Ancestry| 106 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: WA L3 in tract anterior thalamic radiation (L) | — | — | R²: 0.27842 [0.24234, 0.3145] Incremental R2 (full-covars): 0.01005 PGS R2 (no covariates): 0.01671 [0.00466, 0.02875] | age, sex, UKB array type, Genotype PCs | — |
| PPM006287 | PSS006123| European Ancestry| 1,651 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: WA L3 in tract anterior thalamic radiation (L) | — | — | R²: 0.2488 [0.23949, 0.25811] Incremental R2 (full-covars): 0.00462 PGS R2 (no covariates): 0.00577 [0.0039, 0.00765] | age, sex, UKB array type, Genotype PCs | — |
| PPM006288 | PSS006124| South Asian Ancestry| 299 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: WA L3 in tract anterior thalamic radiation (L) | — | — | R²: 0.13516 [0.12108, 0.14924] Incremental R2 (full-covars): -0.00016 PGS R2 (no covariates): 0.00053 [-0.00049, 0.00154] | age, sex, UKB array type, Genotype PCs | — |
| PPM006289 | PSS006125| European Ancestry| 5,120 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: WA L3 in tract anterior thalamic radiation (L) | — | — | R²: 0.2017 [0.19629, 0.20712] Incremental R2 (full-covars): 0.00642 PGS R2 (no covariates): 0.006 [0.00484, 0.00716] | 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
|
|---|---|---|---|---|---|---|---|---|
| PSS006121 | — | — | 182 individuals | — | African unspecified | — | UKB | — |
| PSS006122 | — | — | 106 individuals | — | East Asian | — | UKB | — |
| PSS006123 | — | — | 1,651 individuals | — | European | non-white British ancestry | UKB | — |
| PSS006124 | — | — | 299 individuals | — | South Asian | — | UKB | — |
| PSS006125 | — | — | 5,120 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |