Predicted Trait | |
Reported Trait | Mean ICVF in external capsule on FA skeleton (R) |
Mapped Trait(s) | |
Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25376 |
Score Construction | |
PGS Name | GBE_INI25376 |
Development Method | |
Name | snpnet |
Parameters | NR |
Variants | |
Original Genome Build | GRCh37 |
Number of Variants | 1,316 |
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 |
---|---|---|---|---|---|---|---|---|
PPM005810 | PSS005646| African Ancestry| 182 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in external capsule on FA skeleton (R) | — | — | R²: 0.15873 [0.14244, 0.17502] Incremental R2 (full-covars): 0.0182 PGS R2 (no covariates): 0.01188 [0.00664, 0.01711] |
age, sex, UKB array type, Genotype PCs | — |
PPM005811 | PSS005647| East Asian Ancestry| 106 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in external capsule on FA skeleton (R) | — | — | R²: 0.11455 [0.08615, 0.14295] Incremental R2 (full-covars): 0.00275 PGS R2 (no covariates): 0.0101 [0.00067, 0.01953] |
age, sex, UKB array type, Genotype PCs | — |
PPM005812 | PSS005648| European Ancestry| 1,651 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in external capsule on FA skeleton (R) | — | — | R²: 0.20266 [0.19375, 0.21158] Incremental R2 (full-covars): 0.02892 PGS R2 (no covariates): 0.02446 [0.02067, 0.02825] |
age, sex, UKB array type, Genotype PCs | — |
PPM005813 | PSS005649| South Asian Ancestry| 299 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in external capsule on FA skeleton (R) | — | — | R²: 0.07303 [0.06194, 0.08412] Incremental R2 (full-covars): 0.01191 PGS R2 (no covariates): 0.0131 [0.0081, 0.0181] |
age, sex, UKB array type, Genotype PCs | — |
PPM005814 | PSS005650| European Ancestry| 5,120 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Mean ICVF in external capsule on FA skeleton (R) | — | — | R²: 0.11812 [0.11354, 0.12269] Incremental R2 (full-covars): 0.01656 PGS R2 (no covariates): 0.0167 [0.01478, 0.01862] |
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 |
---|---|---|---|---|---|---|---|---|
PSS005646 | — | — | 182 individuals | — | African unspecified | — | UKB | — |
PSS005647 | — | — | 106 individuals | — | East Asian | — | UKB | — |
PSS005648 | — | — | 1,651 individuals | — | European | non-white British ancestry | UKB | — |
PSS005649 | — | — | 299 individuals | — | South Asian | — | UKB | — |
PSS005650 | — | — | 5,120 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |