| Predicted Trait | |
| Reported Trait | Mean FA in tapetum on FA skeleton (R) |
| Mapped Trait(s) | |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25102 |
| Score Construction | |
| PGS Name | GBE_INI25102 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 1,948 |
| 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
|
Sample Numbers
|
Sample Ancestry
|
Cohort(s)
|
Phenotype Definitions & Methods
|
Age of Study Participants
|
Participant Follow-up Time
|
Additional Ancestry Description
|
Additional Sample/Cohort Information
|
|---|---|---|---|---|---|---|---|---|
| — | 21,081 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 |
|---|---|---|---|---|---|---|---|---|
| PPM005660 | PSS005496| African Ancestry| 182 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Mean FA in tapetum on FA skeleton (R) | — | — | R²: 0.10141 [0.08751, 0.11532] Incremental R2 (full-covars): -0.01563 PGS R2 (no covariates): 0.00142 [-0.00041, 0.00325] | age, sex, UKB array type, Genotype PCs | — |
| PPM005661 | PSS005497| East Asian Ancestry| 106 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Mean FA in tapetum on FA skeleton (R) | — | — | R²: 0.15212 [0.12079, 0.18346] Incremental R2 (full-covars): -0.0191 PGS R2 (no covariates): 0.0007 [-0.0018, 0.0032] | age, sex, UKB array type, Genotype PCs | — |
| PPM005662 | PSS005498| European Ancestry| 1,651 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Mean FA in tapetum on FA skeleton (R) | — | — | R²: 0.11162 [0.10425, 0.11899] Incremental R2 (full-covars): 0.01157 PGS R2 (no covariates): 0.01191 [0.00924, 0.01459] | age, sex, UKB array type, Genotype PCs | — |
| PPM005663 | PSS005499| South Asian Ancestry| 299 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Mean FA in tapetum on FA skeleton (R) | — | — | R²: 0.11679 [0.10343, 0.13016] Incremental R2 (full-covars): 0.01156 PGS R2 (no covariates): 0.02313 [0.01655, 0.02971] | age, sex, UKB array type, Genotype PCs | — |
| PPM005664 | PSS005500| European Ancestry| 5,120 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Mean FA in tapetum on FA skeleton (R) | — | — | R²: 0.10139 [0.09707, 0.10571] Incremental R2 (full-covars): 0.02101 PGS R2 (no covariates): 0.02025 [0.01815, 0.02236] | 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
|
|---|---|---|---|---|---|---|---|---|
| PSS005496 | — | — | 182 individuals | — | African unspecified | — | UKB | — |
| PSS005497 | — | — | 106 individuals | — | East Asian | — | UKB | — |
| PSS005498 | — | — | 1,651 individuals | — | European | non-white British ancestry | UKB | — |
| PSS005499 | — | — | 299 individuals | — | South Asian | — | UKB | — |
| PSS005500 | — | — | 5,120 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |