| Predicted Trait | |
| Reported Trait | Mean FA in tapetum on FA skeleton (L) |
| Mapped Trait(s) | |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25103 |
| Score Construction | |
| PGS Name | GBE_INI25103 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 1,202 |
| 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 |
|---|---|---|---|---|---|---|---|---|
| PPM005665 | PSS005501| African Ancestry| 182 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Mean FA in tapetum on FA skeleton (L) | — | — | R²: 0.0991 [0.08531, 0.11288] Incremental R2 (full-covars): -0.01681 PGS R2 (no covariates): 0.0001 [-0.00039, 0.0006] | age, sex, UKB array type, Genotype PCs | — |
| PPM005666 | PSS005502| East Asian Ancestry| 106 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Mean FA in tapetum on FA skeleton (L) | — | — | R²: 0.1938 [0.16016, 0.22743] Incremental R2 (full-covars): 0.00884 PGS R2 (no covariates): 0.03771 [0.02, 0.05542] | age, sex, UKB array type, Genotype PCs | — |
| PPM005667 | PSS005503| European Ancestry| 1,651 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Mean FA in tapetum on FA skeleton (L) | — | — | R²: 0.05996 [0.05424, 0.06568] Incremental R2 (full-covars): 0.00962 PGS R2 (no covariates): 0.00947 [0.00707, 0.01186] | age, sex, UKB array type, Genotype PCs | — |
| PPM005668 | PSS005504| South Asian Ancestry| 299 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Mean FA in tapetum on FA skeleton (L) | — | — | R²: 0.11853 [0.10509, 0.13197] Incremental R2 (full-covars): 0.01153 PGS R2 (no covariates): 0.0186 [0.01267, 0.02452] | age, sex, UKB array type, Genotype PCs | — |
| PPM005669 | PSS005505| European Ancestry| 5,120 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Mean FA in tapetum on FA skeleton (L) | — | — | R²: 0.04881 [0.04563, 0.05198] Incremental R2 (full-covars): 0.01602 PGS R2 (no covariates): 0.01632 [0.01442, 0.01821] | 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
|
|---|---|---|---|---|---|---|---|---|
| PSS005501 | — | — | 182 individuals | — | African unspecified | — | UKB | — |
| PSS005502 | — | — | 106 individuals | — | East Asian | — | UKB | — |
| PSS005503 | — | — | 1,651 individuals | — | European | non-white British ancestry | UKB | — |
| PSS005504 | — | — | 299 individuals | — | South Asian | — | UKB | — |
| PSS005505 | — | — | 5,120 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |