| Predicted Trait | |
| Reported Trait | HTLV-1 gag antigen for Human T-Lymphotropic Virus 1 |
| Mapped Trait(s) | blood protein measurement (EFO_0007937) |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI23022 |
| Score Construction | |
| PGS Name | GBE_INI23022 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 66 |
| 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% 5,368 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
|
|---|---|---|---|---|---|---|---|---|
| — | 5,368 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 |
|---|---|---|---|---|---|---|---|---|
| PPM005345 | PSS005021| African Ancestry| 119 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: HTLV-1 gag antigen for Human T-Lymphotropic Virus 1 | — | — | R²: 0.18173 [0.16477, 0.19868] Incremental R2 (full-covars): 0.00586 PGS R2 (no covariates): 0.02091 [0.01403, 0.02779] | age, sex, UKB array type, Genotype PCs | — |
| PPM005346 | PSS005022| East Asian Ancestry| 41 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: HTLV-1 gag antigen for Human T-Lymphotropic Virus 1 | — | — | R²: 0.22757 [0.19265, 0.26249] Incremental R2 (full-covars): 0.01155 PGS R2 (no covariates): 0.00849 [-0.00017, 0.01714] | age, sex, UKB array type, Genotype PCs | — |
| PPM005347 | PSS005023| European Ancestry| 471 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: HTLV-1 gag antigen for Human T-Lymphotropic Virus 1 | — | — | R²: 0.08759 [0.08088, 0.0943] Incremental R2 (full-covars): 0.02612 PGS R2 (no covariates): 0.03168 [0.0274, 0.03596] | age, sex, UKB array type, Genotype PCs | — |
| PPM005348 | PSS005024| South Asian Ancestry| 164 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: HTLV-1 gag antigen for Human T-Lymphotropic Virus 1 | — | — | Incremental R2 (full-covars): 0.0038 R²: 0.22286 [0.20661, 0.2391] PGS R2 (no covariates): 0.01447 [0.00922, 0.01972] | age, sex, UKB array type, Genotype PCs | — |
| PPM005349 | PSS005025| European Ancestry| 1,275 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: HTLV-1 gag antigen for Human T-Lymphotropic Virus 1 | — | — | R²: 0.03666 [0.03387, 0.03944] Incremental R2 (full-covars): 0.01644 PGS R2 (no covariates): 0.01753 [0.01557, 0.0195] | 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
|
|---|---|---|---|---|---|---|---|---|
| PSS005021 | — | — | 119 individuals | — | African unspecified | — | UKB | — |
| PSS005022 | — | — | 41 individuals | — | East Asian | — | UKB | — |
| PSS005023 | — | — | 471 individuals | — | European | non-white British ancestry | UKB | — |
| PSS005024 | — | — | 164 individuals | — | South Asian | — | UKB | — |
| PSS005025 | — | — | 1,275 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |