| Predicted Trait | |
| Reported Trait | Lymphocyte count |
| Mapped Trait(s) | lymphocyte count (EFO_0004587) |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI30120 |
| Score Construction | |
| PGS Name | GBE_INI30120 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 4,212 |
| 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% 261,890 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
|
Cohort(s)
|
Phenotype Definitions & Methods
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Age of Study Participants
|
Participant Follow-up Time
|
Additional Ancestry Description
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Additional Sample/Cohort Information
|
|---|---|---|---|---|---|---|---|---|
| — | 261,890 individuals | European | UKB | — | — | — | white British ancestry | — |
PGS Performance Metric ID (PPM) |
PGS Sample Set ID (PSS) |
Performance Source
|
Trait
|
PGS Effect Sizes (per SD change) |
Classification Metrics
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Other Metrics
|
Covariates Included in the Model
|
PGS Performance: Other Relevant Information |
|---|---|---|---|---|---|---|---|---|
| PPM008614 | PSS006966| African Ancestry| 6,120 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Lymphocyte count | — | — | R²: 0.01509 [0.00921, 0.02097] Incremental R2 (full-covars): 0.0048 PGS R2 (no covariates): 0.00655 [0.00264, 0.01046] | age, sex, UKB array type, Genotype PCs | — |
| PPM008615 | PSS006967| East Asian Ancestry| 1,654 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Lymphocyte count | — | — | R²: 0.07751 [0.05317, 0.10185] Incremental R2 (full-covars): 0.02783 PGS R2 (no covariates): 0.0308 [0.01468, 0.04692] | age, sex, UKB array type, Genotype PCs | — |
| PPM008616 | PSS006968| European Ancestry| 24,129 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Lymphocyte count | — | — | R²: 0.04047 [0.03568, 0.04526] Incremental R2 (full-covars): 0.03437 PGS R2 (no covariates): 0.03502 [0.03053, 0.0395] | age, sex, UKB array type, Genotype PCs | — |
| PPM008617 | PSS006969| South Asian Ancestry| 7,491 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Lymphocyte count | — | — | R²: 0.04041 [0.03187, 0.04896] Incremental R2 (full-covars): 0.02891 PGS R2 (no covariates): 0.02928 [0.02192, 0.03663] | age, sex, UKB array type, Genotype PCs | — |
| PPM008618 | PSS006970| European Ancestry| 65,520 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Lymphocyte count | — | — | R²: 0.02566 [0.0233, 0.02801] Incremental R2 (full-covars): 0.02051 PGS R2 (no covariates): 0.02072 [0.01859, 0.02285] | 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
|
|---|---|---|---|---|---|---|---|---|
| PSS006966 | — | — | 6,120 individuals | — | African unspecified | — | UKB | — |
| PSS006967 | — | — | 1,654 individuals | — | East Asian | — | UKB | — |
| PSS006968 | — | — | 24,129 individuals | — | European | non-white British ancestry | UKB | — |
| PSS006969 | — | — | 7,491 individuals | — | South Asian | — | UKB | — |
| PSS006970 | — | — | 65,520 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |