Predicted Trait | |
Reported Trait | Basophil percentage |
Mapped Trait(s) | basophil percentage of leukocytes (EFO_0007992) |
Additional Trait Information | http://ipgs.mit.edu/tanigawakellis2023/INI30220 |
Score Construction | |
PGS Name | INI30220 |
Development Method | |
Name | snpnet |
Parameters | inclusive PGS |
Variants | |
Original Genome Build | GRCh37 |
Number of Variants | 3,472 |
Effect Weight Type | beta |
PGS Source | |
PGS Catalog Publication (PGP) ID | PGP000502 |
Citation (link to publication) | Tanigawa Y et al. AJHG (2023) |
Ancestry Distribution | |
Score Development/Training | |
PGS Evaluation |
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 |
---|---|---|---|---|---|---|---|---|
— | 315,527 individuals | European, South Asian, African unspecified, Other admixed ancestry | UKB | — | — | — | European, South Asian, African unspecified, Other admixed ancestry | — |
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 |
---|---|---|---|---|---|---|---|---|
PPM019044 | PSS011139| European Ancestry| 65,814 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Basophil percentage | — | — | R²: 0.01773 [0.01576, 0.01971] PGS R2 (no covariates): 0.01574 [0.01388, 0.0176] Incremental R2 (full-covars): 0.01546 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM019046 | PSS011112| South Asian Ancestry| 1,428 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Basophil percentage | — | — | R²: 0.00464 [-0.00224, 0.01152] PGS R2 (no covariates): 0.00472 [-0.00221, 0.01166] Incremental R2 (full-covars): 0.00423 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM019047 | PSS011154| African Ancestry| 1,154 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Basophil percentage | — | — | R²: 0.00436 [-0.00302, 0.01174] PGS R2 (no covariates): 0.002 [-0.00301, 0.007] Incremental R2 (full-covars): 0.00188 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM019048 | PSS011168| Multi-ancestry (excluding European)| 7,732 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Basophil percentage | — | — | R²: 0.02293 [0.01645, 0.02941] PGS R2 (no covariates): 0.01249 [0.00766, 0.01732] Incremental R2 (full-covars): 0.01169 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM019045 | PSS011110| European Ancestry| 2,810 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Basophil percentage | — | — | R²: 0.02094 [0.01063, 0.03125] PGS R2 (no covariates): 0.01757 [0.00809, 0.02705] Incremental R2 (full-covars): 0.01716 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
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 |
---|---|---|---|---|---|---|---|---|
PSS011110 | — | — | 2,810 individuals | — | European (non-white British ancestry) |
— | UKB | — |
PSS011112 | — | — | 1,428 individuals | — | South Asian | — | UKB | — |
PSS011154 | — | — | 1,154 individuals | — | African unspecified | — | UKB | — |
PSS011168 | — | — | 7,732 individuals | — | East Asian, Other admixed ancestry | East Asian, Other admixed ancestry | UKB | — |
PSS011139 | — | — | 65,814 individuals | — | European (white British ancestry) |
— | UKB | — |