Experimental Factor Ontology (EFO) Information | |
Identifier | EFO_0007992 |
Description | A calculated measurement in which the number of basophil granulocytes is divided by the number of all white blood cells in a specified sample of peripheral venous blood, and the result presented as a ratio, fraction, quotient or percentage. A basophil is a granular leukocyte with an irregularly shaped, relatively pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm containing coarse granules of variable size that stain bluish-black when exposed to basic dyes. | Trait categories |
Hematological measurement
Inflammatory measurement
|
Synonyms |
5 synonyms
|
Mapped term | CMO:0000368 |
Polygenic Score ID & Name | PGS Publication ID (PGP) | Reported Trait | Mapped Trait(s) (Ontology) | Number of Variants |
Ancestry distribution GWAS Dev Eval |
Scoring File (FTP Link) |
---|---|---|---|---|---|---|
PGS000089 (baso_p) |
PGP000051 | Xu Y et al. Cell Genom (2022) |
Basophil percentage of white cells | basophil percentage of leukocytes | 5,248 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000089/ScoringFiles/PGS000089.txt.gz | |
PGS000164 (baso_p) |
PGP000078 | Vuckovic D et al. Cell (2020) |
Basophil percentage of white cells | basophil percentage of leukocytes | 150 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000164/ScoringFiles/PGS000164.txt.gz |
PGS001377 (GBE_INI30220) |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Basophil percentage | basophil percentage of leukocytes | 3,205 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001377/ScoringFiles/PGS001377.txt.gz |
PGS003945 (INI30220) |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Basophil percentage | basophil percentage of leukocytes | 3,472 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003945/ScoringFiles/PGS003945.txt.gz |
PGS Performance Metric ID (PPM) |
Evaluated Score |
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 |
---|---|---|---|---|---|---|---|---|---|
PPM000210 | PGS000089 (baso_p) |
PSS000154| European Ancestry| 80,906 individuals |
PGP000051 | Xu Y et al. Cell Genom (2022) |
Reported Trait: Basophil percentage of white cells | — | — | Pearson correlation coefficent (r): 0.18838 | age, sex, 10 PCs of ancestry, lifestyle factors (diet, smoking, alcohol consumption), technical covariates (the time between venepuncture and full blood cell analysis, seasonal effects, centre of sample collection, time dependent drift of equipment, systematic differences in equipment) | UKB Testing Set - these samples were held out from Score Development (regression training) but overlap with the samples used for variant selection (GWAS) |
PPM000211 | PGS000089 (baso_p) |
PSS000128| European Ancestry| 40,133 individuals |
PGP000051 | Xu Y et al. Cell Genom (2022) |
Reported Trait: Basophil percentage of white cells | — | — | Pearson correlation coefficent (r): 0.17123 | age, sex, 10 PCs of ancestry, lifestyle factors (diet, smoking, alcohol consumption), technical covariates (the time between venepuncture and full blood cell analysis, seasonal effects, centre of sample collection, time dependent drift of equipment, systematic differences in equipment) | — |
PPM000520 | PGS000164 (baso_p) |
PSS000291| European Ancestry| 39,260 individuals |
PGP000078 | Vuckovic D et al. Cell (2020) |
Reported Trait: Basophil percentage of white cells | — | — | R²: 0.02544 | sex, age, 10 genetic PCs | — |
PPM007058 | PGS001377 (GBE_INI30220) |
PSS007014| South Asian Ancestry| 7,491 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Basophill % | — | — | R²: 0.01668 [0.01106, 0.0223] Incremental R2 (full-covars): 0.01178 PGS R2 (no covariates): 0.01253 [0.00763, 0.01742] |
age, sex, UKB array type, Genotype PCs | — |
PPM007059 | PGS001377 (GBE_INI30220) |
PSS007015| European Ancestry| 65,520 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Basophill % | — | — | R²: 0.01674 [0.01482, 0.01866] Incremental R2 (full-covars): 0.01485 PGS R2 (no covariates): 0.01504 [0.01321, 0.01686] |
age, sex, UKB array type, Genotype PCs | — |
PPM007055 | PGS001377 (GBE_INI30220) |
PSS007011| African Ancestry| 6,120 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Basophill % | — | — | R²: 0.00639 [0.00253, 0.01025] Incremental R2 (full-covars): 0.00238 PGS R2 (no covariates): 0.00249 [0.00007, 0.00491] |
age, sex, UKB array type, Genotype PCs | — |
PPM007056 | PGS001377 (GBE_INI30220) |
PSS007012| East Asian Ancestry| 1,654 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Basophill % | — | — | R²: 0.01523 [0.00371, 0.02675] Incremental R2 (full-covars): 0.00867 PGS R2 (no covariates): 0.00896 [0.00007, 0.01786] |
age, sex, UKB array type, Genotype PCs | — |
PPM007057 | PGS001377 (GBE_INI30220) |
PSS007013| European Ancestry| 24,130 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Basophill % | — | — | R²: 0.01922 [0.01584, 0.0226] Incremental R2 (full-covars): 0.01406 PGS R2 (no covariates): 0.0152 [0.01219, 0.01822] |
age, sex, UKB array type, Genotype PCs | — |
PPM019044 | PGS003945 (INI30220) |
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 | PGS003945 (INI30220) |
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 | PGS003945 (INI30220) |
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 | PGS003945 (INI30220) |
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 | PGS003945 (INI30220) |
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 | — |
PSS000291 | — | — | 39,260 individuals | — | European | — | INTERVAL | — |
PSS007011 | — | — | 6,120 individuals | — | African unspecified | — | UKB | — |
PSS007012 | — | — | 1,654 individuals | — | East Asian | — | UKB | — |
PSS007014 | — | — | 7,491 individuals | — | South Asian | — | UKB | — |
PSS007015 | — | — | 65,520 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |
PSS007013 | — | — | 24,130 individuals | — | European | non-white British ancestry | UKB | — |
PSS011154 | — | — | 1,154 individuals | — | African unspecified | — | UKB | — |
PSS011168 | — | — | 7,732 individuals | — | East Asian, Other admixed ancestry | East Asian, Other admixed ancestry | UKB | — |
PSS000154 | — | — | 80,906 individuals, 46.0 % Male samples |
Mean = 57.2 years Range = [40.18, 72.91] years |
European | — | UKB | — |
PSS000128 | — | — | 40,133 individuals, 50.0 % Male samples |
Mean = 43.92 years Range = [18.0, 76.4] years |
European | — | INTERVAL | — |
PSS011139 | — | — | 65,814 individuals | — | European (white British ancestry) |
— | UKB | — |