Trait: basophil count

Experimental Factor Ontology (EFO) Information
Identifier EFO_0005090
Description
  • The number of granulocytes (polymorphonuclear leukocytes) in a specified volume of blood, usually 1 cubic millimeter.
  • quantification of basophils in the blood
Trait categories
Hematological measurement
Inflammatory measurement
Synonym blood basophil count
Mapped terms 4 mapped terms
  • CMO:0000034
  • CMO:0000111
  • MedDRA:10049695
  • SNOMEDCT:42351005
Child trait(s) basophil percentage of leukocytes

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Note: This table shows all PGS for "basophil count" and any child terms of this trait in the EFO hierarchy by default.
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution Scoring File (FTP Link)
PGS000088
(baso)
PGP000051 |
Xu Y et al. Cell Genom (2022)
Basophil count basophil count 9,121
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000088/ScoringFiles/PGS000088.txt.gz
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
PGS000163
(baso)
PGP000078 |
Vuckovic D et al. Cell (2020)
Basophil count basophil count 185
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000163/ScoringFiles/PGS000163.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)
Basophill % basophil percentage of leukocytes 3,205
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001377/ScoringFiles/PGS001377.txt.gz
PGS001378
(GBE_INI30160)
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Basophill count basophil count 3,050
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001378/ScoringFiles/PGS001378.txt.gz

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

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
PPM000208 PGS000088
(baso)
PSS000153|
European Ancestry|
80,944 individuals
PGP000051 |
Xu Y et al. Cell Genom (2022)
Reported Trait: Basophil count Pearson correlation coefficent (r): 0.20539 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)
PPM000209 PGS000088
(baso)
PSS000127|
European Ancestry|
39,986 individuals
PGP000051 |
Xu Y et al. Cell Genom (2022)
Reported Trait: Basophil count Pearson correlation coefficent (r): 0.20489 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)
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)
PPM000546 PGS000163
(baso)
PSS000290|
European Ancestry|
2,314 individuals
PGP000078 |
Vuckovic D et al. Cell (2020)
Reported Trait: Basophil count : 0.0089 sex, age, 10 genetic PCs
PPM000519 PGS000163
(baso)
PSS000291|
European Ancestry|
39,260 individuals
PGP000078 |
Vuckovic D et al. Cell (2020)
Reported Trait: Basophil count : 0.02691 sex, age, 10 genetic PCs
PPM000520 PGS000164
(baso_p)
PSS000291|
European Ancestry|
39,260 individuals
PGP000078 |
Vuckovic D et al. Cell (2020)
Reported Trait: Basophil percentage of white cells : 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 % : 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 % : 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 % : 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 % : 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 % : 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
PPM007045 PGS001378
(GBE_INI30160)
PSS006986|
African Ancestry|
6,120 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Basophill count : 0.0091 [0.0045, 0.01369]
Incremental R2 (full-covars): 0.00051
PGS R2 (no covariates): 0.00175 [-0.00028, 0.00379]
age, sex, UKB array type, Genotype PCs
PPM007046 PGS001378
(GBE_INI30160)
PSS006987|
East Asian Ancestry|
1,654 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Basophill count : 0.01746 [0.00516, 0.02976]
Incremental R2 (full-covars): 0.00946
PGS R2 (no covariates): 0.00963 [0.00042, 0.01883]
age, sex, UKB array type, Genotype PCs
PPM007047 PGS001378
(GBE_INI30160)
PSS006988|
European Ancestry|
24,129 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Basophill count : 0.01903 [0.01567, 0.0224]
Incremental R2 (full-covars): 0.01496
PGS R2 (no covariates): 0.01602 [0.01293, 0.01911]
age, sex, UKB array type, Genotype PCs
PPM007048 PGS001378
(GBE_INI30160)
PSS006989|
South Asian Ancestry|
7,491 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Basophill count : 0.01814 [0.01228, 0.02399]
Incremental R2 (full-covars): 0.01206
PGS R2 (no covariates): 0.01266 [0.00775, 0.01758]
age, sex, UKB array type, Genotype PCs
PPM007049 PGS001378
(GBE_INI30160)
PSS006990|
European Ancestry|
65,520 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Basophill count : 0.01717 [0.01523, 0.01911]
Incremental R2 (full-covars): 0.01451
PGS R2 (no covariates): 0.01475 [0.01294, 0.01655]
age, sex, UKB array type, Genotype PCs

Evaluated Samples

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
PSS000290 2,314 individuals European
(French Canadian)
CARTaGENE
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
PSS006986 6,120 individuals African unspecified UKB
PSS006987 1,654 individuals East Asian UKB
PSS006988 24,129 individuals European non-white British ancestry UKB
PSS006989 7,491 individuals South Asian UKB
PSS006990 65,520 individuals European white British ancestry UKB Testing cohort (heldout set)
PSS000153 80,944 individuals,
46.0 % Male samples
Mean = 57.21 years
Range = [40.05, 70.91] years
European UKB
PSS000154 80,906 individuals,
46.0 % Male samples
Mean = 57.2 years
Range = [40.18, 72.91] years
European UKB
PSS000127 39,986 individuals,
50.0 % Male samples
Mean = 43.87 years
Range = [18.0, 76.4] years
European INTERVAL
PSS000128 40,133 individuals,
50.0 % Male samples
Mean = 43.92 years
Range = [18.0, 76.4] years
European INTERVAL