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
GWAS
Dev
Eval
 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)
 Basophil percentage 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)
 Basophil count basophil count 3,050
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001378/ScoringFiles/PGS001378.txt.gz
PGS003940
(INI30160)
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Basophil count basophil count 4,184
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003940/ScoringFiles/PGS003940.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
PGS004727
(Basophils_PRSmix_eur)
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Basophil count basophil count 6,503
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004727/ScoringFiles/PGS004727.txt.gz
PGS004728
(Basophils_PRSmix_sas)
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Basophil count basophil count 6,132,012
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004728/ScoringFiles/PGS004728.txt.gz
PGS004729
(Basophils_PRSmixPlus_eur)
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Basophil count basophil count 1,538,675
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004729/ScoringFiles/PGS004729.txt.gz
PGS004730
(Basophils_PRSmixPlus_sas)
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Basophil count basophil count 6,132,012
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004730/ScoringFiles/PGS004730.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 — — R²: 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 — — R²: 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 — — 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 —
PPM007045 PGS001378
(GBE_INI30160)
 PSS006986|
African Ancestry|
6,120 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Basophill count — — R²: 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 — — R²: 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 — — R²: 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 — — R²: 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 — — R²: 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 —
PPM019019 PGS003940
(INI30160)
 PSS011139|
European Ancestry|
65,814 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Basophil count — — R²: 0.01943 [0.01737, 0.02149]
PGS R2 (no covariates): 0.01516 [0.01334, 0.01699]
Incremental R2 (full-covars): 0.01498		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM019021 PGS003940
(INI30160)
 PSS011112|
South Asian Ancestry|
1,428 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Basophil count — — R²: 0.00683 [-0.00149, 0.01515]
PGS R2 (no covariates): 0.00551 [-0.00198, 0.013]
Incremental R2 (full-covars): 0.00504		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM019020 PGS003940
(INI30160)
 PSS011110|
European Ancestry|
2,810 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Basophil count — — R²: 0.02167 [0.01119, 0.03216]
PGS R2 (no covariates): 0.01847 [0.00876, 0.02818]
Incremental R2 (full-covars): 0.01766		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM019022 PGS003940
(INI30160)
 PSS011154|
African Ancestry|
1,154 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Basophil count — — R²: 0.00981 [-0.00119, 0.02082]
PGS R2 (no covariates): 0.00446 [-0.003, 0.01192]
Incremental R2 (full-covars): 0.00447		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM019023 PGS003940
(INI30160)
 PSS011168|
Multi-ancestry (excluding European)|
7,732 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Basophil count — — R²: 0.02131 [0.01506, 0.02757]
PGS R2 (no covariates): 0.01354 [0.00851, 0.01856]
Incremental R2 (full-covars): 0.01229		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
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) —
PPM020952 PGS004727
(Basophils_PRSmix_eur)
 PSS011482|
European Ancestry|
3,385 individuals
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Reported Trait: Basophil count — — Incremental R2 (Full model versus model with only covariates): 0.014 [0.006, 0.022] age, sex, PC1, PC2, PC3, PC4, PC5, PC6, PC7, PC8, PC9, PC10 Incremental R2 (Full model versus model with only covariates)
PPM020953 PGS004728
(Basophils_PRSmix_sas)
 PSS011463|
South Asian Ancestry|
7,096 individuals
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Reported Trait: Basophil count — — Incremental R2 (Full model versus model with only covariates): 0.018 [0.012, 0.024] age, sex, PC1, PC2, PC3, PC4, PC5, PC6, PC7, PC8, PC9, PC10 Incremental R2 (Full model versus model with only covariates)
PPM020954 PGS004729
(Basophils_PRSmixPlus_eur)
 PSS011482|
European Ancestry|
3,385 individuals
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Reported Trait: Basophil count — — Incremental R2 (Full model versus model with only covariates): 0.023 [0.013, 0.033] age, sex, PC1, PC2, PC3, PC4, PC5, PC6, PC7, PC8, PC9, PC10 Incremental R2 (Full model versus model with only covariates)
PPM020955 PGS004730
(Basophils_PRSmixPlus_sas)
 PSS011463|
South Asian Ancestry|
7,096 individuals
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Reported Trait: Basophil count — — Incremental R2 (Full model versus model with only covariates): 0.03 [0.022, 0.038] age, sex, PC1, PC2, PC3, PC4, PC5, PC6, PC7, PC8, PC9, PC10 Incremental R2 (Full model versus model with only covariates)

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
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)
PSS011154 — — 1,154 individuals — African unspecified — UKB —
PSS011463 — — 7,096 individuals — South Asian — G&H —
PSS011168 — — 7,732 individuals — East Asian, Other admixed ancestry East Asian, Other admixed ancestry UKB —
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 —
PSS011482 — — 3,385 individuals — European — AllofUs —
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 —
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 —
PSS011110 — — 2,810 individuals — European
(non-white British ancestry)		 — UKB —
PSS011112 — — 1,428 individuals — South Asian — UKB —
PSS011139 — — 65,814 individuals — European
(white British ancestry)		 — UKB —