Trait: basophil count

Experimental Factor Ontology (EFO) Information
Identifier EFO_0005090
Description
  • quantification of basophils in the blood
  • The number of granulocytes (polymorphonuclear leukocytes) in a specified volume of blood, usually 1 cubic millimeter.
Trait category
Hematological measurement
Synonyms blood basophil count
Mapped term(s) 3 mapped terms
  • SNOMEDCT:42351005
  • CMO:0000111
  • CMO:0000034

Associated Polygenic Score(s)

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Number of Variants PGS Scoring File (FTP Link)
PGS000088 baso PGP000051
Xu Y et al. bioRxiv (2020)
Pre
Basophil count 198 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000088/ScoringFiles/PGS000088.txt.gz
PGS000163 baso PGP000078
Vuckovic D et al. medRxiv (2020)
Pre
Basophil count 185 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000163/ScoringFiles/PGS000163.txt.gz

PGS 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 ID)
Evaluated Score PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000208 PGS000088 (baso) PSS000153 PGP000051
Xu Y et al. (2020)
Pre
Reported Trait: Basophil count Pearson correlation coefficent (r): 0.2021 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 PGP000051
Xu Y et al. (2020)
Pre
Reported Trait: Basophil count Pearson correlation coefficent (r): 0.1804 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 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Basophil count : 0.0088977112141824 sex, age, 10 genetic PCs
PPM000519 PGS000163 (baso) PSS000291 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Basophil count : 0.0269108302450236 sex, age, 10 genetic PCs

Evaluated Samples

PGS Sample Set ID
(PSS ID)
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000127 39,986 individuals,
50.0 % Male samples
Mean = 43.87 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
PSS000290 2,314 individuals European
(French Canadian)
CARTaGENE
PSS000291 39,260 individuals European INTERVAL