Trait: neutrophil count

Experimental Factor Ontology (EFO) Information
Identifier EFO_0004833
Description
  • Is a quantification of neutrophils in blood.
  • The number of granulocytes (polymorphonuclear leukocytes) in a specified volume of blood, usually 1 cubic millimeter.
Trait category
Hematological measurement
Synonyms blood neutrophil count
Mapped term(s) 3 mapped terms
  • CMO:0000030
  • NCIt:C51950
  • SNOMEDCT:30630007
Child trait(s) neutrophil 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 "neutrophil 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 PGS Scoring File (FTP Link)
PGS000105
(neut)
 PGP000051 |
Xu Y et al. bioRxiv (2020)
|Pre		 Neutrophil count neutrophil count 512
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000105/ScoringFiles/PGS000105.txt.gz
PGS000106
(neut_p)
 PGP000051 |
Xu Y et al. bioRxiv (2020)
|Pre		 Neutrophil percentage of white cells neutrophil percentage of leukocytes 452
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000106/ScoringFiles/PGS000106.txt.gz
PGS000182
(neut)
 PGP000078 |
Vuckovic D et al. Cell (2020)
 Neutrophil count neutrophil count 492
-
 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000182/ScoringFiles/PGS000182.txt.gz
PGS000183
(neut_p)
 PGP000078 |
Vuckovic D et al. Cell (2020)
 Neutrophil percentage of white cells neutrophil percentage of leukocytes 437
-
 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000183/ScoringFiles/PGS000183.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
PPM000242 PGS000105
(neut)
 PSS000170|
European Ancestry|
81,358 individuals
 PGP000051 |
Xu Y et al. bioRxiv (2020)
|Pre		 Reported Trait: Neutrophil count — — Pearson correlation coefficent (r): 0.3359 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)
PPM000243 PGS000105
(neut)
 PSS000144|
European Ancestry|
39,138 individuals
 PGP000051 |
Xu Y et al. bioRxiv (2020)
|Pre		 Reported Trait: Neutrophil count — — Pearson correlation coefficent (r): 0.3159 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) —
PPM000244 PGS000106
(neut_p)
 PSS000171|
European Ancestry|
81,423 individuals
 PGP000051 |
Xu Y et al. bioRxiv (2020)
|Pre		 Reported Trait: Neutrophil percentage of white cells — — Pearson correlation coefficent (r): 0.2924 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)
PPM000245 PGS000106
(neut_p)
 PSS000145|
European Ancestry|
39,190 individuals
 PGP000051 |
Xu Y et al. bioRxiv (2020)
|Pre		 Reported Trait: Neutrophil percentage of white cells — — Pearson correlation coefficent (r): 0.2774 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) —
PPM000556 PGS000182
(neut)
 PSS000290|
European Ancestry|
2,314 individuals
 PGP000078 |
Vuckovic D et al. Cell (2020)
 Reported Trait: Neutrophil count — — R²: 0.06859 sex, age, 10 genetic PCs —
PPM000536 PGS000182
(neut)
 PSS000291|
European Ancestry|
39,260 individuals
 PGP000078 |
Vuckovic D et al. Cell (2020)
 Reported Trait: Neutrophil count — — R²: 0.08009 sex, age, 10 genetic PCs —
PPM000537 PGS000183
(neut_p)
 PSS000291|
European Ancestry|
39,260 individuals
 PGP000078 |
Vuckovic D et al. Cell (2020)
 Reported Trait: Neutrophil percentage of white cells — — R²: 0.06432 sex, age, 10 genetic 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 —
PSS000170 — — 81,358 individuals,
45.0 % Male samples
 Mean = 57.19 years
Range = [40.19, 72.44] years		 European — UKB —
PSS000171 — — 81,423 individuals,
46.0 % Male samples
 Mean = 57.25 years
Range = [39.99, 70.5] years		 European — UKB —
PSS000291 — — 39,260 individuals — European — INTERVAL —
PSS000144 — — 39,138 individuals,
50.0 % Male samples
 Mean = 43.84 years
Range = [18.0, 76.4] years		 European — INTERVAL —
PSS000145 — — 39,190 individuals,
50.0 % Male samples
 Mean = 43.83 years
Range = [18.0, 76.4] years		 European — INTERVAL —