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Neutrophils

Shah A

Type
Biomarker
ID
PH347
Version ID
694
Data Sources
Valid event data range
01/01/1999 - 01/07/2016
Sex
Female, Male
Agreement Date
2012-11-23
Coding system
Read codes v2
Tags /Collections
Phenotype Library

Definition

We used information in the primary care and hospitalization records to classify the patient state on the date of the differential leukocyte count. These criteria were based on the recommendations of the eMERGE consortium (http://phenotype.mc.vanderbilt.edu/group/emerge-phenotype-wg) for studies to identify genetic determinants of the underlying stable leukocyte count. The eMERGE criteria were modified to be suitable for a cohort study, avoiding the use of clinical events after the index date in order to avoid immortal time bias. The criteria for an 'acute' patient state were: in hospital on the date of blood test, vaccination in the previous 7 days, anemia diagnosis within the previous 30 days, symptoms or diagnosis of infection within the previous 30 days, prior diagnosis of myelodysplastic syndrome, prior diagnosis of hemoglobinopathy, cancer chemotherapy or G-CSF within 6 months before index date, or the use of drugs affecting the immune system such as methotrexate or steroids within the previous 3 months.

Values with missing units frequently have zero recorded, but this is not the case if units are provided. It is theoretically possible to have a neutrophil count measured as zero (severely immunosuppressed patients, or if white cell count is below the lower limit of detection). It is up to the analyst to remove zero values if desired.

In the Clinical Practice Research Datalink (CPRD, primary care data) we extracted neutrophil measurements using the structured data component of the test CPRD table (entity type 184) combined with a list of Read terms (see below). The value was extracted from the data2 field where the units data3 field were set as 37 [109/L], 153 [109], 17 [/L]. We filtered any values less than 50 10^9/L.

Implementation


Publications

Clinical Code List

Rows: 6
Code Description CALIBER category
42J..00 Neutrophil count Neutrophil count
42J1.00 Neutrophil count normal Neutrophil count
42J2.00 Neutropenia Neutrophil count
42J3.00 Neutrophilia Neutrophil count
42J4.00 Neutrophil count abnormal Neutrophil count
42JZ.00 Neutrophil count NOS Neutrophil count

API

To Export Phenotype Details:

Format API
XML site_root/api/v1/public/phenotypes/PH347/version/694/detail/?format=xml
JSON site_root/api/v1/public/phenotypes/PH347/version/694/detail/?format=json
R Package

# Download here

library(ConceptLibraryClient)


# Connect to API

client = connect_to_API(public=TRUE)


# Get details of phenotype

details = get_phenotype_detail_by_version('PH347', '694', api_client=client)

To Export Phenotype Code List:

Format API
XML site_root/api/v1/public/phenotypes/PH347/version/694/export/codes/?format=xml
JSON site_root/api/v1/public/phenotypes/PH347/version/694/export/codes/?format=json
CSV site_root/phenotypes/PH347/version/694/export/codes/
R Package

# Download here

library(ConceptLibraryClient)


# Connect to API

client = connect_to_API(public=TRUE)


# Get codelists of phenotype

codelists = get_phenotype_code_list('PH347', '694', api_client=client)

Version History

Version
ID
Name Owner Publish date
694 Neutrophils ieuan.scanlon 2021-10-06 currently shown

Export - export all codes into a csv file/JSON/XML for the current phenotype version.

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