Estimation of Eosinophil Cells in Cord Blood with References Based on Blood in Adults via Bayesian Measurement Error Modeling.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
09 Nov 2019
09 Nov 2019
Historique:
received:
22
01
2019
revised:
05
11
2019
accepted:
07
11
2019
entrez:
12
11
2019
pubmed:
12
11
2019
medline:
12
11
2019
Statut:
aheadofprint
Résumé
Eosinophils are phagocytic white blood cells with a variety of roles in the immune system. In situations where actual counts are not available, high quality approximations of their cell proportions using indirect markers are critical. We develop a Bayesian measurement error model to estimate proportions of eosinophils in cord blood, using the cord blood DNA methylation profiles, based on markers of eosinophil cell heterogeneity in blood of adults. The proposed method can be directly extended to other cells across different reference panels. We demonstrate the method's estimation accuracy using B cells and show that the findings support the proposed approach. The method has been incorporated into the estimateCellCounts function in the minfi package to estimate eosinophil cells proportions in cord blood. estimateCellCounts function is implemented and available in Bioconductor package minfi. Supplementary data are available at Bioinformatics online.
Identifiants
pubmed: 31710672
pii: 5618719
doi: 10.1093/bioinformatics/btz839
pmc: PMC10251766
pii:
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : NIOSH CDC HHS
ID : T42 OH008455
Pays : United States
Organisme : NICHD NIH HHS
ID : R03 HD092776
Pays : United States
Organisme : NIMHD NIH HHS
ID : R01 MD013299
Pays : United States
Organisme : NIEHS NIH HHS
ID : R01 ES025574
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI121226
Pays : United States
Organisme : NIEHS NIH HHS
ID : R01 ES025531
Pays : United States
Organisme : NIA NIH HHS
ID : R01 AG055406
Pays : United States
Organisme : NIEHS NIH HHS
ID : P30 ES017885
Pays : United States
Organisme : NIEHS NIH HHS
ID : R24 ES028533
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL132321
Pays : United States
Informations de copyright
© The Author(s) (2019). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
Références
Methods Mol Biol. 2014;1178:81-92
pubmed: 24986609
Bioinformatics. 2014 May 15;30(10):1363-9
pubmed: 24478339
Clin Exp Immunol. 2016 Jan;183(1):57-64
pubmed: 26291602
Curr Environ Health Rep. 2015 Jun;2(2):145-54
pubmed: 26231364
Clin Immunol. 2014 May-Jun;152(1-2):68-76
pubmed: 24607604