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Estimation of eosinophil cells in cord blood with references based on blood in adults via Bayesian measurement error modeling

Estimation of eosinophil cells in cord blood with references based on blood in adults via Bayesian measurement error modeling
Estimation of eosinophil cells in cord blood with references based on blood in adults via Bayesian measurement error modeling

MOTIVATION: 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.

RESULTS: 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.

AVAILABILITY: estimateCellCounts function is implemented and available in Bioconductor package minfi.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

1367-4803
Jiang, Yu
4fa0a27b-8c06-4988-832a-8f5fb3a3f1ec
Zhang, Hongmei
9f774048-54d6-4321-a252-3887b2c76db0
Andrews, Shan V
5f42ca35-9842-48fb-8bcc-d3ebf5ad724b
Arshad, Hasan
917e246d-2e60-472f-8d30-94b01ef28958
Ewart, Susan
28667421-3cf7-43d7-b1c3-ca27564938f7
Holloway, John W.
4bbd77e6-c095-445d-a36b-a50a72f6fe1a
Fallin, M. Daniele
01b22b82-bb05-46c5-9ea3-5449d336fec9
Bakulski, Kelly M.
4643d0da-a3dd-47a5-825d-920d42a6dbd7
Karmaus, Wilfried
281d0e53-6b5d-4d38-9732-3981b07cd853
Jiang, Yu
4fa0a27b-8c06-4988-832a-8f5fb3a3f1ec
Zhang, Hongmei
9f774048-54d6-4321-a252-3887b2c76db0
Andrews, Shan V
5f42ca35-9842-48fb-8bcc-d3ebf5ad724b
Arshad, Hasan
917e246d-2e60-472f-8d30-94b01ef28958
Ewart, Susan
28667421-3cf7-43d7-b1c3-ca27564938f7
Holloway, John W.
4bbd77e6-c095-445d-a36b-a50a72f6fe1a
Fallin, M. Daniele
01b22b82-bb05-46c5-9ea3-5449d336fec9
Bakulski, Kelly M.
4643d0da-a3dd-47a5-825d-920d42a6dbd7
Karmaus, Wilfried
281d0e53-6b5d-4d38-9732-3981b07cd853

Jiang, Yu, Zhang, Hongmei, Andrews, Shan V, Arshad, Hasan, Ewart, Susan, Holloway, John W., Fallin, M. Daniele, Bakulski, Kelly M. and Karmaus, Wilfried (2019) Estimation of eosinophil cells in cord blood with references based on blood in adults via Bayesian measurement error modeling. Bioinformatics. (doi:10.1093/bioinformatics/btz839).

Record type: Article

Abstract

MOTIVATION: 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.

RESULTS: 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.

AVAILABILITY: estimateCellCounts function is implemented and available in Bioconductor package minfi.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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CellProportionMeasurementErrorModelingPublished - Accepted Manuscript
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More information

Accepted/In Press date: 7 November 2019
e-pub ahead of print date: 9 November 2019

Identifiers

Local EPrints ID: 435969
URI: http://eprints.soton.ac.uk/id/eprint/435969
ISSN: 1367-4803
PURE UUID: dc5bfff3-dd6b-490b-bbd3-816276f5ff8e
ORCID for John W. Holloway: ORCID iD orcid.org/0000-0001-9998-0464

Catalogue record

Date deposited: 25 Nov 2019 17:30
Last modified: 18 Feb 2021 16:49

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