Yu Jiang1, Hongmei Zhang1, Shan V Andrews2, Hasan Arshad3, Susan Ewart4, John W Holloway5, M Daniele Fallin6, Kelly M Bakulski7, Wilfried Karmaus1. 1. Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA. 2. Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA. 3. Clinical and Experimental Sciences, University of Southampton, Southampton, UK. 4. Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, MI, USA. 5. Human Development and Health, University of Southampton, Southampton, UK. 6. Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA. 7. Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA.
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.
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.
Authors: S Hasan Arshad; Veeresh Patil; Frances Mitchell; Stephen Potter; Hongmei Zhang; Susan Ewart; Linda Mansfield; Carina Venter; John W Holloway; Wilfried J Karmaus Journal: Int J Epidemiol Date: 2020-08-01 Impact factor: 7.196