@article{ff2ea053f7764876bf77e131a0ff3de7,
title = "Host gene expression in nose and blood for the diagnosis of viral respiratory infection",
abstract = "Background: Recently there has been a growing interest in the potential for host transcriptomic analysis to augment the diagnosis of infectious diseases. Methods: We compared nasal and blood samples for evaluation of the host transcriptomic response in children with acute respiratory syncytial virus (RSV) infection, symptomatic non-RSV respiratory virus infection, asymptomatic rhinovirus infection, and virus-negative asymptomatic controls. We used nested leave-one-pair-out cross-validation and supervised principal components analysis to define small sets of genes whose expression patterns accurately classified subjects. We validated gene classification scores using an external data set. Results: Despite lower quality of nasal RNA, the number of genes detected by microarray in each sample type was equivalent. Nasal gene expression signal derived mainly from epithelial cells but also included a variable leukocyte contribution. The number of genes with increased expression in virus-infected children was comparable in nasal and blood samples, while nasal samples also had decreased expression of many genes associated with ciliary function and assembly. Nasal gene expression signatures were as good or better for discriminating between symptomatic, asymptomatic, and uninfected children. Conclsusions: Our results support the use of nasal samples to augment pathogen-based tests to diagnose viral respiratory infection.",
keywords = "Diagnosis, Human gene expression, Microarray, Respiratory viruses, Viral infection",
author = "Jinsheng Yu and Peterson, {Derick R.} and Baran, {Andrea M.} and Soumyaroop Bhattacharya and Wylie, {Todd N.} and Falsey, {Ann R.} and Mariani, {Thomas J.} and Storch, {Gregory A.}",
note = "Funding Information: This work was funded by the National Institute of Allergy and Infectious Diseases, Division of Microbiology and Infectious Diseases, NIH, Department of Health and Human Services, under Contract No. HHSN272201200005C. The Genome Technology Access Center is partially funded by National Cancer Institute Cancer Center Support Grant No. P30 CA91842 to the Siteman Cancer Center and by Institute of Clinical and Translational Sciences/Clinical and Translational Sciences Award Grant No. UL1TR002345 from the NCRR, a component of NIH, and NIH Roadmap for Medical Research. Funding Information: Clinical and Translational Sciences Award Grant No. UL1TR002345 from the NCRR, a component of NIH, and NIH Roadmap for Medical Research. Potential conflicts of interest. G. A. S. has been a consultant for BioFire Diagnostics (Salt Lake City, UT) and Luminex Corporation (Austin, TX). A. R. F. has received research funding from Merck Sharpe and Dohme, Janssen Pharmaceuticals Inc., Gilead Sciences Inc., Sanofi Pasteur, Pfizer, and Medimmune and has served as an unpaid advisor for Sanofi Pasteur, Pfizer, Novavax, and Gilead Sciences. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed. Funding Information: Financial support. This work was funded by the National Institute of Allergy and Infectious Diseases, Division of Microbiology and Infectious Diseases, NIH, Department of Health and Human Services, under Contract No. HHSN272201200005C. The Genome Technology Access Center is partially funded by National Cancer Institute Cancer Center Support Grant No. P30 CA91842 to the Siteman Cancer Center and by Institute of Clinical and Translational Sciences/ Publisher Copyright: {\textcopyright} The Author(s) 2018. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved.",
year = "2019",
month = mar,
day = "15",
doi = "10.1093/infdis/jiy608",
language = "English",
volume = "219",
pages = "1151--1161",
journal = "Journal of Infectious Diseases",
issn = "0022-1899",
number = "7",
}