Host gene expression classifiers diagnose acute respiratory illness etiology

Ephraim L. Tsalik; Ricardo Henao; Marshall Nichols; Thomas Burke; Emily R. Ko; Micah T. McClain; Lori L. Hudson; Anna Mazur; Debra H. Freeman; Tim Veldman; Raymond J. Langley; Eugenia B. Quackenbush; Seth W. Glickman; Charles B. Cairns; Anja K. Jaehne; Emanuel P. Rivers; Ronny M. Otero; Aimee K. Zaas; Stephen F. Kingsmore; Joseph Lucas; Vance G. Fowler; Lawrence Carin; Geoffrey S. Ginsburg; Christopher W. Woods

doi:10.1126/scitranslmed.aad6873

Research ArticleInfectious Disease

Host gene expression classifiers diagnose acute respiratory illness etiology

Ephraim L. Tsalik¹,²,³,*,
Ricardo Henao¹,⁴,*,
Marshall Nichols¹,
Thomas Burke¹,
Emily R. Ko¹,⁵,
Micah T. McClain¹,³,⁶,
Lori L. Hudson¹,
Anna Mazur¹,
Debra H. Freeman¹,³,
Tim Veldman¹,
Raymond J. Langley⁷,
Eugenia B. Quackenbush⁸,
Seth W. Glickman⁸,
Charles B. Cairns⁸,⁹,
Anja K. Jaehne¹⁰,
Emanuel P. Rivers¹⁰,
Ronny M. Otero¹⁰,
Aimee K. Zaas¹,³,
Stephen F. Kingsmore¹¹,
Joseph Lucas¹,
Vance G. Fowler Jr³,
Lawrence Carin¹,⁴,
Geoffrey S. Ginsburg¹,† and
Christopher W. Woods¹,³,⁶,†

¹Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA.
²Emergency Medicine Service, Durham Veteran’s Affairs Medical Center, Durham, NC 27705, USA.
³Division of Infectious Diseases and International Health, Department of Medicine, Duke University, Durham, NC 27710, USA.
⁴Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA.
⁵Duke Regional Hospital, Department of Medicine, Duke University, Durham, NC 27710, USA.
⁶Section for Infectious Diseases, Medicine Service, Durham Veteran’s Affairs Medical Center, Durham, NC 27705, USA.
⁷Immunology Division, Lovelace Respiratory Research Institute, Albuquerque, NM 87108, USA.
⁸Department of Emergency Medicine, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.
⁹Department of Emergency Medicine, University of Arizona Health Sciences Center, Tucson, AZ 85724, USA.
¹⁰Department of Emergency Medicine, Henry Ford Hospital, Wayne State University, Detroit, MI 48202, USA.
¹¹Rady Pediatric Genomic and Systems Medicine Institute, Rady Children’s Hospital, San Diego, CA 92123, USA.

↵†Corresponding author. E-mail: geoffrey.ginsburg{at}duke.edu (G.S.G.); chris.woods{at}duke.edu (C.W.W.)

↵* These authors contributed equally to this work.

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Science Translational Medicine 20 Jan 2016:
Vol. 8, Issue 322, pp. 322ra11
DOI: 10.1126/scitranslmed.aad6873

Ephraim L. Tsalik

1Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA.

2Emergency Medicine Service, Durham Veteran’s Affairs Medical Center, Durham, NC 27705, USA.

3Division of Infectious Diseases and International Health, Department of Medicine, Duke University, Durham, NC 27710, USA.

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Ricardo Henao

1Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA.

4Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA.

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Marshall Nichols

1Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA.

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Thomas Burke

1Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA.

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Emily R. Ko

1Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA.

5Duke Regional Hospital, Department of Medicine, Duke University, Durham, NC 27710, USA.

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Micah T. McClain

1Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA.

3Division of Infectious Diseases and International Health, Department of Medicine, Duke University, Durham, NC 27710, USA.

6Section for Infectious Diseases, Medicine Service, Durham Veteran’s Affairs Medical Center, Durham, NC 27705, USA.

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Lori L. Hudson

1Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA.

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Anna Mazur

1Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA.

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Debra H. Freeman

1Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA.

3Division of Infectious Diseases and International Health, Department of Medicine, Duke University, Durham, NC 27710, USA.

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Tim Veldman

1Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA.

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Raymond J. Langley

7Immunology Division, Lovelace Respiratory Research Institute, Albuquerque, NM 87108, USA.

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Eugenia B. Quackenbush

8Department of Emergency Medicine, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.

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Seth W. Glickman

8Department of Emergency Medicine, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.

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Charles B. Cairns

8Department of Emergency Medicine, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.

9Department of Emergency Medicine, University of Arizona Health Sciences Center, Tucson, AZ 85724, USA.

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Anja K. Jaehne

10Department of Emergency Medicine, Henry Ford Hospital, Wayne State University, Detroit, MI 48202, USA.

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Emanuel P. Rivers

10Department of Emergency Medicine, Henry Ford Hospital, Wayne State University, Detroit, MI 48202, USA.

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Ronny M. Otero

10Department of Emergency Medicine, Henry Ford Hospital, Wayne State University, Detroit, MI 48202, USA.

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Aimee K. Zaas

1Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA.

3Division of Infectious Diseases and International Health, Department of Medicine, Duke University, Durham, NC 27710, USA.

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Stephen F. Kingsmore

11Rady Pediatric Genomic and Systems Medicine Institute, Rady Children’s Hospital, San Diego, CA 92123, USA.

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Joseph Lucas

1Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA.

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Vance G. Fowler Jr

3Division of Infectious Diseases and International Health, Department of Medicine, Duke University, Durham, NC 27710, USA.

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Lawrence Carin

1Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA.

4Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA.

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Geoffrey S. Ginsburg

1Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA.

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For correspondence: geoffrey.ginsburg@duke.edu chris.woods@duke.edu

Christopher W. Woods

1Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA.

3Division of Infectious Diseases and International Health, Department of Medicine, Duke University, Durham, NC 27710, USA.

6Section for Infectious Diseases, Medicine Service, Durham Veteran’s Affairs Medical Center, Durham, NC 27705, USA.

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For correspondence: geoffrey.ginsburg@duke.edu chris.woods@duke.edu

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