Whole blood gene expression profiling of neonates with confirmed bacterial sepsis.
Neonatal infection remains a primary cause of infant morbidity and mortality worldwide and yet our understanding of how human neonates respond to infection remains incomplete. Changes in host gene expression in response to infection may occur in any part of the body, with the continuous interaction between blood and tissues allowing blood cells to act as biosensors for the changes. In this study we have used whole blood transcriptome profiling to systematically identify signatures and the pathway biology underlying the pathogenesis of neonatal infection. Blood samples were collected from neonates at the first clinical signs of suspected sepsis alongside age matched healthy control subjects. Here we report a detailed description of the study design, including clinical data collected, experimental methods used and data analysis workflows and which correspond with data in Gene Expression Omnibus (GEO) data sets (GSE25504). Our data set has allowed identification of a patient invariant 52-gene classifier that predicts bacterial infection with high accuracy and lays the foundation for advancing diagnostic, prognostic and therapeutic strategies for neonatal sepsis.
Division of Infection and Pathway Medicine, Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK ; SynthSys-Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3JD, UK.
Paul
P
Dickinson
Neonatal Unit, Simpson Centre for Reproductive Health, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK.
Claire L
CL
Smith
Division of Infection and Pathway Medicine, Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK ; SynthSys-Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3JD, UK.
Thorsten
T
Forster
Division of Infection and Pathway Medicine, Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK.
Marie
M
Craigon
Division of Infection and Pathway Medicine, Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK.
Alan J
AJ
Ross
Division of Infection and Pathway Medicine, Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK.
Mizan R
MR
Khondoker
Fios Genomics Ltd., Edinburgh BioQuater, Edinburgh EH16 4SB, UK.
Alasdair
A
Ivens
Animal & Bioscience Research Department, AGRIC, Teagasc, Grange, Dunsany, Co. Meath, Ireland.
David J
DJ
Lynn
Neonatal Unit, Simpson Centre for Reproductive Health, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK.
Judith
J
Orme
Neonatal Unit, Simpson Centre for Reproductive Health, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK.
Allan
A
Jackson
Division of Infection and Pathway Medicine, Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK.
Paul
P
Lacaze
MRC Research Laboratories, Atlantic Boulevard, PO Box 273, Fajara, Gambia.
Katie L
KL
Flanagan
Neonatal Unit, Simpson Centre for Reproductive Health, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK.
Benjamin J
BJ
Stenson
Division of Infection and Pathway Medicine, Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK ; SynthSys-Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3JD, UK.
Peter
P
Ghazal
Gene expression profiling; Microarray; Neonatal sepsis; Whole blood