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Title: Towards microarray diagnosis of infection in the newborn
Author: Smith, Claire Lindsay
Awarding Body: University of Edinburgh
Current Institution: University of Edinburgh
Date of Award: 2010
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Background & Aims: Infection causes significant morbidity and mortality in newborn infants. Current methods for diagnosing infection are unreliable. It would be beneficial if a test could be found that could diagnose infection sensitively, accurately and reliably - particularly if more rapid and from smaller samples. Microarrays are a useful means of global analysis of gene expression. One particularly exciting application of microarrays could be in diagnosing infection by detecting alteration in host RNA phenotype in response to infection. I set out to investigate whether small volumes of neonatal blood could yield RNA of sufficient quality and quantity to carry out microarray analysis and to identify suitable methods of sample handling and RNA extraction. I then went on to determine if differences in gene expression profiles could be detected between infants with confirmed infection and a group of controls using microarray technology. Methods: Umbilical cord blood was used to optimise blood collection tube, RNA extraction method and sample storage conditions. RNA quality and yield were assessed for each. RNA samples from neonatal blood taken from infants with confirmed infection and controls were then run on microarray: initially on CodeLink™ Whole Human Genome Microarray and later on Illumina® Human Whole-Genome Expression BeadChips. Normalised, validated microarray data was analysed to examine differences between control and infected samples. Functional annotation according to gene ontology and pathway analysis was performed. Results: High quality RNA yields sufficient for microarray work were obtained. The optimum blood collection tube, RNA extraction method and sample handling conditions are described. Results from the Codelink™ arrays are presented along with discussion of problems encountered using this platform. Results from 28 infected and 35 control samples run on the Illumina® platform are presented. 6221 features were significantly differentially expressed between infected and control groups (adjusted p-value < 0.001). 448 features had > 2-fold up-regulation and 341 features > 2-fold down-regulation (p < 0.001). Functional annotation and pathway analysis revealed a notable proportion of these are involved in immune functions. Conclusions: Sufficient high quality RNA for microarray analysis can be obtained from small neonatal blood samples. Differential RNA expression profiles of host response can be detected between infected and non-infected infants. Such data may provide an alternative way for diagnosing infection in infants in the future. Large-scale studies are required to explore this further.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (M.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available