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Open Access Research

Using gene expression data to identify certain gastro-intestinal diseases

Philip S Crooke1*, John T Tossberg2, Sara N Horst3, John L Tauscher1, Melodie A Henderson3, Dawn B Beaulieu3, David A Schwartz3, Nancy J Olsen4 and Thomas M Aune35

Author Affiliations

1 Department of Mathematics, Vanderbilt University, Nashville, TN, USA

2 Research Department, ArthroChip, LLC, Franklin, TN, USA

3 Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA

4 Department of Medicine, Penn State Hershey Medical Center, Hershey, PA, USA

5 Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA

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Journal of Clinical Bioinformatics 2012, 2:20  doi:10.1186/2043-9113-2-20

Published: 21 November 2012

Abstract

Background

Inflammatory bowel diseases, ulcerative colitis and Crohn’s disease are considered to be of autoimmune origin, but the etiology of irritable bowel syndrome remains elusive. Furthermore, classifying patients into irritable bowel syndrome and inflammatory bowel diseases can be difficult without invasive testing and holds important treatment implications. Our aim was to assess the ability of gene expression profiling in blood to differentiate among these subject groups.

Methods

Transcript levels of a total of 45 genes in blood were determined by quantitative real-time polymerase chain reaction (RT-PCR). We applied three separate analytic approaches; one utilized a scoring system derived from combinations of ratios of expression levels of two genes and two different support vector machines.

Results

All methods discriminated different subject cohorts, irritable bowel syndrome from control, inflammatory bowel disease from control, irritable bowel syndrome from inflammatory bowel disease, and ulcerative colitis from Crohn’s disease, with high degrees of sensitivity and specificity.

Conclusions

These results suggest these approaches may provide clinically useful prediction of the presence of these gastro-intestinal diseases and syndromes.