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  • Bioinformatic approaches for candidate gene selection and association analysis in patients with inflammatory bowel diseases [Elektronski vir]
    Potočnik, Uroš, 1969- ; Mitrovič, Mitja ; Glavač, Damjan
    The aim of our study was to design and evaluate the efficiency of different bioinformatic approaches for selection of candidate genes associated with the human inflammatory bowel diseases (IBD), and ... to perform association study in IBD patients and controls for selcted candidate genes. We used several bioinformatics approaches including literature data mining tools, microarray expression data analysis and pathway analysis to create candidate gene lists. Meta analysis of candidate gene lists revealed 35 potential IBD genes. Literature search showed 20/35 potential IBD genes were already tested in IBD patients and 14/20 genes showed positive association with IBD. In addition 15 novel candidate genes were identified which have not been tested in IBD patients yet. Genes confirmed in several independent association studies include genes associated with Crohn disease (NOD2/CARD15, OCTN1, OCTN2), with ulcerative colitis (MDR1/ABCB1) or with both diseases (DLG5, ICAM-1, TLR4). We have selected NOD2/CARD15 as gene with the highest number of positive association studies reported and ABCB1/MDR1 as gene with highest number of conflicting association studies reported for genotyping and association study in Slovenian IBD patients and controls. Our study confirmed an association between polymorphisms in NOD2/CARD15 gene and Crohn disease patients and association between polymorphisms and haplotypes in the multidrug resistance 1(MDR1) gene coding for P-glycoprotein (P-gp), and refractory Crohn disease (CD) patients with severe forms of Crohn disease, which develop fistulas and do not respond to standard therapy as well as with patients with ulcerative colitis. This results suggest bioinformatics approaches were able to efficiently identify candidate genes associated with IBD. The identification of novel IBD susceptibility genes will lead to better understanding disease pathophysiology, discovery of new therapeutic targets and in better disease management.
    Vir: Scientific journal on applied information technology [Elektronski vir] : IT as a tool for research, education and presentation. - ISSN 1683-1373 (Vol. 3, iss. 1, 2007, str. [1-6])
    Vrsta gradiva - e-članek ; neleposlovje za odrasle
    Leto - 2007
    Jezik - angleški
    COBISS.SI-ID - 11540758

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