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The study of conserved sequence tags (CSTs) within the context of genes related to genetically transmitted diseases, may result in the identification of novel elements involved in the molecular mechanisms underlying the disease. Cystic fibrosis is a well known monogenic disease, caused by reduced activity of the CFTR chloride channel. Molecular diagnosis is based on the identification of mutations affecting the coding sequence in both alleles. In 10% of CF patients it is not identified a mutation in the exonic sequence. This sub-group of CF patients is a good candidate for CST analysis.

In collaboration with another group located at CEINGE, we carried out a low level analysis of the CSTs contained within the intronic regions of the human CFTR gene. The study led to the identification of many polymorphic sites within the gene. A specific tool was created for the characterization of the polymorphic sites, where the tested sequences are compared to the wild type ones and polymorphic sites are identified, highlighted and named according to the current standards. In addition, each variation is evaluated on the basis of the list of previously known single nucleotide polimorfisms (SNPs) and, accordingly, classified either as a novel or as an already reported one.

The results of this analysis are collected in a database and made accessible through a web interface.

According to the frequency of mutations, CSTs has been classified in different groups. Strongly conserved regions, showing the wild type sequence in all subjects. CST regions containing mutation(s) either randomly distributed among the tested subjects, with no correlation to pathology, or limited to specific subsets of subjects. Finally, some mutations tend to concentrate in a subset of patients, carrying alleles characterized by absence of mutations within the coding sequence, and are therefore suggestive of a potential functional role played by the CST containing sequence, possibly related to the disease.

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Bioinformatics: Research DB: DG-CST - KINWEB - ONCOEMAT - EYEDIS - CFTR
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