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BITS2007 Meeting
BITS2007 Meeting



26-28 April 2007 Napoli, Italy

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CST analysis in the characterization of cystic fibrosis patients
 
Motivation
Conserved sequence tags (CSTs) are genomic sequences, generally believed to 
be the result of selective evolutionary pressure for conservation due to a 
possible functional role, and are therefore considered as a potential resource 
for the discovery of novel functional elements. The study of such sequences 
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.


Methods
Selection of CSTs was carried out by using an extension of a pipeline, 
previously developed in our laboratory (Nucleic Acids Res. 2005; 33 - D505-10). 
Basically sequences were compared by BLASTZ, and sequences showing at 
least 70% identity over at least 100 bp were extracted and fully annotated. A 
protocol was devised for selecting PCR primers, able to cover all CST containing 
genomic segments while keeping at a minimum the number of multiplex 
reactions and the synthesized oligonucleotides. Primers selected in this way 
were synthesized and used to analyze the CFTR genomic region of CF patients 
and controls.
A PostgreSql database was used to hold data from the analysis, including all 
the details of the analyzed genomic regions, and additional information 
concerning the CFTR genotype and phenotype of the source subjects. 
Information about CFTR wild type sequence, exons and known SNPs were 
taken from the ENSEMBL (http://www.ensembl.org) web site.
The web site, used to access the data, has been developed by using the PHP 
scripting language, and includes the tools used to identify and classify the 
mutations.


Results
A low level analysis of the CSTs contained within the intronic regions of the 
human CFTR gene was carried out. 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.
Analysis of 56 intronic CSTs from 70 CF patients and 20 control subjects 
resulted in the identification of 76 different polymorphic sites, including novel 
and previously described ones. According to the frequency of mutations, CSTs 
can be classified in different groups. About a quarter of the CSTs are strongly 
conserved regions, showing the wild type sequence in all subjects. Other CST 
regions contain mutation(s) either randomly distributed among the tested 
subjects, with no correlation to pathology, or limited to specific subsets of 
subjects. A number of these mutations are probably located on specific 
pathologic alleles, being typically found in patients carrying one or two alleles 
containing nonsense or missense mutations. 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.
 
Id: 169
Place: Napoli, Italy
Centro Congressi "Federico II"
Via Partenope 36
Napoli
Starting date:
-- not yet scheduled --   
Duration: 20'
Contribution type: Oral
Primary Authors: BOCCIA, Angelo (Universita` degli Studi di Napoli `Federico II`, Napoli; CEINGE Biotecnologie Avanzate, Napoli)
Co-Authors: ELCE, Ausilia (CEINGE Biotecnologie Avanzate, Napoli)
TOMAIUOLO, Rossella (Universita` degli Studi di Napoli `Federico II`, Napoli; CEINGE Biotecnologie Avanzate, Napoli)
CASTALDO, Giuseppe (Universita` degli Studi di Napoli `Federico II`, Napoli; CEINGE Biotecnologie Avanzate, Napoli)
PAOLELLA, Giovanni (Universita` degli Studi di Napoli `Federico II`, Napoli; CEINGE Biotecnologie Avanzate, Napoli)
Presenters: BOCCIA, Angelo
 
Included in session: Session 4: Biomedical Informatics
Included in track: Biomedical informatics
 




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