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International Journal of Computational Bioinformatics and In Silico Modeling
2014: Volume-3 Issue-6
ISSN: 2320-0634

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ABSTRACT   REFERENCES  
International Journal of Computational Bioinformatics and In Silico Modeling 3(6) 2014: 531-537

Computational Detection of Deleterious Single Nucleotide Polymorphisms in Human Adenomatous Polyposis Coli Gene the Gate-Keeper of Colorectal Carcinoma



Shahenaz S. Salih1*, Ibtihal M. Abdelhag2, Wafaa M. Abdalla3, Altaf S. Mosad4, Mohamed M. Hassan5, Mohamed A. Hassan5,6

1 Department of Histopathology & Cytology, Sudan University for Sciences and Technology, Sudan
2 Department of Histopathology & Cytology, Omdurman Islamic University, Sudan
3 Department of Microbiology, Sudan University for Sciences and Technology, Sudan
4 Department of Clinical Pathology, Sudan University for Sciences and Technology, Sudan
5 Department of Bioinformatics, Africa City of Technology, Sudan University of Medical Science and Technology, Sudan
6 Division of Molecular Genetics, Institute of Human Genetics, University of Tubingen, Germany

* Corresponding Author

ABSTRACT

Colorectal cancer (CRC) is one of the most diffuse cancers worldwide; evidences showed that Adenomatous Polyposis Coli (APC) is a multifunctional tumor suppressor gene that regulates and controls many biological functions; mutations in this gene has been reported in many cases of CRC. SNPs contribute to gene mutations and expression variations justifying phenotypic variations among population and hence such SNPs would be potential biological targets for identification and analysis; therefore this work focused on analysis of SNPs in the coding regions of APC gene found as non-synonymous variants (nsSNP) and those in the 3'un-translated region (3'UTR) affecting miRNA binding using computational methods. 333 nsSNPs were analyzed by tools that concerning structural and functional aberrations and measure degrees and scores of alterations; and then the protein variants were subjected to structural modeling to highlight the impact of amino acid substitution upon protein phenotype. Analysis with Sift and Polyphen resulted in 15 damaging nsSNPs out of a total and marked 5 amino acid substitutions (E142G, R99W, R24N, L680S and W157T) with probably high deleterious scores, while analysis of 51 3'UTR SNPs by its special tool PolymiRTS resulted in no single nucleotide variant at that region could disturb the conserved sites of miRNA. It has been found that the use of such computational analysis tools was highly valuable and critical to highlight life threatening mutations and early sounds for APC gene aberrations causing truncated products with adverse outcomes.

 


Copyright © 2014 | AIZEON publishers | All rights reserved

 

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Citation: Shahenaz S. Salih et al. (2014). Computational Detection of Deleterious Single Nucleotide Polymorphisms in Human Adenomatous Polyposis Coli Gene the Gate-Keeper of Colorectal Carcinoma. Int J Comput Bioinfo In Silico Model 3(6): 531-537

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