| Abstract: |
Introduction: Single nucleotide polymorphisms (SNPs) exists as a type of genetic variation that can be either pathogenic or non pathogenic based on their influence on phenotype. At the date of the writing of this paper, there are four hundred and two single nucleotide polymorphisms present in the fusion gene of the intronic regions of human PAX7, which is found on chromosome one. Of those seventy-five are present in the intronic gene region of PAX7 present in the fusion gone alveolar rhabdomyosarcoma (ARMS) mainly found in the three prime regions of introns five, six, seven and eight. The aim of this research is to identify those SNPS most likely to affect PAX7 mediated tumorigenicity, particulary for alveolar rhabdomyosarcoma with which PAX7 is associated. The research elucidated in this paper also examines the efficacy and ease of using in silico biological methods prior to the commencement of bench work to increase the success rate of SNP detection and allele quantification. Results: In Silico Biology and Pyrosequencing technologies are shown to be faster, more cost-efficient than conventional PCR and Sanger sequencing and provide excellent adjunct techniques to identify alterations in gene sequence. For PAX7, seventy-five intronic SNPS were identified to be within close vicinity (fifty to one hundred nucleotides) of intronic cis regulatory elements and some of these remain whithin the PAX7 gene region present in the PAX7-FOX1, the fusion gene of alveolar rhabdomyosarcoma. Of these seventy-five, five were found to be different in alveolar rhabdomyosarcoma patients, both by conventional PCR, Sanger sequencing and Pyrosequencing. Change due to LOH were revealed by the current genotyping results obtained by in silico means from the NCBI website and thus may provide an indication of altered sequences that contribute substantially to increase tumorigenicity. Conclusions: Morever, six SNPs were within a conserved in introns five and eight of PAX7 that is highly conserved in homologous Pax7 genes of several animal phyla as well as in the exon/intron twenty-three regions of NF-1 and intron seven of PAX3. © EuroJournals Publishing, Inc. 2007. |
