Identification of common SNPs in the chromosome 11region: from 12,535,356 to 12,377,571

Identification of common SNPs in the chromosome 11region: from 12,535,356 to 12,377,571
Mahyar Ansari,^1,*
1. shahid bahonar university
Introduction: Nowaday , with the development of bioinformatics, it is possible to diagnose and treat many diseases . For example, snp can be identified by using bioinformatics. SNP or single nucleotide polymorphism is one of the factors of phenotypic change within a species and it is considered as an important genetic marker. SNPs can affect a person's risk of developing cancer. There are several bioinformatics tools for identifying SNP. One of these sites is the galaxy bioinformatics site . This program allows researchers to perform bioinformatics work and analysis without the need to use coding. The aim of this study was to identify the most common types of SNP in a part of the chromosome 11 region: from 12,535,356 to 12,377,571
Methods: 1-First, the coding sequences data of the desired area was extracted from the ucsc site with the ncbi refseq source and loaded on the galaxy site. 2-Then, the SNP sequences data of the whole genome in the desired region were extracted from the ucsc site 3-After that, we joined the two extracted data together 4-Using the statistic option on the galaxy site on the joined data, the count operation was performed and then sorted 5- Finally, we compared the obtained data with the initial data of the coding of the desired area
Results: The extracted coding data had 26 regions and the extracted SNP data had 34,617 regions. After merging the two extracted data, the data with 698 regions was created. This data indicates the amount of overlapping between exons and SNP. After counting, the data with 26 lines was obtained, which shows the number of SNP for each exon. By sorting the data, they are sorted based on the maximum amount of SNP for each exon. Compared to the sorted data with the initial coding data, 25 exons were classified based on the highest SNP value. The highest density was 46 in the target area.
Conclusion: In the chromosome 11 region: from 12,535,356 to 12,377,571, the PARVA gene is located .The PARVA gene is one of the oncogenes of lung cancer and can induce VEGF expression. Also the VEGF gene is involved in the cancer angiogenesis process. Therefore, recognizing common SNPs of PARVA genes can be important and provide a way to identify or treat cancer. Also, by laboratory examination of these SNPs and genetic manipulation of them , we can better understand the mechanism of cancer
Keywords: SNP, CANCER. BIOINFORMATICS