Basic bioinformatics tools for genotyping
studies. A practical exercise with type 2
diabetes mellitus
Alessandro Brito dos Santos1, J�?�?�?©ssica Nayara G�?�?�?³es de Ara�?�?�?ºjo1, Rafael Caetano Bastos1, Andr�?�?�?© Ducati Luchessi1, Adriana Augusto de Rezende�?�??�?¹, Mario Hiroyuki Hirata2, Rosario

Dominguez Crespo Hirata; Vivian Nogueira Silbiger

International Research Journal of Biochemistry and Bioinformatics

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Basic bioinformatics tools for genotyping studies. A practical exercise with type 2 diabetes mellitus Alessandro Brito dos Santos1, J�?�?�?©ssica Nayara G�?�?�?³es de Ara�?�?�?ºjo1, Rafael Caetano Bastos1, Andr�?�?�?© Ducati Luchessi1, Adriana Augusto de Rezende�?�??�?¹, Mario Hiroyuki Hirata2, Rosario

Abstract

Dominguez Crespo Hirata and Vivian Nogueira Silbiger

The knowledge of bioinformatics tools is essential to investigate the molecular basis of complex diseases, such as type 2 diabetes mellitus (T2DM). The aims of this study were select single nucleotide polymorphisms (SNPs) of candidate genes and elaborate genotyping strategies of T2DM using bioinformatics tools. The genes were selected searching in PubMed/NCBI for articles published from 2007 to 2011 involving T2DM studies. Interactions among the selected genes were studied using the software Ingenuity Pathway Analysis (IPA). SNPs with frequencies higher than 10% were chose according data available at dbSNP/NCBI. Genotyping strategies were based on TaqMan�?�??�?® real-time PCR, PCR-RFLP and sequencing methods, in this order of priority. Primers, probes or enzymes for genotyping strategies were determined using websites and free software. Among the 56 selected genes by PubMed/NCBI research, 32 and 7 were direct and indirectly associated with T2DM, respectively. Five genes were selected to elaborate the genotyping strategies, ADCY5, AGER, IRS2, KCNQ1 and PREX1, for each gene were possible to select 7, 10, 9, 9 and 11 SNPs, respectively. It was possible to select primers and probes for TaqMan�?�??�?® real time-PCR in 65.2% (30/46) of the SNPs selected. Seven of the sixteen SNPs remaining (43.8 %) were viable to genotype by PCR-RFLP, the second strategy. The others nine SNPs were test by third option and just one of them could not be genotype by pyrosequencing, following for the last strategy by Sanger conventional sequencing. In conclusion, this study shows that bioinformatics tools allow the development of a set of genotype strategies for application in future gene candidate association studies for T2DM.

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