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Development of ARMS-PCR assay for genotyping of Pro12Ala SNP of PPARG gene: a cost effective way for case–control studies of type 2 diabetes in developing countries

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Abstract

Type 2 diabetes (T2D) is a prevalent metabolic disorder across the globe. Research is underway on various aspects including genetics to understand and control the global epidemic of diabetes. Recently, several SNPs in various genes have been associated with T2D. These association studies are mainly carried out in the developed countries through Genome Wide Association Scans, with follow-up replication/validation studies by high-throughput genotyping techniques (e.g. Taqman Technology). Although, similar studies could be conducted in developing countries, however, the limiting factors are the associated cost and expertise. These factors hamper research into the genetic association and replication studies from low-income countries to figure out the role of putatively associated SNPs in diabetes. Although, there are several SNP detection methods (e.g. Taqman assay, Dot-blot, PCR-RFLP, DGGE, SSCP) but these are either expensive or labor intensive or less sensitive. Hence, our aim was to develop a low-cost method for the validation of PPARG (Pro12Ala, CCA>GCA) SNP (rs1801282) for its association with T2D. Here, we developed a cost-effective and rapid amplification refractory mutation specific-PCR (ARMS-PCR) method for this SNP detection. We successfully genotyped PPARG SNPs (Pro12Ala) in human samples and the validity of this method was confirmed by DNA sequencing of a few representative samples for the three different genotypes. Furthermore, ARMS-PCR was applied to T2D patients and control samples for the screening of this SNP.

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Acknowledgments

All authors declare that there is no conflict of interest regarding this publication. This work was supported by the student grant from Higher Education Commission (HEC), Pakistan. Use of research facilities of National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan are greatly appreciated. We are also thankful to all our colleagues for their help during this study. We thank all patients and hospital staff who participated in this study.

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Authors and Affiliations

  1. Diabetes and Cardio-Metabolic Disorders Laboratory, Human Molecular Genetics and Metabolic Disorders Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, P.O. Box 577, Faisalabad, Pakistan

    Mehboob Islam, Fazli Rabbi Awan & Shahid Mahmood Baig

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  1. Mehboob Islam
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  2. Fazli Rabbi Awan
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  3. Shahid Mahmood Baig
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Correspondence to Fazli Rabbi Awan.

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Islam, M., Awan, F.R. & Baig, S.M. Development of ARMS-PCR assay for genotyping of Pro12Ala SNP of PPARG gene: a cost effective way for case–control studies of type 2 diabetes in developing countries. Mol Biol Rep 41, 5585–5591 (2014). https://doi.org/10.1007/s11033-014-3213-7

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  • DOI: https://doi.org/10.1007/s11033-014-3213-7

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