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Development of Novel High-Resolution Melting-Based Assays for Genotyping Two Alu Insertion Polymorphisms (FXIIIB and PV92)

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Abstract

Insertion/Deletion polymorphisms (InDels) are a common type of genetic variation, with a growing role in population genetics and applied genomics. There is the need for the development of novel cost-effective assays for genotyping InDels of high importance. The main objective of this study was to develop high-resolution melting-based assays for genotyping two commonly studied Alu insertion polymorphisms: FXIIIB and PV92 (rs70942849 and rs3138523). Three primers (two forward and one reverse) were designed for each marker, and high-resolution melting (HRM) analyses in a qPCR platform were performed, using EvaGreen fluorescent dye. For each one of the two Alu insertion polymorphisms, HRM analyses identified distinguishable peaks for the three genotypes, allowing a robust genotyping. Results were validated using 96 DNA samples previously genotyped and the assays worked with different DNA concentrations. In this study, we developed novel cost-effective assays, using qPCR, for genotyping two Alu insertion polymorphisms (widely used as ancestry markers). Our results highlight the feasibility of using HRM analyses for genotyping InDel polymorphisms of medical and biotechnological importance.

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Acknowledgments

This study was supported by a research Grant from Universidad Antonio Nariño (VCTI-UAN, project # 20131080). Y.G.-G. was supported by a fellowship from Colciencias (Young Scientists Program). Funding sources had no involvement in study design, analysis of data, writing of the report, or in the decision to submit the manuscript.

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Correspondence to Diego A. Forero.

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All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards.

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Informed consent was obtained from all individual participants included in this study.

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Yeimy González-Giraldo and Marisol Rodríguez-Dueñas have contributed equally to this work.

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González-Giraldo, Y., Rodríguez-Dueñas, M. & Forero, D.A. Development of Novel High-Resolution Melting-Based Assays for Genotyping Two Alu Insertion Polymorphisms (FXIIIB and PV92). Mol Biotechnol 58, 197–201 (2016). https://doi.org/10.1007/s12033-016-9915-4

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  • DOI: https://doi.org/10.1007/s12033-016-9915-4

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