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

详细信息    查看全文

• 作者：Yeimy González-Giraldo ; Marisol Rodríguez-Dueñas…
• 关键词：High ; resolution melting ; Insertion/Deletion polymorphisms ; Genotyping assays ; Molecular genetics ; Real ; time PCR ; Ancestry informative markers
• 刊名：Molecular Biotechnology
• 出版年：2016
• 出版时间：March 2016
• 年：2016
• 卷：58
• 期：3
• 页码：197-201
• 全文大小：951 KB
• 参考文献：1.Mullaney, J. M., Mills, R. E., Pittard, W. S., & Devine, S. E. (2010). Small insertions and deletions (INDELs) in human genomes. Human Molecular Genetics, 19, R131–R136.CrossRef
  2.Lu, J. T., Wang, Y., Gibbs, R. A., & Yu, F. (2012). Characterizing linkage disequilibrium and evaluating imputation power of human genomic insertion-deletion polymorphisms. Genome Biology, 13, R15.CrossRef
  3.Genomes Project Consortium, Abecasis, G. R., Auton, A., Brooks, L. D., DePristo, M. A., Durbin, R. M., et al. (2012). An integrated map of genetic variation from 1,092 human genomes. Nature, 491, 56–65.CrossRef
  4.Antunez-de-Mayolo, G., Antunez-de-Mayolo, A., Antunez-de-Mayolo, P., Papiha, S. S., Hammer, M., Yunis, J. J., et al. (2002). Phylogenetics of worldwide human populations as determined by polymorphic Alu insertions. Electrophoresis, 23, 3346–3356.CrossRef
  5.Rigat, B., Hubert, C., Corvol, P., & Soubrier, F. (1992). PCR detection of the insertion/deletion polymorphism of the human angiotensin converting enzyme gene (DCP1) (dipeptidyl carboxypeptidase 1). Nucleic Acids Research, 20, 1433.CrossRef
  6.LaRue, B. L., Ge, J., King, J. L., & Budowle, B. (2012). A validation study of the Qiagen Investigator DIPplex(R) kit; An INDEL-based assay for human identification. International Journal of Legal Medicine, 126, 533–540.CrossRef
  7.Bhangale, T. R., Stephens, M., & Nickerson, D. A. (2006). Automating resequencing-based detection of insertion-deletion polymorphisms. Nature Genetics, 38, 1457–1462.CrossRef
  8.Koyama, R. G., Castro, R. M., De Mello, M. T., Tufik, S., & Pedrazzoli, M. (2008). Simple detection of large InDeLS by DHPLC: The ACE gene as a model. Journal of Biomedicine and Biotechnology, 2008, 562183.CrossRef
  9.Robledo, R., Beggs, W., & Bender, P. (2003). A simple and cost-effective method for rapid genotyping of insertion/deletion polymorphisms. Genomics, 82, 580–582.CrossRef
  10.Sawyer, S. L., Howell, W. M., & Brookes, A. J. (2003). Scoring insertion-deletion polymorphisms by dynamic allele-specific hybridization. BioTechniques, 35(292–296), 298.
  11.Sasayama, T., Kato, M., Aburatani, H., Kuzuya, A., & Komiyama, M. (2006). Simultaneous genotyping of indels and SNPs by mass spectroscopy. Journal of the American Society for Mass Spectrometry, 17, 3–8.CrossRef
  12.Mathot, L., Falk-Sorqvist, E., Moens, L., Allen, M., Sjoblom, T., & Nilsson, M. (2012). Automated genotyping of biobank samples by multiplex amplification of insertion/deletion polymorphisms. PLoS ONE, 7, e52750.CrossRef
  13.Oka, K., Asari, M., Omura, T., Yoshida, M., Maseda, C., Yajima, D., et al. (2014). Genotyping of 38 insertion/deletion polymorphisms for human identification using universal fluorescent PCR. Molecular and Cellular Probes, 28, 13–18.CrossRef
  14.Ragoussis, J. (2009). Genotyping technologies for genetic research. Annual Review of Genomics and Human Genetics, 10, 117–133.CrossRef
  15.Er, T. K., & Chang, J. G. (2012). High-resolution melting: Applications in genetic disorders. Clinica Chimica Acta, 414, 197–201.CrossRef
  16.Ojeda, D. A., Lopez-Leon, S., & Forero, D. A. (2014). A novel cost-effective assay based on real-time PCR for COMT Val158Met genotyping. Biomarkers, 19, 567–570.CrossRef
  17.Lin, M. H., Tseng, C. H., Tseng, C. C., Huang, C. H., Chong, C. K., & Tseng, C. P. (2001). Real-time PCR for rapid genotyping of angiotensin-converting enzyme insertion/deletion polymorphism. Clinical Biochemistry, 34, 661–666.CrossRef
  18.Untergasser, A., Cutcutache, I., Koressaar, T., Ye, J., Faircloth, B. C., Remm, M., & Rozen, S. G. (2012). Primer3–new capabilities and interfaces. Nucleic Acids Research, 40, e115.CrossRef
  19.Kass, D. H., Aleman, C., Batzer, M. A., & Deininger, P. L. (1994). Identification of a human specific Alu insertion in the factor XIIIB gene. Genetica, 94, 1–8.CrossRef
  20.Radvansky, J., Resko, P., Surovy, M., Minarik, G., Ficek, A., & Kadasi, L. (2010). High-resolution melting analysis for genotyping of the myotonic dystrophy type 1 associated Alu insertion/deletion polymorphism. Analytical Biochemistry, 398, 126–128.CrossRef
  21.Kibbe, W. A. (2007). OligoCalc: An online oligonucleotide properties calculator. Nucleic Acids Research, 35, W43–W46.CrossRef
  22.Morales, L. C., Arboleda, G., Rodriguez, Y., Forero, D. A., Ramirez, N., Yunis, J. J., & Arboleda, H. (2009). Absence of Lamin A/C gene mutations in four Wiedemann-Rautenstrauch syndrome patients. American Journal of Medical Genetics A, 149A, 2695–2699.CrossRef
  23.Gonzalez-Giraldo, Y., Gonzalez-Reyes, R. E., Mueller, S. T., Piper, B. J., Adan, A., & Forero, D. A. (2015). Differences in planning performance, a neurocognitive endophenotype, are associated with a functional variant in PER3 gene. Chronobiology International, 32, 591–595.CrossRef
  24.Ojeda, D. A., Perea, C. S., Nino, C. L., Gutierrez, R. M., Lopez-Leon, S., Arboleda, H., et al. (2013). A novel association of two non-synonymous polymorphisms in PER2 and PER3 genes with specific diurnal preference subscales. Neuroscience Letters, 553, 52–56.CrossRef
  25.Watkins, W. S., Ricker, C. E., Bamshad, M. J., Carroll, M. L., Nguyen, S. V., Batzer, M. A., et al. (2001). Patterns of ancestral human diversity: An analysis of Alu-insertion and restriction-site polymorphisms. American Journal of Human Genetics, 68, 738–752.CrossRef
  26.Hernandez, H. G., Tse, M. Y., Pang, S. C., Arboleda, H., & Forero, D. A. (2013). Optimizing methodologies for PCR-based DNA methylation analysis. BioTechniques, 55, 181–197.
  27.Hiratsuka, M., Kishikawa, Y., Narahara, K., Inoue, T., Hamdy, S. I., Agatsuma, Y., et al. (2001). Detection of angiotensin-converting enzyme insertion/deletion polymorphisms using real-time polymerase chain reaction and melting curve analysis with SYBR Green I on a GeneAmp 5700. Analytical Biochemistry, 289, 300–303.CrossRef
  28.Vaughn, C. P., & Elenitoba-Johnson, K. S. (2004). High-resolution melting analysis for detection of internal tandem duplications. Journal of Molecular Diagnostics, 6, 211–216.CrossRef
  29.Mamedov, I. Z., Shagina, I. A., Kurnikova, M. A., Novozhilov, S. N., Shagin, D. A., & Lebedev, Y. B. (2010). A new set of markers for human identification based on 32 polymorphic Alu insertions. European Journal of Human Genetics, 18, 808–814.CrossRef
  30.Ojeda, D. A., Perea, C. S., Suarez, A., Nino, C. L., Gutierrez, R. M., Lopez-Leon, S., et al. (2014). Common functional polymorphisms in SLC6A4 and COMT genes are associated with circadian phenotypes in a South American sample. Neurological Sciences, 35, 41–47.CrossRef
  31.Alaerts, M., Ceulemans, S., Forero, D., Moens, L. N., De Zutter, S., Heyrman, L., et al. (2009). Detailed analysis of the serotonin transporter gene (SLC6A4) shows no association with bipolar disorder in the Northern Swedish population. American Journal of Medical Genetics Part B, Neuropsychiatric Genetics, 150B, 585–592.CrossRef
  32.Ojeda, D. A., Nino, C. L., Lopez-Leon, S., Camargo, A., Adan, A., & Forero, D. A. (2014). A functional polymorphism in the promoter region of MAOA gene is associated with daytime sleepiness in healthy subjects. Journal of the Neurological Sciences, 337, 176–179.CrossRef
  33.Santos, N. P., Ribeiro-Rodrigues, E. M., Ribeiro-Dos-Santos, A. K., Pereira, R., Gusmao, L., Amorim, A., et al. (2010). Assessing individual interethnic admixture and population substructure using a 48-insertion-deletion (INSEL) ancestry-informative marker (AIM) panel. Human Mutation, 31, 184–190.CrossRef
  
• 作者单位：Yeimy González-Giraldo (1) (2)
  Marisol Rodríguez-Dueñas (2) (3)
  Diego A. Forero (2)
  
  1. Department of Nutrition and Biochemistry, School of Sciences, Pontificia Universidad Javeriana, Bogotá, Colombia
  2. Laboratory of NeuroPsychiatric Genetics, Biomedical Sciences Research Group, School of Medicine, Universidad Antonio Nariño, Bogotá, Colombia
  3. Faculty of Science, Universidad Antonio Nariño, Bogotá, Colombia
  
• 刊物主题：Biotechnology; Biochemistry, general; Cell Biology; Protein Science; Biological Techniques; Human Genetics;
• 出版者：Springer US
• ISSN：1559-0305

文摘

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.