Chapter 9
Mutation Scanning and Genotyping in Plants by High-Resolution DNA Melting
Jason T. McKinney,
Lyle M. Nay,
David De Koeyer,
Gudrun H. Reed,
Mikeal Wall,
Robert A. Palais,
Robert L. Jarret,
Carl T. Wittwer,
Jason T. McKinney
Idaho Technology, Genotyping Applications Division, 390 Wakara Way, Salt Lake City, UT 84108, USA
Search for more papers by this authorLyle M. Nay
Idaho Technology, Genotyping Applications Division, 390 Wakara Way, Salt Lake City, UT 84108, USA
Search for more papers by this authorDavid De Koeyer
Agriculture and Agri-Food Canada, Potato Research Centre, 850 Lincoln Road, Fredericton, New Brunswick E3B 4Z7, Canada
Search for more papers by this authorGudrun H. Reed
University of Utah, Department of Pathology, 50N. Medical Drive, Salt Lake City, UT 84109, USA
Search for more papers by this authorMikeal Wall
Idaho Technology, Genotyping Applications Division, 390 Wakara Way, Salt Lake City, UT 84108, USA
Search for more papers by this authorRobert A. Palais
University of Utah, Department of Mathematics, 155S. 1400E., Salt Lake City, UT 84112, USA
Search for more papers by this authorRobert L. Jarret
US Department of Agriculture/Agricultural Research Service, Plant Genetic Resources Unit, 1109 Experiment Street, Griffin, GA 30224, USA
Search for more papers by this authorCarl T. Wittwer
University of Utah, Department of Pathology, 50N. Medical Drive, Salt Lake City, UT 84109, USA
Search for more papers by this authorJason T. McKinney,
Lyle M. Nay,
David De Koeyer,
Gudrun H. Reed,
Mikeal Wall,
Robert A. Palais,
Robert L. Jarret,
Carl T. Wittwer,
Jason T. McKinney
Idaho Technology, Genotyping Applications Division, 390 Wakara Way, Salt Lake City, UT 84108, USA
Search for more papers by this authorLyle M. Nay
Idaho Technology, Genotyping Applications Division, 390 Wakara Way, Salt Lake City, UT 84108, USA
Search for more papers by this authorDavid De Koeyer
Agriculture and Agri-Food Canada, Potato Research Centre, 850 Lincoln Road, Fredericton, New Brunswick E3B 4Z7, Canada
Search for more papers by this authorGudrun H. Reed
University of Utah, Department of Pathology, 50N. Medical Drive, Salt Lake City, UT 84109, USA
Search for more papers by this authorMikeal Wall
Idaho Technology, Genotyping Applications Division, 390 Wakara Way, Salt Lake City, UT 84108, USA
Search for more papers by this authorRobert A. Palais
University of Utah, Department of Mathematics, 155S. 1400E., Salt Lake City, UT 84112, USA
Search for more papers by this authorRobert L. Jarret
US Department of Agriculture/Agricultural Research Service, Plant Genetic Resources Unit, 1109 Experiment Street, Griffin, GA 30224, USA
Search for more papers by this authorCarl T. Wittwer
University of Utah, Department of Pathology, 50N. Medical Drive, Salt Lake City, UT 84109, USA
Search for more papers by this authorBook Editor(s):Prof. Dr. Khalid Meksem,
Prof. Dr. Günter Kahl,
Prof. Dr. Khalid Meksem
Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901-4415, USA
Search for more papers by this authorProf. Dr. Günter Kahl
GenXPro GmbH, Research Innovation Center (FIZ) Biotechnology, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
Search for more papers by this authorSummary
This chapter contains sections titled:
-
Introduction
-
Methods and Protocols
-
Applications
-
Perspectives
-
References
References
- Ririe, K.M., Rasmussen, R.P., and Wittwer, C.T. (1997) Product differentiation by analysis of DNA melting curves during the polymerase chain reaction. Anal. Biochem., 245, 154–160.
- Herrmann, M.G., Durtschi, J.D., Bromley, L.K., Wittwer, C.T., and Voelkerding, K.V. (2006) Amplicon DNA melting analysis for mutation scanning and genotyping: cross-platform comparison of instruments and dyes. Clin. Chem., 52, 494–503.
- Herrmann, M.G., Durtschi, J.D., Bromley, L.K., Wittwer, C.T., and Voelkerding, K.V. (2007) Instrument comparison for heterozygote scanning of single and double heterozygotes: a correction and extension of Herrmann et al., Clin Chem 2006;52:494–503. Clin. Chem., 53, 150–152.
- Herrmann, M.G., Durtschi, J.D., Wittwer, C.T., and Voelkerding, K.V. (2007) Expanded instrument comparison of amplicon DNA melting analysis for mutation scanning and genotyping. Clin. Chem., 53, 1544–1548.
- Dujols, V.E., Kusukawa, N., McKinney, J.T., Dobrowolski, S.F., and Wittwer, C.T. (2006) High-resolution melting analysis for scanning and genotyping, in Real-Time PCR (ed. M.T. Dorak), Garland, New York.
- Dobrowolski, S.F., McKinney, J.T., Amat di San Filippo, C., Giak Sim, K., Wilcken, B., and Longo, N. (2005) Validation of dye-binding/high-resolution thermal denaturation for the identification of mutations in the SLC22A5 gene. Hum. Mutat., 25, 306–313.
- McKinney, J.T., Longo, N., Hahn, S.H., Matern, D., Rinaldo, P., Strauss, A.W., and Dobrowolski, S.F. (2004) Rapid, comprehensive screening of the human medium chain acyl-CoA dehydrogenase gene. Mol. Genet. Metab., 82, 112–120.
- Montgomery, J., Wittwer, C.T., Kent, J.O., and Zhou, L. (2007) Scanning the cystic fibrosis transmembrane conductance regulator gene using high-resolution DNA melting analysis. Clin. Chem., 53, 1891–1898.
- Reed, G.H. and Wittwer, C.T. (2004) Sensitivity and specificity of single-nucleotide polymorphism scanning by high-resolution melting analysis. Clin. Chem., 50, 1748–1754.
- Dames, S., Pattison, D.C., Bromley, L.K., Wittwer, C.T., and Voelkerding, K.V. (2007) Unlabeled probes for the detection and typing of herpes simplex virus. Clin. Chem., 53, 1847–1854.
- Erali, M., Palais, R., and Wittwer, C.T. (2008) SNP genotyping by unlabeled probe melting analysis, in Molecular Beacons: Signalling Nucleic Acid Probes, Methods and Protocols (eds O. Seitz and A. Marx), Humana Press, Totowa, NJ.
- Zhou, L., Myers, A.N., Vandersteen, J.G., Wang, L., and Wittwer, C.T. (2004) Closed-tube genotyping with unlabeled oligonucleotide probes and a saturating DNA dye. Clin. Chem., 50, 1328–1335.
- Graham, R., Liew, M., Meadows, C., Lyon, E., and Wittwer, C.T. (2005) Distinguishing different DNA heterozygotes by high-resolution melting. Clin. Chem., 51, 1295–1298.
- Liew, M., Nelson, L., Margraf, R., Mitchell, S., Erali, M., Mao, R., Lyon, E., and Wittwer, C. (2006) Genotyping of human platelet antigens 1 to 6 and 15 by high-resolution amplicon melting and conventional hybridization probes. J. Mol. Diagn., 8, 97–104.
- Liew, M., Pryor, R., Palais, R., Meadows, C., Erali, M., Lyon, E., and Wittwer, C. (2004) Genotyping of single-nucleotide polymorphisms by high-resolution melting of small amplicons. Clin. Chem., 50, 1156–1164.
- Wittwer, C.T., Reed, G.H., Gundry, C.N., Vandersteen, J.G., and Pryor, R.J. (2003) High-resolution genotyping by amplicon melting analysis using LCGreen. Clin. Chem., 49, 853–860.
- Erali, M., Voelkerding, K.V., and Wittwer, C.T. (2008) High resolution melting applications for clinical laboratory medicine. Exp. Mol. Pathol., 85, 50–58.
- Reed, G.H., Kent, J.O., and Wittwer, C.T. (2007) High-resolution DNA melting analysis for simple and efficient molecular diagnostics. Pharmacogenomics, 8, 597–608.
- Chateigner-Boutin, A.L. and Small, I. (2007) A rapid high-throughput method for the detection and quantification of RNA editing based on high-resolution melting of amplicons. Nucleic Acids Res., 35, e114.
- Mackay, J.F., Wright, C.D., and Bonfiglioli, R.G. (2008) A new approach to varietal identification in plants by microsatellite high resolution melting analysis: application to the verification of grapevine and olive cultivars. Plant Methods, 4, 8.
- Lehmensiek, A., Sutherland, M.W., and McNamara, R.B. (2008) The use of high resolution melting (HRM) to map single nucleotide polymorphism markers linked to a covered smut resistance gene in barley. Theor. Appl. Genet., 117, 721–728.
- Chagne, D., Gasic, K., Crowhurst, R.N., Han, Y., Bassett, H.C., Bowatte, D.R., Lawrence, T.J., Rikkerink, E.H., Gardiner, S.E., and Korban, S.S. (2008) Development of a set of SNP markers present in expressed genes of the apple. Genomics, 92, 353–358.
- Wu, S.B., Wirthensohn, M.G., Hunt, P., Gibson, J.P., and Sedgley, M. (2008) High resolution melting analysis of almond SNPs derived from ESTs. Theor. Appl. Genet., 118, 1–14.
- Croxford, A.E., Rogers, T., Caligari, P.D., and Wilkinson, M.J. (2008) High-resolution melt analysis to identify and map sequence-tagged site anchor points onto linkage maps: a white lupin (Lupinus albus) map as an exemplar. New Phytol., 180, 594–607.
- Nomoto, K., Tsuta, K., Takano, T., Fukui, T., Fukui, T., Yokozawa, K., Sakamoto, H., Yoshida, T., Maeshima, A.M., Shibata, T., Furuta, K., Ohe, Y., and Matsuno, Y. (2006) Detection of EGFR mutations in archived cytologic specimens of non-small cell lung cancer using high-resolution melting analysis. Am. J. Clin. Pathol., 126, 608–615.
- Dames, S., Margraf, R.L., Pattison, D.C., Wittwer, C.T., and Voelkerding, K.V. (2007) Characterization of aberrant melting peaks in unlabeled probe assays. J. Mol. Diagn., 9, 290–296.
- Bennett, C.D., Campbell, M.N., Cook, C.J., Eyre, D.J., Nay, L.M., Nielsen, D.R., Rasmussen, R.P., and Bernard, P.S. (2003) The LightTyper: high-throughput genotyping using fluorescent melting curve analysis. Biotechniques, 34, 1288–1295.
-
Highsmith, W.E., Jr.,
Nataraj, A.J.,
Jin, Q.,
O'Connor, J.M.,
El-Nabi, S.H.,
Kusukawa, N., and
Garner, M.M.
(1999)
Use of DNA toolbox for the characterization of mutation scanning methods. II: evaluation of single-strand conformation polymorphism analysis.
Electrophoresis,
20,
1195–1203.
10.1002/(SICI)1522-2683(19990101)20:6<1195::AID-ELPS1195>3.0.CO;2-A CAS PubMed Web of Science® Google Scholar
- De Leeneer, K., Coene, I., Poppe, B., De Paepe, A., and Claes, K. (2008) Rapid and sensitive detection of BRCA1/2 mutations in a diagnostic setting: comparison of two high-resolution melting platforms. Clin. Chem., 54, 982–989.
- Dobrowolski, S.F., Ellingson, C., Coyne, T., Martin, R., Grey, J., Naylor, E.W., Koch, R., and Levy, H. (2007) Mutations in the phenylalanine hydroxylase gene identified in 95 patients with phenylketonuria using novel systems of mutation scanning and specific genotyping based upon thermal melt profiles. Mol. Genet. Metabol., 91, 218–227.
- Dobrowolski, S.F., Ellingson, C.E., Caldovic, L., and Tuchman, M. (2007) Streamlined assessment of gene variants by high resolution melt profiling utilizing the ornithine transcarbamylase gene as a model system. Hum. Mutat., 28, 1133–1140.
- Lin, S.Y., Su, Y.N., Hung, C.C., Tsay, W., Chiou, S.S., Chang, C.T., Ho, H.N., and Lee, C.N. (2008) Mutation spectrum of 122 hemophilia A families from Taiwanese population by LD-PCR, DHPLC, multiplex PCR and evaluating the clinical application of HRM. BMC Med. Genet., 9, 53.
- Vandersteen, J.G., Bayrak-Toydemir, P., Palais, R.A., and Wittwer, C.T. (2007) Identifying common genetic variants by high-resolution melting. Clin. Chem., 53, 1191–1198.
- Gundry, C.N., Vandersteen, J.G., Reed, G.H., Pryor, R.J., Chen, J., and Wittwer, C.T. (2003) Amplicon melting analysis with labeled primers: a closed-tube method for differentiating homozygotes and heterozygotes. Clin. Chem., 49, 396–406.
- Montgomery, J., Wittwer, C.T., Palais, R.A., and Zhou, L. (2007) Simultaneous mutation scanning and genotyping by high-resolution DNA melting analysis. Nature Prot., 2, 59–66.
- Palais, R.A., Liew, M.A., and Wittwer, C.T. (2005) Quantitative heteroduplex analysis for single nucleotide polymorphism genotyping. Anal. Biochem., 346, 167–175.
- Gundry, C.N., Dobrowolski, S.F., Martin, Y.R., Robbins, T.C., Nay, L.M., Boyd, N., Coyne, T., Wall, M.D., Wittwer, C.T., and Teng, D.H. (2008) Base-pair neutral homozygotes can be discriminated by calibrated high-resolution melting of small amplicons. Nucleic Acids Res., 36, 3401–3408.
- Margraf, R.L., Mao, R., and Wittwer, C.T. (2006) Masking selected sequence variation by incorporating mismatches into melting analysis probes. Hum. Mutat., 27, 269–278.
- Zhou, L., Errigo, R.J., Lu, H., Poritz, M.A., Seipp, M.T., and Wittwer, C.T. (2008) Snapback primer genotyping with saturating DNA dye and melting analysis. Clin. Chem., 54, 1648–1656.
- De Jong, W.S., De Jong, D.M., and Bodis, M. (2003) A fluorogenic 5′ nuclease (TaqMan) assay to assess dosage of a marker tightly linked to red skin color in autotetraploid potato. Theor. Appl. Genet., 107, 1384–1390.
