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High-resolution DNA melting analysis for simple and efficient molecular diagnostics

    Gudrun H Reed

    Department of Pathology, University of Utah Medical Center, 5B418, 50 North Medical Drive, Salt Lake City, UT 84132, USA.

    ,
    Jana O Kent

    Department of Pathology, University of Utah Medical Center, 5B418, 50 North Medical Drive, Salt Lake City, UT 84132, USA.

    &
    Carl T Wittwer

    † Author for correspondence

    Department of Pathology, University of Utah Medical Center, 5B418, 50 North Medical Drive, Salt Lake City, UT 84132, USA.

    Published Online:https://doi.org/10.2217/14622416.8.6.597

    High-resolution melting of DNA is a simple solution for genotyping, mutation scanning and sequence matching. The melting profile of a PCR product depends on its GC content, length, sequence and heterozygosity and is best monitored with saturating dyes that fluoresce in the presence of double-stranded DNA. Genotyping of most variants is possible by the melting temperature of the PCR products, while all variants can be genotyped with unlabeled probes. Mutation scanning and sequence matching depend on sequence differences that result in heteroduplexes that change the shape of the melting curve. High-resolution DNA melting has several advantages over other genotyping and scanning methods, including an inexpensive closed tube format that is homogenous, accurate and rapid. Owing to its simplicity and speed, the method is a good fit for personalized medicine as a rapid, inexpensive method to predict therapeutic response.

    Papers of special note have been highlighted as either of interest (•) or of considerable interest (••) to readers.

    Bibliography

    • Wittwer CT, Herrmann MG: Rapid thermal cycling and PCR kinetics. In: PCR Methods Manual.Innis M, Gelfand D, Sninsky J (Eds). Academic Press, San Diego, CA, USA 211–229 (1999).• Review of rapid temperature cycling for PCR.
    • Carlquist JF, Horne BD, Muhlestein JB et al.: Genotypes of the cytochrome p450 isoform, CYP2C9, and the vitamin K epoxide reductase complex subunit 1 conjointly determine stable warfarin dose: a prospective study. J. Thromb. Thrombolysis22,191–197 (2006).
    • Slinger R, Bellfoy D, Desjardins M, Chan F: High-resolution melting assay for the detection of gyrA mutations causing quinolone resistance in Salmonella enterica serovars Typhi and Paratyphi. Diagn. Microbiol. Infect. Dis.57,455–458 (2007).
    • Wittwer CT, Kusukawa N: Real-time PCR. In: Diagnostic Molecular Microbiology; Principles and Applications. Persing DH, Tenover FC, Versalovic J et al. (Eds). ASM Press, Washington DC, USA 71–84 (2004).•• Technical review of real-time PCR methods.
    • Wittwer CT, Herrmann MG, Moss AA, Rasmussen RP: Continuous fluorescence monitoring of rapid cycle DNA amplification. Biotechniques22,130–131, 134–138 (1997).•• Introduction of SYBR Green I and hybridization probes to real-time PCR.
    • Wittwer CT, Ririe KM, Andrew RV, David DA, Gundry RA, Balis UJ: The LightCycler: a microvolume multisample fluorimeter with rapid temperature control. Biotechniques22,176–181 (1997).
    • Ririe KM, Rasmussen RP, Wittwer CT: Product differentiation by analysis of DNA melting curves during the polymerase chain reaction. Anal. Biochem.245,154–160 (1997).• First use of fluorescent melting analysis for PCR product differentiation.
    • Pirulli D, Boniotto M, Puzzer D, Spano A, Amoroso A, Crovella S: Flexibility of melting temperature assay for rapid detection of insertions, deletions, and single-point mutations of the AGXT gene responsible for type 1 primary hyperoxaluria. Clin. Chem.46,1842–1844 (2000).
    • Lipsky RH, Mazzanti CM, Rudolph JG et al.: DNA melting analysis for detection of single nucleotide polymorphisms. Clin. Chem.47,635–644 (2001).
    • 10  Dufresne SD, Belloni DR, Wells WA, Tsongalis GJ: BRCA1 and BRCA2 mutation screening using SmartCycler II high-resolution melt curve analysis. Arch. Pathol. Lab. Med.130,185–187 (2006).
    • 11  von Ahsen N, Oellerich M, Schutz E: Limitations of genotyping based on amplicon melting temperature. Clin. Chem.47,1331–1332 (2001).
    • 12  Gundry CN, Vandersteen JG, Reed GH, Pryor RJ, Chen J, Wittwer CT: Amplicon melting analysis with labeled primers: a closed-tube method for differentiating homozygotes and heterozygotes. Clin. Chem.49,396–406 (2003).•• First use of high-resolution melting analysis.
    • 13  Wittwer CT, Reed GH, Gundry CN, Vandersteen JG, Pryor RJ: High-resolution genotyping by amplicon melting analysis using LCGreen. Clin. Chem.49,853–860 (2003).•• Introduction of saturating dyes.
    • 14  Krypuy M, Newnham GM, Thomas DM, Conron M, Dobrovic A: High resolution melting analysis for the rapid and sensitive detection of mutations in clinical samples: KRAS codon 12 and 13 mutations in non-small cell lung cancer. BMC Cancer6,295 (2006).
    • 15  Wojdacz TK, Dobrovic A: Methylation-sensitive high resolution melting (MS-HRM): a new approach for sensitive and high-throughput assessment of methylation. Nucleic Acids Res.35,e41 (2007).
    • 16  McKinney JT, Longo N, Hahn SH et al.: Rapid, comprehensive screening of the human medium chain acyl-CoA dehydrogenase gene. Mol. Genet. Metab.82,112–120 (2004).• First mutation scanning of a complex gene with saturation dyes.
    • 17  Reed GH, Wittwer CT: Sensitivity and specificity of single-nucleotide polymorphism scanning by high-resolution melting analysis. Clin. Chem.50,1748–1754 (2004).
    • 18  Willmore C, Holden JA, Zhou L, Tripp S, Wittwer CT, Layfield LJ: Detection of c-kit-activating mutations in gastrointestinal stromal tumors by high-resolution amplicon melting analysis. Am. J. Clin. Pathol.122,206–216 (2004).
    • 19  Zhou L, Vandersteen J, Wang L et al.: High-resolution DNA melting curve analysis to establish HLA genotypic identity. Tissue Antigens64,156–164 (2004).
    • 20  Kennerson ML, Warburton T, Nelis E et al.: Mutation scanning the GJB1 gene with high-resolution melting analysis: implications for mutation scanning of genes for Charcot-Marie-Tooth disease. Clin. Chem.53,349–352 (2007).
    • 21  Liew M, Seipp M, Durtschi J et al.: Closed-tube SNP genotyping without labeled probes/a comparison between unlabeled probe and amplicon melting. Am. J. Clin. Pathol.127,1–8 (2007).
    • 22  Lonie L, Porter DE, Fraser M et al.: Determination of the mutation spectrum of the EXT1/EXT2 genes in British Caucasian patients with multiple osteochondromas, and exclusion of six candidate genes in EXT negative cases. Hum. Mutat.27,1160 (2006).
    • 23  Zhou L, Wang L, Palais R, Pryor R, Wittwer CT: High-resolution DNA melting analysis for simultaneous mutation scanning and genotyping in solution. Clin. Chem.51,1770–1777 (2005).• Combined mutation scanning and genotyping by melting.
    • 24  Herrmann MG, Durtschi JD, Bromley LK, Wittwer CT, Voelkerding KV: Amplicon DNA melting analysis for mutation scanning and genotyping: cross-platform comparison of instruments and dyes. Clin. Chem.52,494–503 (2006).• Instrument comparison for melting analysis.
    • 25  Herrmann MG, Durtschi JD, Bromley LK, Wittwer CT, Voelkerding KV: 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 (2007).
    • 26  Herrmann MG, Durtschi JD, Wittwer CT, Voelkerding KV: Expanded instrument comparison of amplicon DNA melting analysis for mutation scanning and genotyping. Clin. Chem. (2007) (In Press).
    • 27  Wittwer C, Kusukawa N: Molecular diagnostics technology. In: Clinical Diagnostic Technology, The Total Testing Process, Volume 2: The Analytical Phase. Ward-Cook K, Lehmann C, Schoeff L, Williams R (Eds). AACC Press, Washington, DC, USA, 341–369 (2005).
    • 28  Wittwer CT, Kusukawa N: Nucleic acid techniques. In: Tietz Textbook of Clinical Chemistry and Molecular Diagnostics (4th Edition). Burtis C, Ashwood E, Bruns D (Eds.). Elsevier, New York, NY, USA, 1407–1449 (2005).• General overview of nucleic acid methods.
    • 29  Gingeras TR, Higuchi R, Kricka LJ, Lo YM, Wittwer CT: Fifty years of molecular (DNA/RNA) diagnostics. Clin. Chem.51,661–671 (2005).
    • 30  Dujols VE, Kusukawa N, McKinney JT, Dobrowolski SF, Wittwer CT: High-resolution melting analysis for scanning and genotyping. In: Real-Time PCR. Dorak MT (Ed.). Garland Science, New York, NY, USA 157–171 (2006).
    • 31  Erali M, Palais B, Wittwer C: SNP genotyping by unlabeled probe melting analysis. In: Molecular Beacons – Signaling Nucleic Acid Probes. Seitz O, Marx A (Eds). Humana Press, Totowa, NJ, USA. (2007) (In Press).
    • 32  Dobrowolski SF, Ellingson C, Coyne T et al.: 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. Metab. (2007) (In Press).
    • 33  Lay MJ, Wittwer CT: Real-time fluorescence genotyping of factor V Leiden during rapid-cycle PCR. Clin. Chem.43,2262–2267 (1997).• First use of probes for genotyping by fluorescent melting analysis.
    • 34  Bernard PS, Ajioka RS, Kushner JP, Wittwer CT: Homogeneous multiplex genotyping of hemochromatosis mutations with fluorescent hybridization probes. Am. J. Pathol.153,1055–1061 (1998).
    • 35  Crockett AO, Wittwer CT: Fluorescein-labeled oligonucleotides for real-time PCR: using the inherent quenching of deoxyguanosine nucleotides. Anal. Biochem.290,89–97 (2001).
    • 36  Wittwer CT, Herrmann MG, Gundry CN, Elenitoba-Johnson KS: Real-time multiplex PCR assays. Methods25,430–442 (2001).
    • 37  Herrmann MG, Dobrowolski SF, Wittwer CT: Rapid β-globin genotyping by multiplexing probe melting temperature and color. Clin. Chem.46,425–428 (2000).
    • 38  Liew M, Pryor R, Palais R et al.: Genotyping of single-nucleotide polymorphisms by high-resolution melting of small amplicons. Clin. Chem.50,1156–1164 (2004).•• Introduction of small amplicon genotyping by high-resolution melting.
    • 39  Palais RA, Liew MA, Wittwer CT: Quantitative heteroduplex analysis for single nucleotide polymorphism genotyping. Anal. Biochem.346,167–175 (2005).
    • 40  Graham R, Liew M, Meadows C, Lyon E, Wittwer CT: Distinguishing different DNA heterozygotes by high-resolution melting. Clin. Chem.51,1295–1298 (2005).
    • 41  Vandersteen JG, Bayrak-Toydemir P, Palais RA, Wittwer CT: Identifying common variants in heteroduplex scanning by high-resolution melting. Clin. Chem.53. (2007) (In Press).
    • 42  Margraf RL, Mao R, Highsmith WE, Holtegaard LM, Wittwer CT: RET proto-oncogene genotyping using unlabeled probes, the masking technique, and amplicon high-resolution melting analysis. J. Mol. Diagn.9,184–196 (2007).
    • 43  Chou LS, Lyon E, Wittwer CT: A comparison of high-resolution melting analysis with denaturing high-performance liquid chromatography for mutation scanning: cystic fibrosis transmembrane conductance regulator gene as a model. Am. J. Clin. Pathol.124,330–338 (2005).
    • 44  Seipp MT, Durtschi JD, Liew MA et al.: Unlabeled oligonucleotides as internal temperature controls for genotyping by amplicon melting. J. Mol. Diagn. (2007) (Epub ahead of print).
    • 45  Liew M, Nelson L, Margraf R et al.: 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 (2006).
    • 46  Hill CE, Duncan A, Wirth D, Nolte FS: Detection and identification of cytochrome P-450 2C9 alleles *1, *2, and *3 by high-resolution melting curve analysis of PCR amplicons. Am. J. Clin. Pathol.125,584–591 (2006).
    • 47  Odell ID, Cloud JL, Seipp M, Wittwer CT: Rapid species identification within the Mycobacterium chelonae-abscessus group by high-resolution melting analysis of hsp65 PCR products. Am. J. Clin. Pathol.123,96–101 (2005).
    • 48  Cheng JC, Huang CL, Lin CC et al.: Rapid detection and identification of clinically important bacteria by high-resolution melting analysis after broad-range ribosomal RNA real-time PCR. Clin. Chem.52,1997–2004 (2006).
    • 49  Erali M, Pounder JI, Woods GL, Petti CA, Wittwer CT: Multiplex single-color PCR with amplicon melting analysis for identification of Aspergillus species. Clin. Chem.52,1443–1445 (2006).
    • 50  Zhou L, Myers AN, Vandersteen JG, Wang L, Wittwer CT: Closed-tube genotyping with unlabeled oligonucleotide probes and a saturating DNA dye. Clin. Chem.50,1328–1335 (2004).•• Introduction of unlabeled probe genotyping by melting and saturation dyes.
    • 51  Dames SA, Margraf RL, Pattison D, Wittwer CT, Voelkerding KV: Stabilty of 3´ blocking modifications of unlabeled probes. J. Mol. Diagn. (2007) (In Press).
    • 52  Poulson M, Wittwer CT: Closed-tube genotype of apo E with isolated probe PCR. Biotechniques (2007) (In Press).
    • 53  Margraf RL, Mao R, Wittwer CT: Masking selected sequence variation by incorporating mismatches into melting analysis probes. Hum. Mutat.27,269–278 (2006).
    • 54  Chou LS, Meadows C, Wittwer CT, Lyon E: Unlabeled oligonucleotide probes modified with locked nucleic acids for improved mismatch discrimination in genotyping by melting analysis. Biotechniques39(5),644 (2005).
    • 55  Lazaruk K, Walsh PS, Oaks F et al.: Genotyping of forensic short tandem repeat (STR) systems based on sizing precision in a capillary electrophoresis instrument. Electrophoresis19,86–93 (1998).
    • 56  Wang Y, Ju J, Carpenter BA, Atherton JM, Sensabaugh GF, Mathies RA: Rapid sizing of short tandem repeat alleles using capillary array electrophoresis and energy-transfer fluorescent primers. Anal. Chem.67,1197–1203 (1995).
    • 57  Schmalzing D, Koutny L, Chisholm D, Adourian A, Matsudaira P, Ehrlich D: Two-color multiplexed analysis of eight short tandem repeat loci with an electrophoretic microdevice. Anal. Biochem.270,148–152 (1999).
    • 58  Butler JM: Genetics and genomics of core short tandem repeat loci used in human identity testing. J. Forensic Sci.51,253–265 (2006).
    • 59  Li L, Li CT, Li RY et al.: SNP genotyping by multiplex amplification and microarrays assay for forensic application. Forensic Sci. Int.162,74–79 (2006).
    • 60  Vaughn CP, Elenitoba-Johnson KS: High-resolution melting analysis for detection of internal tandem duplications. J. Mol. Diagn.6,211–216 (2004).
    • 61  Orita M, Iwahana H, Kanazawa H, Hayashi K, Sekiya T: Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proc. Natl Acad. Sci. USA86,2766–2770 (1989).
    • 62  Lerman LS, Silverstein K: Computational simulation of DNA melting and its application to denaturing gradient gel. Electrophoresis Methods Enzymol.155,482–501 (1987).
    • 63  Xiao W, Oefner PJ: Denaturing high-performance liquid chromatography: a review. Hum. Mutat.17,439–474 (2001).
    • 64  Li Q, Liu Z, Monroe H, Culiat CT: Integrated platform for detection of DNA sequence variants using capillary array electrophoresis. Electrophoresis23,1499–1511 (2002).
    • 65  Bocker S: Simulating multiplexed SNP discovery rates using base-specific cleavage and mass spectrometry. Bioinformatics23,e5–12 (2007).
    • 66  Willmore-Payne C, Holden JA, Tripp S, Layfield LJ: Human malignant melanoma: Detection of BRAF- and c-kit-activating mutations by high-resolution amplicon melting analysis. Hum. Pathol.36,486–493 (2005).
    • 67  Willmore-Payne C, Holden JA, Chadwick BE, Layfield LJ: Detection of c-kit exons 11- and 17-activating mutations in testicular seminomas by high-resolution melting amplicon analysis. Mod. Pathol.19,1164–1169 (2006).
    • 68  Willmore-Payne C, Layfield LJ, Holden JA: c-KIT mutation analysis for diagnosis of gastrointestinal stromal tumors in fine needle aspiration specimens. Cancer105,165–170 (2005).
    • 69  Dobrowolski SF, McKinney JT, Amat di San Filippo C, Giak Sim K, Wilcken B, Longo N: Validation of dye-binding/high-resolution thermal denaturation for the identification of mutations in the SLC22A5 gene. Hum. Mutat.25,306–313 (2005).
    • 70  Margraf RL, Mao R, Highsmith WE, Holtegaard LM, Wittwer CT: Mutation scanning of the RET protooncogene using high-resolution melting analysis. Clin. Chem.52,138–141 (2006).
    • 71  Willmore-Payne C, Holden JA, Layfield LJ: Detection of epidermal growth factor receptor and human epidermal growth factor receptor 2 activating mutations in lung adenocarcinoma by high-resolution melting amplicon analysis: correlation with gene copy number, protein expression, and hormone receptor expression. Hum. Pathol.37,755–763 (2006).
    • 72  Willmore-Payne C, Holden JA, Layfield LJ: Detection of EGFR- and HER2-activating mutations in squamous cell carcinoma involving the head and neck. Mod. Pathol.19,634–640 (2006).
    • 73  Nomoto K, Tsuta K, Takano T et al.: 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 (2006).
    • 74  Willmore-Payne C, Volmar KE, Huening MA, Holden JA, Layfield LJ: Molecular diagnostic testing as an adjunct to morphologic evaluation of pancreatic ductal system brushings: Potential augmentation for diagnostic sensitivity. Diagn. Cytopathol.35,218–224 (2007).