Denaturing high-performance liquid chromatography (DHPLC) for nucleic acid analysis

Molecular Biomethods Handbook: Second Edition

Volumn , Issue , 2008, Pages 89-106

  Leung, Kim Hung ^a   Yip, Shea Ping ^a  

^a HONG KONG POLYTECHNIC UNIVERSITY   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 79952187877     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-60327-375-6_7     Document Type: Chapter

References (49)

1. The International SNP Map Working Group (2001) A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 49:928-933
2. Cotton RGH (1997) Mutation Detection. Oxford University Press, Oxford
3. Xiao W, Stern D, Jain M, Huber CG, Oefner PJ (2001) Multiplex capillary denaturing high-performance liquid chromatography with laser-induced fluorescence detection. Biotechniques 30:1332-1338
4. Xiao WH, Oefner PJ (2001) Denaturing high-performance liquid chromatography: a review. Hum Mutat 17:439-474
5. Gjerde DT, Hanna CP, Hornby D (2002) DNA chromatography. Wiley-VCH, Weinheim
6. Hung CC, Su YN, Lin CY, Yang CC, Lee WT, Chien SC, Lin WL, Lee CN (2005) Denaturing HPLC coupled with multiplex PCR for rapid detection of large deletions in Duchenne muscular dystrophy carriers. Clin Chem 51:1252-1256
7. Dehainault C, Lauge A, Caux-Moncoutier V, Pages-Berhouet S, Doz F, Desjardins L, Couturier J, Gauthier-Villars M, Stoppa-Lyonnet D, Houdayer C (2004) Multiplex PCR/liquid chromatography assay for detection of gene rearrangements: application to RB1 gene. Nucleic Acids Res 32:e139
8. Han W, Yip SP, Wang J, and Yap MKH (2004) Using denaturing HPLC for SNP discovery and genotyping, and establishing the linkage disequilibrium pattern for the all-Trans-retinol dehydrogenase (RDH8) gene. J Hum Genet 49:16-23
9. Ravnik-Glavac M, Atkinson A, Glavac D, Dean M (2002) DHPLC screening of cystic fibrosis gene mutations. Hum Mutat 19:374-383
10. Yip SP, Pun SF, Leung KH, Lee SY (2003) Rapid simultaneous genotyping of five common Southeast Asian -Thalassemia mutations by multiplex minisequencing and denaturing HPLC. Clin Chem 49:1656-1659
11. Chu MY (2003) Mutational analysis of the RLBP1 and CHM genes in Chinese patients with retinal degeneration. MSc Dissertation. The Hong Kong Polytechnic University, Hong Kong SAR, China
12. Colosimo A, Guida V, De Luca A, Cappabianca MP, Bianco I, Palka G, and Dallapiccola B. (2002) Reliability of DHPLC in mutational screening of betaglobin (HBB) alleles. Hum Mutat 19:287-295
13. Lilleberg SL, Durocher J, Sanders C, Walters K, Culver K (2004) High sensitivity scanning of colorectal tumors and matched plasma DNA for mutations in APC, TP53, K-RAS, and BRAF genes with a novel DHPLC fluorescence detection platform. Ann NY Acad Sci 1022:250-256
14. zur Stadt U, Rischewski J, Schneppenheim R, Kabisch H (2001) Denaturing HPLC for identification of clonal T-cell receptor gamma rearrangements in newly diagnosed acute lymphoblastic leukemia. Clin Chem 47:2003-2011
15. Hoogendoorn B, Owen MJ, Oefner PJ, Williams N, Austin J, ODonovan MC (1999) Genotyping single nucleotide polymorphisms by primer extension and high performance liquid chromatography. Hum Genet 104:89-93
16. Liang Q, Davis PA, Thompson BH, Simpson JT (2001) High-performance liquid chromatography multiplex detection of two single nucleotide mutations associated with hereditary hemochromatosis. J Chromatogr B Biomed Sci Appl 754: 265-270
17. Devaney JM, Pettit EL, Kaler SG, Vallone PM, Butler JM, Marino MA (2001) Genotyping of two mutations in the HFE gene using single-base extension and high-performance liquid chromatography. Anal Chem 73:620-624
18. Wu G, Hua L, Zhu J, Mo QH, Xu XM (2003) Rapid, accurate genotyping of betathalassaemia mutations using a novel multiplex primer extension/denaturing highperformance liquid chromatography assay. Br J Haematol 122:311-316
19. Hoogendoorn B, Norton N, Kirov G, Williams N, Hamshere ML, Spurlock G, Austin J, Stephens MK, Buckland PR, Owen MJ, ODonovan MC (2000) Cheap, accurate and rapid allele frequency estimation of single nucleotide polymorphisms by primer extension and DHPLC in DNA pools. Hum Genet 107:488-493
20. Lewis CM (2002) Genetic association studies: design, analysis and interpretation. Brief Bioinform 3:146-153
21. Norton N, Williams NM, ODonovan MC, Owen MJ (2004) DNA pooling as a tool for large-scale association studies in complex traits. Ann Med 36:146-152
22. Hannachi-MZali F, Ambler JE, Taylor CF, Hawkey PM (2002) Examination of single and multiple mutations involved in resistance to quinolones in Staphylococcus aureus by a combination of PCR and denaturing high-performance liquid chromatography (DHPLC). J Antimicrob Chemother 50:649-655
23. Eaves DJ, Liebana E, Woodward MJ, Piddock LJ (2002) Detection of gyrA mutations in quinolone-resistant Salmonella enterica by denaturing high-performance liquid chromatography. J Clin Microbiol 40:4121-4125
24. Randall LP, Coldham NG, Woodward MJ (2005) Detection of mutations in Salmonella enterica gyrA, gyrB, parC and parE genes by denaturing high performance liquid chromatography (DHPLC) using standard HPLC instrumentation. J Antimicrob Chemother 56:619-623
25. Hurtle W, Lindler L, Fan W, Shoemaker D, Henchal E, Norwood D (2003) Detection and identification of ciprofloxacin-resistant Yersinia pestis by denaturing high-performance liquid chromatography. J Clin Microbiol 41:3273-3283
26. Perez-Perez FJ Hanson ND (2002) Detection of plasmid-mediated AmpC betalactamase genes in clinical isolates by using multiplex PCR. J Clin Microbiol 40: 2153-2162
27. Shi R, Otomo K, Yamada H, Tatsumi T, Sugawara I (2006) Temperature-mediated heteroduplex analysis for the detection of drug-resistant gene mutations in clinical isolates of Mycobacterium tuberculosis by denaturing HPLC, SURVEYOR nuclease. Microbes Infect 8:128-135
28. Hurtle W, Shoemaker D, Henchal E, Norwood D (2002) Denaturing HPLC for identifying bacteria. Biotechniques 33:386-391
29. Evans JT, Hawkey PM, Smith EG, Boese KA, Warren RE, Hong G (2004) Automated high-Throughput mycobacterial interspersed repetitive unit typing of Mycobacterium tuberculosis strains by a combination of PCR and nondenaturing high-performance liquid chromatography. J Clin Microbiol 42:4175-4180
30. Goldenberg O, Herrmann S, Adam T, Marjoram G, Hong G, Gobel UB, Graf B (2005) Use of denaturing high-performance liquid chromatography for rapid detection and identification of seven Candida species. J Clin Microbiol 43:5912-5915
31. Domann E, Hong G, Imirzalioglu C, Turschner S, Kuhle J, Watzel C, Hain T, Hossain H, Chakraborty T (2003) Culture-independent identification of pathogenic bacteria and polymicrobial infections in the genitourinary tract of renal transplant recipients. J Clin Microbiol 41:5500-5510
32. Goldenberg O, Herrmann S, Marjoram G, Noyer-Weidner M, Hong G, Bereswill S, Gobel UB (2007) Molecular monitoring of the intestinal flora by denaturing high performance liquid chromatography. J Microbiol Methods (in press)
33. Barlaan EA, Sugimori M, Furukawa S, Takeuchi K (2005) Profiling and monitoring of microbial populations by denaturing high-performance liquid chromatography. J Microbiol Methods 61:399-412
34. Becker-Andre M, Hahlbrock K (1989) Absolute mRNA quantification using the polymerase chain reaction (PCR). A novel approach by a PCR aided transcript titration assay (PATTY). Nucleic Acids Res 17: 9437-9446
35. Freeman WM, Walker SJ, Vrana KE (1999) Quantitative RT-PCR: pitfalls and potential. Biotechniques 26:112-125
36. Leerkes MR, Caballero OL, Mackay A, Torloni H, OHare MJ, Simpson AJ, de Souza SJ (2002) In silico comparison of the transcriptome derived from purified normal breast cells and breast tumor cell lines reveals candidate upregulated genes in breast tumor cells. Genomics 79:257-265
37. Hayward AL, Hinojos CA, Nurowska B, Hewetson A, Sabatini S, Oefner PJ, Doris PA (1999) Altered sodium pump alpha and gamma subunit gene expression in nephron segments from hypertensive rats. J Hypertens 17:1081-1087
38. Hecker KH, Green SM, Kobayashi K (2000) Analysis and purification of nucleic acids by ion-pair reversed-phase high-performance liquid chromatography. J Biochem Biophys Methods 46:83-93
39. Dickman M, Hornby DP (2000) Isolation of single-stranded DNA using denaturing DNA chromatography. Anal Biochem 284:164-167
40. Azarani A, Hecker KH (2001) RNA analysis by ion-pair reversed-phase high performance liquid chromatography. Nucleic Acids Res 29:e7
41. Robertson KD, Wolffe AP (2000) DNA methylation in health and disease. Nat Rev Genet 1:11-19
42. Frommer M, McDonald LE, Millar DS, Collis CM, Watt F, Grigg GW, Molloy PL, Paul CL (1992) A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci USA 89: 1827-1831
43. Southern EM (1975) Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol 98:503-517
44. Singer-Sam J, Grant M, LeBon JM, Okuyama K, Chapman V, Monk M, Riggs AD (1990) Use of a HpaII-polymerase chain reaction assay to study DNA methylation in the Pgk-1 CpG island of mouse embryos at the time of X-chromosome inactivation. Mol Cell Biol 10:4987-4989
45. Baumer A (2002) Analysis of the methylation status of imprinted genes based on methylation-specific polymerase chain reaction combined with denaturing highperformance liquid chromatography. Methods 27:139-143
46. El-Maarri O, Herbiniaux U, Walter J, Oldenburg J (2002) A rapid, quantitative, non-radioactive bisulfite-SNuPE-IP RP HPLC assay for methylation analysis at specific CpG sites. Nucleic Acids Res 30:e25
47. Couvert P, Poirier K, Carrie A, Chalas C, Jouannet P, Beldjord C, Bienvenu T, Chelly J, Kerjean A (2003) DHPLC-based method for DNA methylation analysis of differential methylated regions from imprinted genes. Biotechniques 34: 356-362
48. Holland MM, Parsons TJ (1999) Mitochondrial DNA Sequence Analysis: validation and use for forensic casework. Forensic Sci Rev 11:21-50
49. LaBerge GS, Shelton RJ, Danielson PB (2003) Forensic utility of mitochondrial DNA analysis based on denaturing high-performance liquid chromatography. Croat Med J 44:281-288