Detection of DNA mutations by fluorescence resonance energy transfer-based preferential homoduplex formation assay

Analytical Biochemistry

Volumn 408, Issue 2, 2011, Pages 197-205

  Kitano, Shiro ^a   Nakayama, Mashimo ^a   Yamane, Akio ^a   Tsukahara, Yusuke ^b   Amano, Masahiko ^a  

^a Life Science Research Laboratory   (Japan)

^b RIKEN   (Japan)

Author keywords

Competitive hybridization; FRET; KRAS mutation; PHFA

Indexed keywords

CELL CULTURE; COST EFFECTIVENESS; DNA; ENERGY TRANSFER; RISK ASSESSMENT;

CLINICAL DIAGNOSTICS; COMPETITIVE HYBRIDIZATION; FLUORESCENCE MEASUREMENTS; FLUORESCENCE RESONANCE ENERGY TRANSFER; FRET; KRAS MUTATION; PHFA; REPRODUCIBILITIES;

FORSTER RESONANCE ENERGY TRANSFER;

DOUBLE STRANDED DNA; GENOMIC DNA; K RAS PROTEIN;

ARTICLE; CELL STRAIN MCF 7; CODON; CONTROLLED STUDY; COST EFFECTIVENESS ANALYSIS; DIAGNOSTIC ACCURACY; DIAGNOSTIC KIT; DIAGNOSTIC TEST; DNA DETERMINATION; FLUORESCENCE; FLUORESCENCE RESONANCE ENERGY TRANSFER; HUMAN; HUMAN CELL; INTERMETHOD COMPARISON; MUTATIONAL ANALYSIS; NUCLEOTIDE SEQUENCE; PREFERENTIAL HOMODUPLEX FORMATION ASSAY; PRIORITY JOURNAL; SIMULATION; SOMATIC MUTATION;

EID: 78149412002     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2010.09.012     Document Type: Article

References (36)

1. Amado R.G., Wolf M., Peeters M., Van Cutsem E., Siena S., Freeman D.J., Juan T., Sikorski R., Suggs S., Radinsky R., Patterson S.D., Chang D.D. Wild-type KRAS is required for panitumumab efficacy in patients with metastatic colorectal cancer. J. Clin. Oncol. 2008, 26:1626-1634.
2. Karapetis C.S., Khambata-Ford S., Jonker D.J., O'Callaghan C.J., Tu D., Tebbutt N.C., Simes R.J., Chalchal H., Shapiro J.D., Robitaille S., Price T.J., Shepherd L., Au H.J., Langer C., Moore M.J., Zalcberg J.R. K-ras mutations and benefit from cetuximab in advanced colorectal cancer. N. Engl. J. Med. 2008, 359:1757-1765.
3. van Krieken J.H., Jung A., Kirchner T., Carneiro F., Seruca R., Bosman F.T., Quirke P., Flejou J.F., Plato Hansen T., de Hertogh G., Jares P., Langner C., Hoefler G., Ligtenberg M., Tiniakos D., Tejpar S., Bevilacqua G., Ensari A. KRAS mutation testing for predicting response to anti-EGFR therapy for colorectal carcinoma: proposal for a European quality assurance program. Virchows Arch. 2008, 453:417-431.
4. Brink M., de Goeij A.F., Weijenberg M.P., Roemen G.M., Lentjes M.H., Pachen M.M., Smits K.M., de Bruine A.P., Goldbohm R.A., van den Brandt P.A. K-ras oncogene mutations in sporadic colorectal cancer in the Netherlands Cohort Study. Carcinogenesis 2003, 24:703-710.
5. Chien C.C., Chen S.H., Liu C.C., Lee C.L., Yang R.N., Yang S.H., Huang C.J. Correlation of K-ras codon 12 mutations in human feces and ages of patients with colorectal cancer (CRC). Transl. Res. 2007, 149:96-102.
6. Ogino S., Kawasaki T., Brahmandam M., Yan L., Cantor M., Namgyal C., Mino-Kenudson M., Lauwers G.Y., Loda M., Fuchs C.S. Sensitive sequencing method for KRAS mutation detection by pyrosequencing. J. Mol. Diagn. 2005, 7:413-421.
7. Kumar R., Dunn L.L. Designed diagnostic restriction fragment length polymorphisms for the detection of point mutations in ras oncogenes. Oncogene Res. 1989, 4:235-241.
8. Tyagi S., Bratu D.P., Kramer F.R. Multicolor molecular beacons for allele discrimination. Nat. Biotechnol. 1998, 16:49-53.
9. Marras S.A., Kramer F.R., Tyagi S. Multiplex detection of single-nucleotide variations using molecular beacons. Genet. Anal. 1999, 14:151-156.
10. Newton C.R., Graham A., Heptinstall L.E., Powell S.J., Summers C., Kalsheker N., Smith J.C., Markham A.F. Analysis of any point mutation in DNA: the amplification refractory mutation system (ARMS). Nucleic Acids Res. 1989, 17:2503-2516.
11. Okayama H., Curiel D.T., Brantly M.L., Holmes M.D., Crystal R.G. Rapid, nonradioactive detection of mutations in the human genome by allele-specific amplification. J. Lab. Clin. Med. 1989, 114:105-113.
12. Tatsumi K., Mitani Y., Watanabe J., Takakura H., Hoshi K., Kawai Y., Kikuchi T., Kogo Y., Oguchi-Katayama A., Tomaru Y., Kanamori H., Baba M., Ishidao T., Usui K., Itoh M., Cizdziel P.E., Lezhava A., Ueda M., Ichikawa Y., Endo I., Togo S., Shimada H., Hayashizaki Y. Rapid screening assay for KRAS mutations by the modified smart amplification process. J. Mol. Diagn. 2008, 10:520-526.
13. Kosaka T., Yatabe Y., Endoh H., Yoshida K., Hida T., Tsuboi M., Tada H., Kuwano H., Mitsudomi T. Analysis of epidermal growth factor receptor gene mutation in patients with non-small cell lung cancer and acquired resistance to gefitinib. Clin. Cancer Res. 2006, 12:5764-5769.
14. Shitara K., Yokota T., Takahari D., Shibata T., Ura T., Utsunomiya S., Inaba Y., Yamaura H., Sato Y., Najima M., Kawai H., Tajika M., Sawaki A., Yatabe Y., Muro K. Phase II study of combination chemotherapy with irinotecan and cetuximab for pretreated metastatic colorectal cancer harboring wild-type KRAS. Jpn. J. Clin. Oncol. 2010, 699-701.
15. Do H., Krypuy M., Mitchell P.L., Fox S.B., Dobrovic A. High resolution melting analysis for rapid and sensitive EGFR and KRAS mutation detection in formalin fixed paraffin embedded biopsies. BMC Cancer 2008, 8:142.
16. Fassina A., Gazziero A., Zardo D., Corradin M., Aldighieri E., Rossi G.P. Detection of EGFR and KRAS mutations on trans-thoracic needle aspiration of lung nodules by high resolution melting analysis. J. Clin. Pathol. 2009, 62:1096-1102.
17. Ma E.S., Wong C.L., Law F.B., Chan W.K., Siu D. Detection of KRAS mutations in colorectal cancer by high-resolution melting analysis. J. Clin. Pathol. 2009, 62:886-891.
18. van Eijk R., van Puijenbroek M., Chhatta A.R., Gupta N., Vossen R.H., Lips E.H., Cleton-Jansen A.M., Morreau H., van Wezel T. Sensitive and specific KRAS somatic mutation analysis on whole-genome amplified DNA from archival tissues. J. Mol. Diagn. 2010, 12:27-34.
19. Dieterle C.P., Conzelmann M., Linnemann U., Berger M.R. Detection of isolated tumor cells by polymerase chain reaction-restriction fragment length polymorphism for K-ras mutations in tissue samples of 199 colorectal cancer patients. Clin. Cancer Res. 2004, 10:641-650.
20. Jacobson D.R., Mills N.E. A highly sensitive assay for mutant ras genes and its application to the study of presentation and relapse genotypes in acute leukemia. Oncogene 1994, 9:553-563.
21. McLean P.A., Wink D.A., Chapman S.K., Hickman A.B., McKillop D.M., Orme-Johnson W.H. A new method for extraction of iron-molybdenum cofactor (FeMoco) from nitrogenase adsorbed to DEAE-cellulose: 1. Effects of anions, cations, and preextraction treatments. Biochemistry 1989, 28:9402-9406.
22. Amicarelli G., Shehi E., Makrigiorgos G.M., Adlerstein D. FLAG assay as a novel method for real-time signal generation during PCR: application to detection and genotyping of KRAS codon 12 mutations. Nucleic Acids Res. 2007, 35:e131.
23. Dabritz J., Hanfler J., Preston R., Stieler J., Oettle H. Detection of Ki-ras mutations in tissue and plasma samples of patients with pancreatic cancer using PNA-mediated PCR clamping and hybridisation probes. Br. J. Cancer 2005, 92:405-412.
24. Chen C.Y., Shiesh S.C., Wu S.J. Rapid detection of K-ras mutations in bile by peptide nucleic acid-mediated PCR clamping and melting curve analysis: comparison with restriction fragment length polymorphism analysis. Clin. Chem. 2004, 50:481-489.
25. Luo J.D., Chan E.C., Shih C.L., Chen T.L., Liang Y., Hwang T.L., Chiou C.C. Detection of rare mutant K-ras DNA in a single-tube reaction using peptide nucleic acid as both PCR clamp and sensor probe. Nucleic Acids Res. 2006, 34:e12.
26. Cross J. DxS Ltd. Pharmacogenomics 2008, 9:463-467.
27. Kimura H., Suminoe M., Kasahara K., Sone T., Araya T., Tamori S., Koizumi F., Nishio K., Miyamoto K., Fujimura M., Nakao S. Evaluation of epidermal growth factor receptor mutation status in serum DNA as a predictor of response to gefitinib (IRESSA). Br. J. Cancer 2007, 97:778-784.
28. Kuang Y., Rogers A., Yeap B.Y., Wang L., Makrigiorgos M., Vetrand K., Thiede S., Distel R.J., Janne P.A. Noninvasive detection of EGFR T790M in gefitinib or erlotinib resistant non-small cell lung cancer. Clin. Cancer Res. 2009, 15:2630-2636.
29. Kimura H., Kasahara K., Kawaishi M., Kunitoh H., Tamura T., Holloway B., Nishio K. Detection of epidermal growth factor receptor mutations in serum as a predictor of the response to gefitinib in patients with non-small-cell lung cancer. Clin. Cancer Res. 2006, 12:3915-3921.
30. Terouanne B., Balaguer P., Boussioux A.M., Nicolas J.C. Quantitative and qualitative analysis of amplified DNA sequences by a competitive hybridization assay. Anal. Biochem. 1992, 205:193-199.
31. Oka T., Matsunaga H., Tokunaga K., Mitsunaga S., Juji T., Yamane A. A simple method for detecting single base substitutions and its application to HLA-DPB1 typing. Nucleic Acids Res. 1994, 22:1541-1547.
32. Tada M., Tateishi K., Kawabe T., Sasahira N., Isayama H., Komatsu Y., Shiratori Y., Omata M. Quantity of mutant K-ras gene in pancreatic secretions for diagnosis of pancreatic carcinoma with different assays: analysis of 100 patients. Clin. Chim. Acta 2002, 324:105-111.
33. Cardullo R.A., Agrawal S., Flores C., Zamecnik P.C., Wolf D.E. Detection of nucleic acid hybridization by nonradiative fluorescence resonance energy transfer. Proc. Natl. Acad. Sci. USA 1988, 85:8790-8794.
34. Morrison L.E. Basic principles of fluorescence and energy transfer. Methods Mol. Biol. 2008, 429:3-19.
35. Franklin W.A., Haney J., Sugita M., Bemis L., Jimeno A., Messersmith W.A. KRAS mutation: comparison of testing methods and tissue sampling techniques in colon cancer. J. Mol. Diagn. 2010, 12:43-50.
36. Whitehall V., Tran K., Umapathy A., Grieu F., Hewitt C., Evans T.J., Ismail T., Li W.Q., Collins P., Ravetto P., Leggett B., Salto-Tellez M., Soong R., Fox S., Scott R.J., Dobrovic A., Iacopetta B. A multicenter blinded study to evaluate KRAS mutation testing methodologies in the clinical setting. J. Mol. Diagn. 2009, 11:543-552.