s-RT-MELT for rapid mutation scanning using enzymatic selection and real time DNA-melting: New potential for multiplex genetic analysis

Nucleic Acids Research

Volumn 35, Issue 12, 2007, Pages

  Li, Jin ^a   Berbeco, Ross ^b   Distel, Robert J ^b   Jänne, Pasi A ^b   Wang, Lilin ^a   Makrigiorgos, G Mike ^a,b  

^a BRIGHAM AND WOMEN S HOSPITAL   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE; DNA FRAGMENT; DOUBLE STRANDED DNA; EPIDERMAL GROWTH FACTOR RECEPTOR; OLIGONUCLEOTIDE; PROTEIN P53; CEL I NUCLEASE; DNA; ENDONUCLEASE; UNCLASSIFIED DRUG;

ANALYTIC METHOD; ARTICLE; BASE MISPAIRING; CONTROLLED STUDY; DNA DENATURATION; DNA DETERMINATION; DNA HYBRIDIZATION; DNA SEQUENCE; GENE AMPLIFICATION; GENETIC ANALYSIS; GENETIC CODE; GENETIC SCREENING; GENETIC VARIABILITY; GERM LINE; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN CELL; MUTATIONAL ANALYSIS; NANOTECHNOLOGY; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SINGLE NUCLEOTIDE POLYMORPHISM; SOMATIC MUTATION; WILD TYPE; CELL LINE; CHEMISTRY; DNA MICROARRAY; EXON; GENETICS; METHODOLOGY; NEOPLASM; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; TUMOR SUPPRESSOR GENE; VALIDATION STUDY;

CELL LINE; DNA; DNA MUTATIONAL ANALYSIS; ENDONUCLEASES; EXONS; GENES, P53; HUMANS; NEOPLASMS; NUCLEIC ACID DENATURATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMERASE CHAIN REACTION; RECEPTOR, EPIDERMAL GROWTH FACTOR;

EID: 34547629014     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm403     Document Type: Article

References (48)

1. Baselga,J. (2006) Targeting tyrosine kinases in cancer: The second wave. Science, 312, 1175-1178.
2. Paez,J.G., Janne,P.A., Lee,J.C., Tracy,S., Greulich,H., Gabriel,S., Herman,P., Kaye,F.J., Lindeman,N. et al. (2004) EGFR Mutations in Lung Cancer: Correlation with Clinical Response to Gefitinib Therapy. Science, 304, 1497-1500.
3. Kobayashi,S., Boggon,T.J., Dayaram,T., Janne,P.A., Kocher,O., Meyerson,M., Johnson,B.E., Eck.M.J., Tenen.D.G. et al. (2005) EGFR mutation and resistance of non-small-cell lung cancer to gefitinib. N. Engl. J. Med., 352, 786-792.
4. Lynch,T.J., Bell,D.W., Sordella,R., Gurubhagavatula,S., Okimoto,R.A., Brannigan,B.W., Harris,P.L., Haserlat,S.M., Supko,J.G. et al. (2004) Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib. N. Engl. J. Med., 350, 2129-2139.
5. Pao,W., Miller,V., Zakowski,M., Doherty,J., Politi,K., Sarkaria,I., Singh,B., Heelan,R., Rusch,V. et al. (2004) EGF receptor gene mutations are common in lung cancers from "never smokers" and are associated with sensitivity of tumors to gefitinib and erlotinib. Proc. Natl Acad. Sci. USA, 101, 13306-13311.
6. Shigematsu,H. and Gazdar,A.F. (2006) Somatic mutations of epidermal growth factor receptor signaling pathway in lung cancers., Int. J.Cancer, 118, 257-262.
7. Kheterpal,I. and Mathies.R.A. (1999) Capillary array electrophoresis DNA sequencing. Anal. Chem, 71, 31A-37A.
8. Mitchelson,K.R. (2001) Thc application of capillary electrophoresis for DNA polymorphism analysis. Methods Mol. Biol., 162, 3-26.
9. Hacia, J.G. (1999) Resequencing and mutational analysis using oligonucleotide microarrays. Nat Genet., 21, 42-47.
10. Wong,C.W., Albert,T.J., Vega,V.B., Norton.J.E., Cutler,D.J., Richmond,T.A., Stanton,L.W., Liu,E.T. and Miller,L.D. (2004) Tracking the evolution of the SARS coronavirus using high-throughput, high-density resequencing arrays. Genome Res., 14, 398-405.
11. Ahmadian,A., Ehn,M. and Hober,S. (2006) Pyrosequencing: History, biochemistry and future. Clin. Chim. Acta, 363, 83-94.
12. Thomas,R.K., Nickerson,E., Simons,J.F., Janne,P.A., Tengs,T., Yuza,Y., Garraway,L.A., Laframboise.T., Lee,J.C. et al. (2006) Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing. Nat. Med., 12, 852-855.
13. Margulies,M., Egholm,M., Altman,W.E., Attiya,S., Bader,J.S., Bemben,L.A., Berka,J., Braverman,M.S., Chen,Y.J. et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376-380.
14. Larsen,L.A., Christiansen,M., Vuust,J. and Andersen,P.S. (2001) Recent developments in high-throughput mutation screening. Pharmacogenomics 2, 387-399.
15. Davies,H., Hunter,C., Smith,R., Stephens,P., Greenman,C., Bignell,G., Teague,J., Butler,A., Edkins,S. et al. (2005) Somatic mutations of the protein kinase gene family in human lung cancer. Cancer Res., 65, 7591-7595.
16. Nollau,P. and Wagener,C. (1997) Methods for detection of point mutations: Performance and quality assessment. IFCC Scientific Division, Committee on Molecular Biology Techniques. Clin. Chem., 43, 1114-1128.
17. Yeung,A.T., Hattangadi,D., Blakesley,L. and Nicolas,E. (2005) Enzymatic mutation detection technologies. Biotechniques, 38, 749-758.
18. Cotton,RG. and Campbell,R.D. (1988) Reactivity of cytosine and thymine in single base pair mismatches with hydroxylamine and osmium tetroxide and its application to the study of mutations. Proc. Natl Acad. Sci. USA, 83, 4397-4401.
19. Khrapko,K., Coller,H.A., Li-Sucholeiki,X.C., Andre,P.C. and Thilly,W.G. (2001) High resolution analysis of point mutations by constant denaturant capillary electrophoresis (CDCE). Methods Mol. Biol., 163, 57-72.
20. Chou,L.S., Lyon,E. and Wittwer,C.T. (2005) 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.
21. Maulik,G., Botchway,S., Chakrabarti,S., Tetradis,S., Price,B. and Makrigiorgos,G.M. (1999) Novel non-isotopic detection of MutY enzyme-recognized mismatches in DNA via ultrasensitive detection of aldehydes. Nucleic Acids Res., 27, 1316-1322.
22. Zhang,Y., Kaur,M., Price,B.D., Tetradis,S. and Makrigiorgos,G.M. (2002) An amplification and ligation-based method to scan for unknown mutations in DNA. Hum. Mutal., 20, 139-147.
23. Makrigiorgos,G.M. (2004) PCR-based detection of minority point mutations. Hum. Mutat., 23, 406-412.
24. Youil,R., Kemper,B.W. and Cotton,R.G. (1995) Screening for mutations by enzyme mismatch cleavage with T4 endonuclease VII. Proc. Natl Acad. Sci. USA, 92, 97-91.
25. De Gregorio,L., Gallinari,P., Gariboldi,M., Manenti,G., Pierotti,M.A., Jiricny,J. and Dragani,T.A. (1996) Genetic mapping of thymine DNA glycosylase (Tdg) gene and of one pseudogene in the mouse. Mamm. Genome, 7, 909-910.
26. Yang,B., Wen,X., Kodali,N.S., Oleykowski,C.A., Miller,C.G., Kulinski,J., Besack,D., Yeung,J.A., Kowalski,D. et al. (2000) Purification, cloning, and characterization of the CEL I nuclease. Biochemistry, 39, 3533-3541.
27. Oleykowski,C.A., Bronson Mullins,C.R., Godwin,A.K. and Yeung,A.T. (1998) Mutation detection using a novel plant endonuclease. Nucleic Acids Res., 26, 4597-4602.
28. Janne,P.A., Borras,A.M., Kuang,Y., Rogers,A.M., Joshi,V.A., Liyanage,H., Lindeman,N., Lee,J.C., Halmos,B. et al. (2006) A rapid and sensitive enzymatic method for epidermal growth factor receptor mutation screening. Clin. Cancer Res., 12, 751-758.
29. Till,B.J., Reynolds,S.H., Greene,E.A., Codomo,C.A., Enns,L.C., Johnson,J.E., Burtner,C., Odden,A.R., Young,K. et al. (2003) Large-scale discovery of induced point mutations with high-throughput TILLING. Genome Res., 13, 524-530.
30. Till,B.J., Burtner,C., Comai,L. and Henikoff,S. (2004) Mismatch cleavage by single-strand specific nucleases. Nucleic Acids Res., 32, 2632-2641.
31. Perry,J.A., Wang,T.L., Welham,T.J., Gardner,S., Pike,J.M., Yoshida,S. and Parniske,M. (2003) A TILLING reverse genetics tool and a web-accessible collection of mutants of the legume Lotus japonicus. Plant Physiol., 131, 866-871.
32. Hurlstone,A.F., Haramis,A.P., Wienholds,E., Begthel,H., Korving,J., Van Eeden,F., Cuppen,E., Zivkovic,D., Plasterk,R.H. et al. (2003) The Wnt/beta-catenin pathway regulates cardiac valve formation. Nature 425, 633-637.
33. Till,J., Zerr,T., Bowers,E., Greene,E.A., Comai,L. and Henikoff,S. (2006) High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling. Nucleic Acids Res., 34, e99.
34. Gilchrist,E.J., O'Neil,N.J., Rose,A.M., Zetka,M.C. and Haughn,G.W. (2006) TILLING is an effective reverse genetics technique for Caenorhabditis elegans. BMC Genomics, 7, 262.
35. (2005) Rapid amplification of 5′ complementary DNA ends (5′ RACE). Nat. Methods, 2, 629-630.
36. Morrison,T., Hurley,J., Garcia, J., Yoder,K., Katz,A., Roberts,D., Cho,J., Kanigan,T., Ilyin,S.E. D. et al. (2006) Nanoliter high throughput quantitative PCR. Nucleic Acids Res., 34, e123.
37. Steger,G. (1994) Thermal denaturation of double-stranded nucleic acids: prediction of temperatures critical for gradient gel electrophoresis and polymerase chain reaction. Nucleic Acids Res., 22, 2760-2768.
38. Blake,R.D. and Delcourt,S.G. (1998) Thermal stability of DNA. Nucleic Acids Res., 26, 3323-3332.
39. Behn,M., Qun,S., Pankow,W., Havemann,K. and Schuermann,M. (1998) Frequent detection of ras and p53 mutations in brush cytology samples from lung cancer patients by a restriction fragment length polymorphism- based "enriched PCR" technique. Clin. Cancer Res., 4, 361-371.
40. Kaur,M., Zhang,Y., Liu,W.H., Tetradis,S., Price,B.D. and Makrigiorgos,G.M. (2002) Ligation of a primer at a mutation: A method to detect tow level mutations in DNA. Mutagenesis, 17, 365-374.
41. Liu,W.H., Kaur,M. and Makrigiorgos,G.M. (2003) Detection of hotspot mutations and polymorphisms using an enhanced PCR-RFLP approach. Hum. Mutat., 21, 535-541.
42. Behn,M., Qun,S., Pankow,W., Havemann,K. and Schuermann,M. (1998) Frequent detection of ras and p53 mutations in brush cytology samples from lung cancer patients by a restriction fragment length polymorphism-based "enriched PCR" technique. Clin. Cancer Res., 4, 361-371.
43. Huang,C., Taki,T., Adachi,M., Konishi,J., Higashiyama,M. and Miyake,M. (098) Mutations in exon 7 and 8 of p53 as poor prognostic factors in patients with non-small cell lung cancer. Oncogene, 16, 2469-2477.
44. Huang,C.L., Taki,T., Adachi,M., Konishi,T., Higashiyama,M., Kinoshita,M., Hadama,T. and Miyake,M. (1998) Mutations of p53 and K-ras genes as prognostic factors for non-small cell lung cancer. Int. J. Oncol., 12, 553-563.
45. Steger,G. (1994) Thermal denaturation of double-stranded nucleic acids: prediction of temperatures critical for gradient gel electrophoresis and polymerase chain reaction. Nucleic Acids Res., 22, 2760-2768.
46. Hernandez-Boussard,T., Rodriguez-Tome,P., Montesano,R. and Hainaut,P. (1999) IARC p53 mutation database: A relational database to compile and analyze p53 mutations in human tumors and cell lines. International Agency for Research on Cancer. Hum. Mutat., 14, 1-8.
47. Lipsky,R.H., Mazyanti,C.M. Rudolph,J.G., Xu,K., Vyas,G., Bozak,D., Radel,M.Q. and Goldman,D. (2001) DNA melting analysis ior detection of single nucteotide polymorphisms. Clin. Chem., 47, 635-644.
48. 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.