Sequencing exons 5 to 8 of the p53 gene by MALDI-TOF mass spectrometry

Nature Biotechnology

Volumn 16, Issue 4, 1998, Pages 381-384

  Fu, Dong Jing ^a   Tang, Kai ^a   Braun, Andreas ^a   Reuter, Dirk ^a   Darnhofer Demar, Brigitte ^a   Little, Daniel P ^a   O'Donnell, Maryanne J ^a   Cantor, Charles R ^b   Köster, Hubert ^a  

^a SEQUENOM INC   (United States)

^b BOSTON UNIVERSITY   (United States)

Author keywords

DNA analysis; Gene mutation; Genomics

Indexed keywords

PROTEIN P53;

ARTICLE; CANCER GENETICS; DNA SEQUENCE; EXON; GENE AMPLIFICATION; GENE MUTATION; GENOME; HUMAN; HUMAN CELL; MASS SPECTROMETRY; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; TUMOR SUPPRESSOR GENE;

BASE SEQUENCE; DNA; EXONS; GENES, P53; HETEROZYGOTE DETECTION; HUMANS; MUTATION; POLYMERASE CHAIN REACTION; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 0031959739     PISSN: 10870156     EISSN: None     Source Type: Journal    
DOI: 10.1038/nbt0498-381     Document Type: Article

References (33)

1. Karas, M. and Hillenkamp, F. 1988. Laser desorption ionization of proteins with molecular masses exceeding 10000 Dalton. Anal. Chem. 60:2299-2301.
2. Hillenkamp, F., Karas, M., Beavis, R.C., and Chait, B.T. 1991. Matrix-assisted laser desorption/ionization mass spectrometry of biopolymers. Anal. Chem. 63:1193A-1203A.
3. Nelson, R.W., Thomas, R.M., and Williams, P. 1990. Time-of-flight mass spectrometry of nucleic acids by laser ablation and ionization from frozen aqueous matrix. Rapid Commun. Mass Spectrom. 4:348-351.
4. Spengler, B., Pan, Y., Cotter, R.J., and Kan, L.-S. 1990. Molecular weight determination of underivatized oligodeoxyribonuleotides by positive-ion matrix-assisted ultraviolet laser desorption mass spectrometry. Rapid Commun. Mass Spectrom. 4:99-102.
5. Wu, K.J., Steding, A., and Becker, C.H. 1993. Matrix-assisted laser desorption time-of-flight mass spectrometry of oligonucleotides using 3-hydroxypicolinic acid as an ultraviolet-sensitive matrix. Rapid Commun. Mass Spectrom. 7:142-146.
6. Pieles, U., Zürcher, W., Schär, M., and Moser, H.E. 1993. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry: a powerful tool for the mass and sequence analysis of natural and modified oligonucleotides. Nucl. Acids Res. 21:3191-3196.
7. Colby, S.M., King, T.B., and Reilly, J.P. 1994. Improving the resolution of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry by exploiting the correlation between ion position and velocity. Rapid Commun. Mass Spectrom. 8:865-868.
8. Vestal, M.L., Juhasz, P., and Martin, S.A. 1995. Delayed extraction matrix-assisted laser desorption time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 9:1044-1050.
9. Whittal, R.M. and Li, L. 1995. High-resolution matrix-assisted laser desorption/ionization in a linear time-of-flight mass spectrometer. Anal. Chem. 67:1950-1954.
10. Köster, H., Tang, K., Fu, D.-J., Braun, A., van den Boom, D., Smith, C.L. et al. 1996. A strategy for rapid and efficient DNA sequencing by mass spectrometry. Nature Biotechnology 14:1123-1128.
11. Tang, K., Taranenko, N.I., Allman, S.L., Chang, L.Y., and Chen, C.H. 1994. Detection of 500-nucleotide DNA by laser desorption mass spectrometry. Rapid Commun. Mass Spectrom. 8:727-730.
12. Jurinke, C., van den Boom, D., Jacob, A., Tang, K., Wörl, R., and Köster, H. 1996. Analysis of ligase chain reaction products via matrix-assisted laser desorption/ionization TOF mass spectrometry. Anal. Biochem. 237:174-181.
13. Taranenko, N.I., Matteson, K.J., Chung, C.N., Zhu, Y.F., Chang, L.Y., Allman, S.L. et al. 1996. Laser desorption mass spectrometry for point mutation detection. Genetic Analysis: Biomolecular Engineering 13:87-94.
14. Liu, Y.-H., Bai, J., Zhu, Y., Liang, X., Siemieniak, D., Venta, P. et al. 1995. Rapid screening of genetic polymorphisms using buccal cell DNA with detection by matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun. Mass Spectrom. 9:735-743.
15. Haff, L.A. and Smirnov, I.P. 1997. Single-nucleotide polymorphism identification assays using a thermostable DNA polymerase and delayed extraction MALDI-TOF mass spectrometry. Genome Res. 7:378-388.
16. Little, D.P., Braun, A., Darnhofer-Demar, B., and Köster, H. 1997. Apolipoprotein E polymorphism identification using temperature cycled primer oligo base extension and mass spectrometry. Eur. J. Clin. Chem. Clin. Biochem. 35:545-548.
17. Braun, A., Little, D.P., and Köster, H. 1997. Detecting CFTR gene mutations using primer oligo base extension and mass spectrometry. Clin. Chem. 43:1151-1158.
18. Little, D.P., Braun, A., Darnhofer-Demar, B., Friling, A., Li, Y., Mclver, R. et al. 1997. Rapid detection of RET proto-oncogene codon 634 mutations using mass spectrometry. J. Mol. Med. 75:745-750.
19. Higgins, G.S., Little, D.P., and Köster, H. 1997. Competitive oligonucleotide single base extension combined with mass spectrometric detection for mutation screening. Biotechniques 23:710-714.
20. Smirnov, I.P., Roskey, M.T., Juhasz, P., Takach, E.J., Martin, S.A., and Haff, L.A. 1996. Sequencing oligonucleotides by exonuclease digestion and delayed extraction matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Anal. Biochem. 238:19-25.
21. Roskey, M.T., Juhasz, P., Smirnov, I.P., Takach, E.J., Martin, S.A., and Haff, L.A. 1996. DNA sequencing by delayed extraction-matrix-assisted laser desorption/ionization time of flight mass spectrometry. Proc. Natl. Acad. Sci. USA 93:4724-4729.
22. Mouradian, S., Rank, D.R., and Smith L.M. 1996. Analyzing sequencing reactions from bacteriophage M13 by matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun. Mass Spectrom. 10:1475-1478.
23. Monforte, J.A. and Becker, C.H. 1997. High-throughput DNA analysis by time-of-flight mass spectrometry. Nat. Med. 3:360-362.
24. Jurinke, C., Zöllner, B., Feucht, H.-H., Jacob, A., Kirchhübel, J., Lüchow, A. et al. 1996. Detection of hepatitis B virus DA in serum samples via nested PCR and MALDI-TOF mass spectrometry. Genetic Analysis: Biomolecular Engineering 13:67-71.
25. Hurst, G.B., Doktycz, M.J., Vass, A.A., and Buchanan, M.V. 1996. Detection of bacterial DNA polymerase chain reaction products by matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun. Mass Spectrom. 10:377-382.
26. Sidransky, D. and Hollstein, M. 1996. Clinical implications of the p53 gene. Annual Review of Medicine 47:285-301.
27. Hainaut, P., Soussi, T., Shomer, B., Hollstein, M., Greenblatt, M., Hovig, E. et al. 1997. Database of p53 gene somatic mutations in human tumor and cell lines: updated compilation and future prospects. Nucl. Acids Res. 25:151-157.
28. Goh, H.S., Yao, J., and Smith, D.R. 1995. p53 point mutation and survival in colorectal cancer patients. Cancer Res. 55:5217-5221.
29. Fu, D.-J., Broude, N.E., Köster, H., Smith, C.L., and Cantor, C.R. 1996. Efficient preparation of short DNA sequence ladders potentially suitable for MALDI-TOF DNA sequencing. Genetic Analysis: Biomolecular Engineering 12:137-142.
30. de la Calle-Martin, O., Fabregat, V., Romero, M., Soler, J., Vives, J., and Yagüe, J. 1990. Ace II polymorphism of the p53 gene. Nucl. Acids Res. 18:4963.
31. Utile, D.P., Cornish, T.J., O'Donnell, M.J., Braun, A., Cotter, R.J., and Köster, H. 1997. MALDI on a chip: Analysis of arrays of low- to sub-femtomole quantities of synthetic oligonucleotides and DNA diagnostic products dispensed by a piezoelectric pipette. Anal. Chem. 69:4540-4546.
32. Sinha, N.D., Biernat, J., and Köster, H. 1983. β-Cyanoethyl N,N-dialkylamino/N-morpholino monochloro phosphoamidites: new phosphitylating agents facilitating ease of deprotection and work-up of synthesized oligonucleotides. Tetrahedron Letters 24:5843-5846.
33. Braun, A., Maier, E., Kammerer, S., Müller, B., and Röscher, A.A. 1996. A novel sequence polymorphism in the promoter region of the human B2-bradykinin receptor gene. Hum. Genet. 97:688-689.