Summary
Dideoxy DNA sequencing is routinely used in research and, increasingly, in clinical care for the detection of DNA sequence variants, single nucleotide changes, or small insertions or deletions, when the spectrum of DNA variation is unknown. DNA sequence variation can be present in tumor tissue that is not present in the normal tissue from the same individual. This somatic DNA sequence variation is often the cause of abnormal cell growth and/or regulation and, ultimately, tumorigenesis. Identification of these oncogenic DNA sequence variants has successfully led to the development of cancer therapies, since the abnormal protein products created from genomic DNA containing mutations can serve as targets for pharmacologic inhibition. Somatic DNA sequence analysis will continue to be a valuable technique for biomarker discovery until the complete spectrum of DNA variation observed in tumor tissue is understood.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsSpringer Nature is developing a new tool to find and evaluate Protocols. Learn more
References
Davies, H., Bignell, G. R., Cox, C., Stephens, P., Edkins, S., Clegg, S., Teague, J., Woffendin, H., Garnett, M. J., Bottomley, W., Davis, N., Dicks, E., Ewing, R., Floyd, Y., Gray, K., Hall, S., Hawes, R., Hughes, J., Kosmidou, V., Menzies, A., Mould, C., Parker, A., Stevens, C., Watt, S., Hooper, S., Wilson, R., Jayatilake, H., Gusterson, B. A., Cooper, C., Shipley, J., Hargrave, D., Pritchard-Jones, K., Maitland, N., Chenevix-Trench, G., Riggins, G. J., Bigner, D. D., Palmieri, G., Cossu, A., Flanagan, A., Nicholson, A., Ho, J. W., Leung, S. Y., Yuen, S. T., Weber, B. L., Seigler, H. F., Darrow, T. L., Paterson, H., Marais, R., Marshall, C. J., Wooster, R., Stratton, M. R., and Futreal, P. A. (2002) Mutations of the BRAF gene in human cancer. Nature 417, 949–54
Strachan, T., and Read, A. P. (2004) Human Molecular Genetics 3, Garland Science, London and New York.
Rozen, S., and Skaletsky, H. (2000) Primer3 on the WWW for general users and for biologist programmers.
Gordon, D., Abajian, C., and Green, P. (1998) Consed: a graphical tool for sequence finishing. Genome Res 8, 195–202.
Gordon, D., Desmarais, C., and Green, P. (2001) Automated finishing with autofinish. Genome Res 11, 614–25.
Gordon, D. (2004) Viewing and Editing Assembled Sequences Using Consed, Wiley, New York.
Greer, C. E., Peterson, S. L., Kiviat, N. B., and Manos, M. M. (1991) PCR amplification from paraffin-embedded tissues. Effects of fixative and fixation time. Am J Clin Pathol 95, 117–24.
Quach, N., Goodman, M. F., and Shibata, D. (2004) In vitro mutation artifacts after formalin fixation and error prone translesion synthesis during PCR. BMC Clin Pathol 4, 1.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Humana Press, a part of Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Farwell, L.M., Joshi, V.A. (2009). DNA Sequencing of Cancer-Related Genes for Biomarker Discovery. In: Tainsky, M. (eds) Tumor Biomarker Discovery. Methods in Molecular Biology, vol 520. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60327-811-9_15
Download citation
DOI: https://doi.org/10.1007/978-1-60327-811-9_15
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-60327-810-2
Online ISBN: 978-1-60327-811-9
eBook Packages: Springer Protocols