Biochip Platforms for DNA Diagnostics
This chapter looks at the use of microlithographically fabricated biochip platforms for DNA diagnostics and prognostics, although protein and RNA biochips are also briefly considered. Biodetection methods such as ion-selective electrodes (ISEs), microelectromechanical systems (MEMS) devices such as microcantilevers, optical, piezoelectric-based acoustic wave, and mass spectrometry are briefly discussed. Emphasis is given to label-free electrochemical (impedimetric, voltammet-ric, and amperometric) detection. The production of DNA biochips is highlighted as are the operation and design of the experiments to reveal gene expression and SNP data. Applications discussed include the monitoring of microbes, cancer classification studies, and patient stratification in drug development. Finally, challenges and issues facing the development of diagnostic and prognostic biochips are discussed in detail.
KeywordsMolecular Diagnostics Severe Acute Respiratory Syndrome Differential Gene Expression Profile Molecular Diagnostics Laboratory Differential Drug Response
This work was supported by the industrial consortium of the Center for Bioelectronics, Biosensors and Biochips and by the Commonwealth Technologies Research Fund (CTRF) Grant SE2002-02. This chapter is dedicated to the memory of Dr. Anil K. Deisingh who passed away on October 21st, 2005 and was at the time a member of the technical staff of the Analytical Chemistry and Microbiology Services Unit, Caribbean Industrial Research Institute, University of the West Indies Campus, St. Augustine, Republic of Trinidad & Tobago.
- 1.Guiseppi-Elie, A. (2003) Biochip platforms for DNA diagnostics. Business Briefing: PharmaTech, London, World Markets Research Centre, p. 87.Google Scholar
- 3.Proudnikov, D., Timofeev, E., and Mirzabekov, A. (1998) Immobilization of DNA in poly-acrylamide gel for the manufacture of DNA and DNA–oligonucleotide microchips. Analytical Biochemistry 259(1), 34–41. Llewellyn, B., Lebed, J., and Chik, V. (2002), www.promega.com/geneticidproc/ussymp11proc/content/llewellyn.pdf.Google Scholar
- 5.Wagner, P. and Kim, R. (May 2002) www.currentdrugdiscovery.com, pp. 23–28.
- 6.Gad-el-Hak, Mohamed, Ed. (2001) The MEMS Handbook. CRC Press, Boca Raton, FL. The MEMS Exchange (2002), http://www.mems-exchange.org/MEMS/what-is.html.
- 7.Christian, G.D. (1994) Analytical Chemistry, 5th ed., Chapter 13. Wiley, New York, 384–397.Google Scholar
- 8.Cunningham, A.J. (1998) Introduction to Bioanalytical Sensors, Techniques in Analytical Chemistry. John Wiley & Sons, Inc. New York.Google Scholar
- 9.A. Guiseppi-Elie and L. Lingerfelt “Impedimetric Detection of DNA Hybridization: Towards Near Patient DNA Diagnostics” In Immobilization of DNA on Chips I (2005); Christine Wittmann, Ed.; Topics in Current Chemistry Vol. 260, Springer Berlin, Heidelberg. pp 161–186.Google Scholar
- 10.Turner, A.P.F. and Newman, J.D. (1998) Biosensors for Food Analysis, A.O. Scott (Ed.). Royal Society of Chemistry, Cambridge, pp. 1–10.Google Scholar
- 13.Hall, E.A.H. (1990) Biosensors. Open University Press, Milton Keynes,UK.Google Scholar
- 16.Schena, M. (2002) Microarray Analysis. Wiley-Liss, New York.Google Scholar
- 17.NCBI (2003) http://www.ncbi.nlm.nih.gov/About/primer/microarrays.html (accessed on May 5th, 2008).
- 19.Vahey, M., Nau, M.E., Barrick, S., Cooley, J.D., Sawyer, R., Sleeker, A.A., Vickerman, P., Bloor, S., Larder, B., Michael, N.L., and Wegner, S.A. (1999) Journal of Clinical Microbiology, 37, 2533–2537.Google Scholar
- 22.Windle, B. and Guiseppi-Elie, A. (2003) Microarrays and gene expression profiling applied to drug research. In Burger's Medicinal Chemistry, 6th ed., D.J. Abraham (Ed.). Wiley, New York.Google Scholar
- 23.Willis, R.C. (2003), Monitoring microbes. Modern Drug Discovery, January, 16–21.Google Scholar
- 26.Hanna, G.J., Johnson, V.A., Kuritzkes, D.R., Richman, D.D., Martinex-Picado, J., Sutton, L., Hazelwood, J.D., and D'Aquila, R.T. (2000) Journal of Clinical Microbiology, 38, 2715–2721.Google Scholar
- 30.Higgins, J.P.T., Shinghal, R., Gill, H., Reese, J.H., Terris, M., Cohen, R.J., Fero, M., Pollack, J.R., vandeRijn, M., and Brooks, J.D. (2003) American Journal of Pathology, 162(3), 925–932.Google Scholar
- 31.Archer, K.J., Dumur, C.I., Scott Taylor, G., Chaplin, M.D., Guiseppi-Elie, A., Buck, G., Grant, G., Ferreira-Gonzalez, A., and Garrett, C. (2008) A disattenuated correlation estimate when variables are measured with error: Illustration estimating cross-platform correlations. Statistics in Medicine, 27(7), 1026–1039.CrossRefGoogle Scholar
- 34.van Brunt, J. (2003) Signals Magazine (online), 25th April 2003, http://www.signalsmag.com/signalsmag.nsf/0/6D4F7034D24D25988256D130011E957?Open.
- 35.SNP Consortium (2001) http://snp.cshl.org/about/2001_TSC_project.overview.shtml. (accessed on May 5th, 2008)
- 36.NIH New Advisory (October 2002) http://www.genome.gov/page.cfm?pageID=10005336. (accessed on May 5th, 2008)
- 37.McNeely, G. (May 5th, 2003) Small Times On-Line IEEE http://www.smalltimes.com/articles/article_display.cfm?Section=ARCHI&C=Profi&ARTICLE_ID=268701&p=109 (accessed on May 5th, 2008)
- 43.Anthony Guiseppi-Elie, Scott Taylor, Louise Lingerfelt, Chris Nixon, Ryan Georgiana, Joy Kim, Stephanie Smith, Brad Mangrum and Nicholas Farell “Studies of the Interaction of Platinum Drugs with DNA Using Oligonucleotide Microarrays” Macromolecular Symposia (2006) 235(1), 115–120CrossRefGoogle Scholar
- 44.CTRF Consortium of Virginia http://www.ctrf-cagenomics.vcu.edu/publiclyavaildata.htm. (accessed on May 5th, 2008)
- 45.Lingerfelt, L., Karlinsey, J., Landers, J., and Guiseppi-Elie, A. (2008) Impedimetric detection for DNA hybridization within microfluidic biochips. In Microchip-Based Assay Systems Methods in Molecular Biology, Pierre N. Floriano, Ed.; Royal Society of Chemistry. Humana Press, NJ. vol. 385, Chapter 8, pp 103–120.Google Scholar
- 48.Guiseppi-Elie, A., Brahim, S., and Wilson, A. (2007) Biosensors based on electrically conducting polymers. In Handbook of Conducting Polymers: Conjugated Polymer Processing and Applications; 3rd ed., T. Skotheim and J.R. Reynolds (Eds.). Taylor and Francis, New York. Chapter 12, pp. 12:1–12:45.Google Scholar
- 50.Williams, E. (2002) Gene Chips: Science and Policy Basics, 2002 Virginia Biotechnology Summit and Governor's Conference on Technology Transfer and University Research, McLean, Virginia, October 14–16.Google Scholar
- 51.Johns, D.J.; Brettwisch, R., and Lebovitz, R. (1991) Patenting DNA: Letter to the editor. Science, 254 (5036), 1276.Google Scholar
- 52.Williams, E.D. (2001) The policy and ethics of DNA chip technologies. In N. Fujiki, M. Sudo, and D.R.J. Macer (Eds.), Bioethics and the Impact of Human Genome Research in the 21st Century: Pharmacogenomics, DNA polymorphism and Medical Genetics Services, 104–109, Eubios Ethics Institute, Tsukuba, Japan.Google Scholar
- 53.Wengel, J. (2004) Analyst, 2, 277–280.Google Scholar