DNA Biochips - past, present, and future: An overview

Biochips as Pathways to Drug Discovery

Volumn , Issue , 2006, Pages 1-14

  Hardiman, Gary ^a,b   Carmen, Andrew ^c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b NATIONAL UNIVERSITY OF IRELAND   (Ireland)

^c JOHNSON AND JOHNSON PHARMACEUTICAL RESEARCH AND DEVELOPMENT   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77949626090     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (42)

1. Cunningham, M.J. Genomics and proteomics: the new millennium of drug discovery and development. J Pharmacol Toxicol Methods 44(1): 291-300, 2000.
2. Kennedy, T. Managing the drug discovery/development interface. Drug Discovery Today 2(10): 436-444, 1997.
3. Avidor, Y., Mabjeesh, N.J., and Matzkin, H. Biotechnology and drug discovery: from bench to bedside. South Med J. 96(12): 1174-1186, 2003.
4. Marton, M.J., DeRisi, J.L., Bennett, H.A., Iyer, V.R., Meyer, M.R., Roberts, C., Stoughton, R., Burchard, J., Slade, D., Dai, H., Bassett, D.E., Jr., Hartwell, L.H., Brown, P.O., and Friend, S.H. Drug target validation and identification of secondary drug target effects using DNA microarrays. Nat. Med. 4: 1293-1301, 1998.
5. Vilo, J. and Kivinen, K. Regulatory sequence analysis: application to the interpretation of gene expression. Eur Neuropsychopharmacol 11: 399-411, 2001.
6. Waring, J.F., Ciurlionis, R., Jolly, R.A., Heindel, M., and Ulrich, R.G. Microarray analysis of hepatotoxins in vitro reveals a correlation between gene expression profiles and mechanisms of toxicity. Toxicol Lett. 120: 359-368, 2001.
7. Hamadeh, H.K., Amin, R.P., Paules, R.S., and Afshari, CA: An overview of toxicogenomics. Curr. Issues Mol. Biol. 4(2): 45-56, 2002.
8. Johnson, J.A. Drug target pharmacogenomics: an overview. Am. J. Pharmacogenomics 1(4): 271-281, 2001.
9. Kruglyak, L. and Nickerson, D.A. Variation is the spice of life. Nat. Genet. 27: 234-236, 2001.
10. Southern, E.M. Blotting at 25. Trends Biochem Sci. 25: 585-588, 2000.
11. Grunstein, M. and Hogness, D.S. Colony hybridization: a method for the isolation of cloned DNAs that contain a specific gene. Proc Natl Acad Sci U S A 72(10):3961-3965, 1975.
12. Williams, J.G. and Patient, R.K. Genetic Engineering. IRL Press, Washington, D.C., 1988.
13. Hardiman, G. and Gannon, F. Differential transferrin gene expression in Atlantic salmon (Salmo salar L.) freshwater parr and seawater smolts. J. Appl. Ichthyol. 12:43-47, 1996.
14. Wallace, R.B., Shaffer, J., Murphy, R.F., Bonner, J., Hirose, T., Itakura, K. Hybridization of synthetic oligodeoxyribonucleotides to phi chi 174 DNA: the effect of single base pair mismatch. Nucl. Acids Res 6: 3543-3557, 1979.
15. Chee, M., Yang, R., Hubbell, E., Berno, A., Huang, X.C., Stern, D., Winkler, J., Lockhart, D.J., Morris, M.S., Fodor, S.P.A. Accessing genetic information with highdensity DNA arrays. Science 274: 610-614, 1996.
16. Schena, M., Shalon, D., Davis, R.W., and Brown, P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467-470, 1995.
17. Bowtell, D.D.L. Options available - from start to finish for obtaining expression data by microarray. Nat. Genet., 21: 25-32, 1999.
18. Hardiman, G. Microarray platforms - comparisons and contrasts. Pharmacogenomics 5(5): 487-502, 2004.
19. Wick, I. and Hardiman, G. Biochip platforms as functional genomics tools for drug discovery. Curr Opin Drug Discov Dev. 8(3): 347-354, 2005.
20. Knight, J. When the chips are down. Nature 410: 6831, 2001.
21. Ramakrishnan, R., Dorris, D., Lublinsky, A., Nguyen, A., Domanus, M., Prokhorova, A., Gieser, L., Touma, E., Lockner, R., Tata, M., Zhu, X., Patterson, M., Shippy, R., Sendera, T.J., and Mazumder, A. An assessment of Motorola CodeLink TM microarray performance for gene expression profiling applications. Nucl. Acids Res. 30: e30, 2002.
22. Hughes, T.R., Mao, M., Jones, A.R., Burchard, J., Marton, M.J., Shannon, K.W., Lefkowitz, S.M., Ziman, M., Schelter, J.M., Meyer, M.R., Kobayashi, S., Davis, C., Dai, H., He, Y.D., Stephaniants, S.B., Cavet, G., Walker, W.L., West, A., Coffey, E., Shoemaker, D.D., Stoughton, R., Blanchard, A.P., Friend, S.H., and Linsley, P.S. Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat. Biotechnol 19: 342-347, 2001.
23. Nuwaysir, E.F., Huang, W., Albert, T.J., Singh, J., Nuwaysir, K., Pitas, A., Richmond, T., Gorski, T., Berg, J.P., Ballin, J., McCormick, M., Norton, J., Pollock, T., Sumwalt, T., Butcher, L., Porter, D., Molla, M., Hall, C., Blattner, F., Sussman, M.R., Wallace, R.L., Cerrina, F., and Green, R.D. Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Res 12: 1749-1755, 2002.
24. Singh-Gasson, S., Green, R.D., Yue, Y., Nelson, C., Blattner, F., Sussman, M.R., and Cerrina, F. Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nat. Biotechnol. 17(10): 974-978, 1999.
25. Gao, X., LeProust, E., Zhang, H., Srivannavit, O., Gulari, E., Yu, P., Nishiguchi, C., Xiang Q, and Zhou X. Aflexible: light-directed DNA chip synthesis gated by deprotection using solution photogenerated acids. Nucl. Acids Res 29, 4744-4750, 2001.
26. Pandey, A. and Mann, M. Proteomics to study genes and genomes. Nature (Insight), 405: 837-846, 2000.
27. Shaw, G. Cheaper chips find a good fit with hit validation. Drug Discovery Dev. 2, 2005.
28. Mitchell, P. Aperspective: on protein microarrays. Nat Biotechnol 20: 225-229, 2002.
29. Service, R.F. Searching for recipes for protein arrays. Science 294: 2080-2082, 2001.
30. Cahill, D. Protein arrays: a high throughput solution for proteomics research? Proteomics:A Trends Guide, Elsevier, London, 2000, pp. 47-51.
31. Zhu, H., Bilgin, M., Bangham, R., Hall, D., Casamayor, A., Bertone, P., Lan, N., Jansen, R., Bidlingmaier, S., Houfel, T., Mitchell, T., Miller, P., Dean, R.A., Gerstein, M., and Snyder, M. Global analysis of protein activities using proteome arrays. Science 293: 2101-2105, 2001.
32. Rouse, R.J., Espinoza, C.R., Niedner, R.H., and Hardiman, G. Development of a microarray assay that measures hybridization stoichiometry in moles. Biotechniques 3: 464-470, 2004.
33. Gygi, S.P., Rochon, Y., Franza, B., and Abersold, R. Correlation between protein and mRNA abundance in yeast. Mol. Cell Biol. 19: 1720-1730, 1999.
34. Rouse, R. and Hardiman, G. Microarray technology: an intellectual property retrospective. Pharmacogenomics 4(5): 623-632, 2003.
35. Hardiman, G. Microarray platforms and drug discovery. Trends in Drug Discovery - Screening 1: 1-4, 2005.
36. Hardiman, G. Microarray platforms - comparisons and contrasts. Pharmacogenomics 5(5): 487-502, 2004.
37. Stafford, P. and Liu, P. Microarray technology comparison, statistical analysis, and experimental design. Microarray Methods and Applications - Nuts and Bolts, DNA Press, Eagleville, PA, 2003, pp. 273-324.
38. Ren, B., Robert, F., Wyrick, J. et al. Genome-wide location and function of DNA associated proteins. Science 290: 2306-2309, 2000. [Description of the Genome-wide location process, which identified all of the known genes for the yeast transcription factor Gal4, as well as several new genes that were confirmed by conventional ChIP assays and additional functional assays.]
39. Kim, T.H., Barrera, L.O., Zheng, M., Qu, C., Singer, M.A., Richmond, T.A., Wu, Y., Green, R.D., and Ren, B. Ahigh: -resolution map of active promoters in the human genome. Nature 436(7052): 876-880, 2005.
40. Wheeler, D.B., Carpenter, A.E., and Sabatini, D.M. Cell microarrays and RNA interference chip away at gene function. Nat. Genet. 37(Suppl.): S25-30, 2005.
41. Espineda, C., Seligson, D.B., James Ball, Jr., W., Rao, J., Palotie, A., Horvath, S., Huang, Y., Shi, T., and Rajasekaran, A.K. Analysis of the Na, K-ATPase alpha- and beta-subunit expression profiles of bladder cancer using tissue microarrays. Cancer 97: 1859-1868, 2003.
42. Mahant, V., Kureshy, F., Vairavan, R., and Hardiman, G. The INFINITI TM system - an automated multiplexing microarray platform for clinical laboratories. Microarray Methods and Applications - Nuts and Bolts, DNA Press, Eagleville, PA, 2003, pp. 325-338.