Microarrays oligonucleotide

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Oligonucleotide microarray analysis of bone marrow samples from patients with IM-sensitive and IM-resistant CML have shown the ability to distinguish IM sensitivity and resistance. Differential gene expression patterns have the potential to identify new gene and protein targets for treatment and may have the potential to be used as a screening tool to identify patients with resistance prior to therapy (68,69,70,71,72). 

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FIGURE 23.1 Schematic representation of genome-scale gene expression analysis with DNA microarrays, (a) DNA microarrays produced by probe deposition (b) Oligonucleotide microarrays produced by in situ probe synthesis (Affymetrix technology). 

Thimmulappa RK, Mai KH, Srisuma S, Kensler TW, Yamamoto M, Biswal S. Identification of Nrf2-regulated genes induced by the chemopreventive agent sulforaphane by oligonucleotide microarray. Cancer Res 2002 62(18) 5196-5203. 

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Schuetz CS, Bonin M, Clare SE, Nieselt K, Sotlar K, Walter M, et al. Progression-specific genes identified by expression profiling of matched ductal carcinomas in situ and invasive breast tumors, combining laser capture microdissection and oligonucleotide microarray analysis. Cancer Res 2006 66(10) 5278—5286. 

In Sections 2 to 4, we review the technology of synthetic oligonucleotide microarrays and describe some of the popular statistical methods that are used to discover genes with differential expression in simple comparative experiments. A novel Bayesian procedure is introduced in Section 5 to analyze differential expression that addresses some of the limitations of current procedures. We proceed, in Section 6, by discussing the issue of sample size and describe two approaches to sample size determination in screening experiments with microarrays. The first approach is based on the concept of reproducibility, and the second approach uses a Bayesian decision-theoretic criterion to trade off information gain and experimental costs. We conclude, in Section 7, with a discussion of some of the open problems in the design and analysis of microarray experiments that need further research. 

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