Oligonucleotide microarray analysis

Kurimoto K, Yabuta Y, Ohinata Y et al. An improved single-cell cDNA amplification method for efficient high-density oligonucleotide microarray analysis. Nucleic Acids Res 2006 34 e42. 

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). 

Roy S., Lado B. H., Khanna S., and Sen C. K. (2002). Vitamin E sensitive genes in the developing rat fetal brain a high-density oligonucleotide microarray analysis. FEBS Lett. 530 17-23. 

Luzzi V, Mahadevappa M, Raja R, Warrington JA, Watson MA. Accurate and reproducible gene expression profiles from laser capture microdissection, transcript amplification, and high density oligonucleotide microarray analysis. J Mol Diagn 2003 5(1) 9-14. 

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. 

Lee JM, Calkins MJ, Chan K, Kan YW, Johnson JA (2003) Identification of the NF-E2-related factor-2-dependent genes conferring protection against oxidative stress in primary cortical astrocytes using oligonucleotide microarray analysis. J Biol Chem 278 12029-12038... 

Kaposi-Novak, R, Lee, J.-S., Mikaelyan, A., Ratel, V., Thorgeirsson, S.S. (2004) Oligonucleotide microarray analysis of aminoallyl-labeled cDNA targets from linear RNA amplification. BioTechniques, 37, 580-588. 

Nishizuka, S., Winokur, S.T., Simon, M., Martin, J., Tsujimoto, H., and Stanbridge, E.J., Oligonucleotide microarray expression analysis of genes whose expression is correlated with tumorigenic and non-tumorigenic phenotype of HeLa X human fibroblast cells. Cancer Lett., 165, 210-209, 2001. 

Hacia JG, Collins FS. Mutational analysis using oligonucleotide microarrays. J Med Genet 1999 36 730-736. 

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). 

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. 

Hacia, J. G. (1999). Resequencing and mutational analysis using oligonucleotide microarrays. Nat. Genet. 21 42-47. 

Guerra CE. Analysis of oligonucleotide microarrays by 3 end labeling using fluorescent nucleotides and terminal transferase. Biotechniques 2006 41 53-56. 

DNA microarrays. The synthesis and applications of oligonucleotide microarrays is a rapidly expanding area. A variety of solid supports have been examined to attach principally ODNs, but also RNA. There have been improvements to attachment, synthesis and analysis of the resultant arrays, and a variety of methods for labelling have been examined. There are also many methods described for the attachment to metal surfaces, especially gold, but also silver and quantum dots. These latter reports are covered in the section on oligonucleotide conjugates. 

Horton JD, Shah NA, Warrington JA, Anderson NN, Park SW, Brown MS, Goldstein JL (2003) Combined analysis of oligonucleotide microarray data from transgenic and knockout mice identifies direct SREBP target genes. Proc Natl Acad Sci US A 100 12027-12032... 

Transcriptome analysis of leukocytes from patients with MCI, AD, and controls by oligonucleotide microarray identified eight genes significantly associated with purine metabolism and the ABC transporters. The ABCB1 gene exhibited significantly positive correlation with Mini-mental State Examination (MMSE) scores [134],... 

Buettner VL, Longmate JA, Barish ME, Mann JR, Singer-Sam J (2004) Analysis of imprinting in mice with uniparental duplication of proximal chromosomes 7 and 15 by use of a custom oligonucleotide microarray. Mamm Genome 15 199-209. 

Sergeev, N., D. Volokhov, V. Chizhikov, and A. Rasooly. Simultaneous analysis of multiple staphylococcal enterotoxin genes by an oligonucleotide microarray assay. J Clin Microbiol. 2004, 42(5), 2134-2143... 

Gitan R S, Shi H, Chen C M, et al. (2002). Methylation-specific oligonucleotide microarray a new potential for high-throughput methylation analysis. Genome Res. 12 158-164. 

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