Microarray oligonucleotide technology

Novagen (ProteoPlex ), S S (FAST Quant), BioSource (Cartesian Array ), and BD Biosciences (BD Clontech Ab Microarrays) have introduced or will soon introduce protein microarray slide formatted products in which antibodies are directly immobilized. Beckman Coulter s protein array products for performing micro-ELlSAS in standard 96-well plate formats are based upon the self-assembly (by hybridization) of oligonucleotide-antibody conjugates to complementary oligonucleotides arrayed in individual wells. HTG s protein array technology was described previously. 

Robert (Bob) Matson, Ph.D., is a senior staff scientist in the Advanced Technology Center at Beckman Coulter, Inc., Fullerton, California. He has been involved in the development of both nucleic acid and protein array-based technology for the past 13 years. His initial introduction to array technology began in collaboration with Sir Edwin Southern in developing an in situ oligonucleotide array synthesis platform for the corporation. Later work by Dr. Matson and his research team produced some of the first plastic microplate-based microarrays. Beckman Coulter recently launched the pi te based upon the microplate "array of arrays" concept. 

Levels of RNA (usually specific mRNAs) in a cell can be measured by well-established techniques such as Northern blot analysis or by polymerase chain reaction (PCR) analysis. However, the recent advent of DNA microarray technology has converted the identification and measurement of specific mRNAs (or other RNAs if required) into a high-throughput process. DNA arrays are also termed oligonucleotide arrays , gene chip arrays or simply, chips . 

Most recent studies in the area of transcriptomics have focused on the utility of microarray technologies which consist of pre-syn-thesized probes (cDNA or oligonucleotides) bound to an appara-... 

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. 

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