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Microarray Technology

Microarrays offer customized options - New probes and assays offer higher throughput and flexibility for diverse applications.

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Microarrays spotted with oligonucleotides, DNA, RNA and proteins have been routinely used as tools for expression profiling for more than a decade. What’s exciting about this technology is that it has continually evolved to incorporate new assays, novel probes and diverse design formats to keep up with advances in science and technology. Over the years, microarray technologies have improved to offer better specificity, sensitivity and reliability. However, one limitation inherent to their design has yet to be overcome: the fact that microarrays cannot be used to find something completely novel, since the arrays consist of a set of predefined, pre-spotted genes or proteins. They can never be a truly hypothesis-free discovery platform.

“Microarrays are a starting point and are rarely sufficient for reaching a true biological conclusion,” says Jon Sherlock, product manager of TaqMan Array Plates and Express Plates in Applied Biosystems’ genomic assays business. “Often, you have to take that information to the next level,” says Sherlock, and according to him, the TaqMan arrays aim to do just that. The TaqMan arrays, offered in a card-like format, consist of 384 pre-spotted probes that measure levels of RNA in a sample, using the PCR-based quantitative TaqMan technology. “The TaqMan provides a definitive, quantitative answer and no validation is necessary with any alternative technology,” says Sherlock.

This technology is also offered in 96-well plates called Taq- Man Express Plates, in which customers can select from more than 50,000 predesigned assays for different targets in rat, human, mouse, dog and other genomes. “[Customers] can select a certain cluster of genes that represent a cellular pathway that they are interested in exploring,” says Sherlock. By May 2009, 130 new assays based on representative gene sets for predesigned pathways—including cytokines; stem cells; kinases; and genes for oncology, inflammation and many others—will be launched on the TaqMan Express Plates.

As companies update their arrays with new sets of assays and probes, customers are looking for more cost-effective options that offer higher flexibility and throughput. Agilent Technologies, Inc., recently expanded beyond its comparative genomic hybridization (CGH) arrays into a new area for measuring copy number variation (CNV). “The CNV arrays are an extension of the CGH platform, where we are still looking for DNA copy number changes,” says Dione Bailey, product manager for the CGH/CNV Microarrays at Agilent. The CNV arrays have probes designed for regions of the genome that are fairly complex or are highly repetitive and not unique. “We have now expanded our probe database and catalog offerings to target those known regions of CNV,” says Bailey.

Using Agilent’s eArray web portal, customers can also design their own CGH arrays using information from a database that contains nearly 24 million probes. “Some customers like to design arrays based on their specific needs, while others like to look at our catalog designs and make some minor modifications to them,” says Bailey. “It doesn’t cost you any more to design a custom array than it does to purchase a catalog array. There is no design fee, setup fee or any minimum quantity to place an order.” The flexibility for customers to design their own arrays and choose from different array formats helps reduce experimental costs. Costs can also be reduced by using a technology in which inter- and intra-assay variabilities are low and the amount of hands-on time is decreased. “Customers should be looking for the best value,” says Sherlock. “Having a technology that will work, getting a result that you can trust—without any pre-validation, optimization or post-validation needed, and without any repeats or failures—is very important.”

Tanuja Koppal, PhD, is a freelance science writer and consultant based in Randolph, N.J.

Agilent
The eArray 5.4 online microarray design tool enables users to design custom microRNA (miRNA) microarrays. Study of miRNA is rapidly emerging as these abundant molecules are increasingly associated with some cancers, heart disease, and other disorders. Researchers can use Agilent’s pre-designed human, mouse or rat miRNA probes, or access miRNA sequences for all 87 species in Sanger 12.0 in the designs of their miRNA microarrays. Each array contains about 15,000 features and arrays are printed eight-perslide, providing low cost per sample. When the design is complete, the file is uploaded to the proprietary SurePrint fabrication platform.
www.agilent.com

Arrayit
The NanoPrint™ LM210, an advanced microarrayer and the only system on the market to offer submicron positional accuracy, is for any format and bio molecule type. Using proprietary linear drive technology, the NanoPrint moves in 500 nanometer steps, offering an exceptional platform for all microarray applications in research, genomics, and diagnostics. The LM210 holds 210 standard glass substrates and comes complete with Arrayit’s patented printing technology and environmental control. Stackers and other options are also available.
www.arrayit.com

Eppendorf Biochip Systems
Eppendorf Biochip Systems’ novel approach to microarrays reflects where research is and what tools help make a more efficient and successful experiment. A complete and integrated system is offered from the microarray to the analyzed data. Products include DualChip® GMO for food and feed investigation, DualChip® TF MAPK and DualChip® TF Stem cell microarrays for transcription factor analysis. Aiming to make life easier for microarray laboratories, the company allows new users as well as established users a fast and convenient start into new opportunities with an optimized, easy-to-use and highly cost-effective microarray platform. Also available are customized and semi-customized microarrays.
www.eppendorf-biochip.com

Tecan
The HS 4800™ Pro hybridization station performs automated, reproducible microarray processing on single- and multi-segment slides. It has been designed to integrate the microarray experiment process— from pre-hybridization, bubble-free hybridization with patented ABS™, up to on-slide nitrogen drying (OSND™). Liquid agitation during hybridization increases sensitivity, stringency and uniformity, and reduces hybridization times. Comprehensive technology minimizes the risk of hybridization artefacts and inter-slide segment carry-over while enhancing consistency of results. Single, dual and QuadChamber ™ options are easily interchangeable.
www.tecan.com

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