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Aug 1, 2008 (Vol. 28, No. 14)

Ancillary Analysis Tools for Microarrays

  • The Geniom® RT Analyzer, a new benchtop microarray processing instrument, was presented by febit at Select Bioscience’s “Advances in Microarray Technology”. The platform complements Geniom® One, the company’s flagship microfluidic microarray system, and is designed to automate the hybridization and analysis of Geniom microfluidic microarrays.

    “Microarray processing has traditionally required separate instruments for hybridization and imaging,” pointed out Peter Roberts, Ph.D., manager at febit. “In contrast, our Geniom RT Analyzer automates sample addition, hybridization, washing, staining, and detection in a single benchtop platform.”

    The system will give labs that do not have the expertise in microarray experimentation a cost-effective and relatively simple route into biochip-based research; all the user has to do is prepare the sample and label it. “We can custom synthesize arrays according to specific requirements for any species,” Dr. Roberts said.

    febit also offers a range of microfluidic microarrays for applications including mRNA profiling and miRNA profiling.

    “Our miRNA arrays are based on the latest Sanger miRBase data,” he explained. “Most suppliers of off-the-shelf arrays produce their chips in large batches with fixed content. This means they can’t always keep up with the latest sequence data in some fields such as microRNAs or other noncoding RNAs.” The miRBase, on the other hand, is updated frequently, Dr. Roberts pointed out. “The flexibility of our microfluidic array technology means we can always produce chips with the most up-to-date content.”

    Synthesis of microarray capture probes is carried out in situ within the chip’s microchannels. Thus researchers can take de novo sequence data, create highly customized microarrays, and synthesize, hybridize, as well as analyze them in 24 hours. “The flexibility also means array design can easily be modified through several refinement rounds to develop the ideal array for a particular application.”

    The industry’s drive to focus on specific targets led febit to develop HybSelectTM, which it aims to launch next year, initially as a service offering. HybSelect is a method for sequence capturing out of DNA to generate samples for next-generation sequencing. “The ability to enrich samples prior to sequencing not only generates better sequencing data but saves the client time and money in terms of resources and reagents.”

    Using HybSelect, febit customizes the microfluidic array so it only captures the DNA of interest. The method can be used in combination with all next-generation sequencing devices. The sample is sent to febit, hybridized to the customized array, and then washed to remove residual, nontarget DNA. The target DNA is then recovered from the array, and the enriched sample shipped back to the customer for incorporation into the protocol of the next-generation sequencing instrument.

    SlidePath, a spin-out from Dublin City University (www.dcu.ie), is focused on software development for digital slide and life science informatics applications. The company’s Distiller solution is a secure, web-based information management solution that enables disparate research data sets to be stored within a central database and shared.

    Ideally suited to the integration and management of high-throughput processes and particularly omics data, the software has utility in clinical research, allowing researchers to integrate data from tissue microarrays (TMAs) and digital slides, explained Donal O’Shea, Ph.D., cofounder and CEO.

    “Used broadly for clinical research in areas such as biomarker validation, TMAs are quite different from gene and protein arrays,” he pointed out. “Whereas one gene array will typically profile gene expression from one sample, TMAs investigate the expression of one protein in many samples.

    “Thus, gene arrays are used to identify putative biomarkers, but it is tissue arrays that are used to validate the findings in clinical cohorts. Distiller allows users to integrate and search through powerful multilayer databases and run complex hypothesis testing on data using the platform’s analytical tools.”

    Distiller’s module plug-in, OpTMA, has been designed to facilitate the analysis of TMAs, automating the entire process of dearraying and associating tissue cores with clinical data. Dearraying is a virtual process, so the original digital slide is never disrupted, and the TMA tissue section can be viewed at any time.

    OpTMA allows the user to dearray entire tissue microarrays with one click, build virtual, patient-centric biomarker arrays from real arrays, and carry out rapid assessment of biomarker panel expression on a patient-by-patient basis, according to SlidePath.

    “We also recently launched a new image analysis product, which allows the high-throughput quantification of immunohistochemical staining in both full-face sections and TMAs,” Dr. O’Shea added. “The software will accurately quantify staining in conventional cell compartments such as membrane, nucleus, and cytoplasm”.

    Image analysis is a new field for SlidePath and required the development of solutions to complexities not present in gene and protein arrays, he admitted. “Unlike gene/protein array analysis, which is concerned with homogeneous spots, in TMAs the spots are by nature heterogeneous in structure due to the presence of different cell types and tissue architectures.”

    Unlike pixel-based image analysis approaches, Definiens’ is based on the Definiens Cognition Network Technology®, which extracts intelligence from digital data in a way that emulates human cognitive processes, according to the firm. “While imaging techniques are becoming ever-more sensitive, issues still surround the ability to assess the specific structures in images and extrapolate them into relevant data and knowledge,” explained Martin Baatz, Ph.D., vp of advanced technology. “Rather than simply examining individual pixels, our technology is capable of identifying objects and making inferences about those objects by looking at them in their local context.”

    To address the specific requirements of the life science industry, the company’s image analysis platform includes Definiens Developer for adapting the platform to any image analysis problem, Definiens Cellenger® for cell-based and high-content assays, and Definiens TissueMap for analyzing histological image data.

  • Managing High-Density Arrays

    Tecan plans to make its 2 µm resolution microarray scanner, the PowerScanner™, available during the second half of 2008. The instrument has been developed to meet the demands of increasingly ultrahigh-density arrays, pointed out Ralph Beneke, Ph.D., product manager, microarrays.

    “With arrays of up to 2 million features already commercially available, and further increases in array density evident for the near future, there is a real need for parallel improvements in microarray analyzers. To address this, the new PowerScanner has been designed by Tecan to offer increased sensitivity, resolution, and accuracy.”

    Features of the PowerScanner include a patent-pending internal system quality control tool, ozone filters to protect samples in the 48-slide autoloader along with a patent-pending acromatic lens and mirror system, online data flow control to provide accuracy, and fully automated Photomultiplier Tube (PMT) adjustment during batch processing along with the ability to carry out adjustments of PMT for each image.

    Tecan’s Infinite® 200 NanoQuant platform, launched at the start of 2008, was developed to allow quantification of nucleic acids and proteins. It reportedly provides labeling efficiency at sample volumes of just 2 µL and at concentrations as low as 1 ng/µL. NanoQuant represents what Tecan claims is the first multimode microplate reader to be developed specifically for absorbance applications with multiple, low-volume samples. “Unlike other low-volume systems on the market the NanoQuant’s multichannel design also uniquely allows the pipetting of 16 samples at a time, both saving time and negating evaporation issues associated with multiple pipetting,” Dr. Beneke said.

  • Calorimetric Detection Technology

    Eppendorf’s Silverquant® colorimetric detection technology for use in protein detection assays is based on the enhancement of silver crystal deposition by nanogold particles. The technology represents a unique approach to microarray analysis, enabling optimal signal-to-background ratio for biotin-labeled molecules, according to Margit Stadler, Ph.D., product line manager.

    “It has also been proven far more sensitive than fluorescence labeling, and Silverquant-stained slides can be archived indefinitely with no degradation of stain. Moreover, as a colorimetric detection device, the Silverquant Scanner is less costly than fluorescence scanners,” she said.



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