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Jan 1, 2009 (Vol. 29, No. 1)

Utilization of DNA Microarrays Increasing

Persistent Doubts about Reproducibility and Compatability of Data Are Being Overcome

  • Focused DNA Microarrays

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    Mirus Bio’s Label IT platform covalently attaches a label to nucleic acids.

    “Oligo GEArrays are an effective alternative to genome-wide microarrays,” says Jeffrey Hung, Ph.D., director of marketing at SABiosciences. He explains that the standard genome-wide array may result in the production of so much data that interpretation becomes a daunting task, requiring elaborate software and complex analytical procedures.

    GEArrays are focused array panels that allow investigators to narrow in on a select group of genes representing a particular biological pathway or disease state. The arrays are constructed with a nylon membrane that is spotted with gene-specific 60 mer oligos for up to 440 specific genes. The arrays operate with as little as 10 pg of RNA, he adds, and are detected with a chemiluminescence method.

    The oligo GEArrays are evaluated for specificity, sequence complexity, secondary structure, melting temperature, GC content, and distance to the 3´ end of the transcript. The company favors nylon membranes as a support structure as opposed to glass or other impermeable materials, reporting that the nylon provides larger probe immobilization and an increased hybridization and detection area.

    The available pathway options cover a wide range of cogent scientific targets, including atherosclerosis, cancer biomarkers, signal transduction pathway markers, and hematology-immunology markers. According to Dr. Hung, the system constitutes a useful research tool for investigators studying gene-expression profiles related to disease states. Discovery of overexpressed genes provides possible drug targets and new ways of looking at pathological states.

    SABiosciences also offers a complement to the microarrays in the form of a methodology for amplifying pictogram amounts of RNA. The TrueLabeling-picoAMP kit takes advantage of a two-round in vitro transcription procedure to amplify and label the cRNA for use in determining gene-expression profiles.

    The kit lends itself especially to situations in which the target RNA is present in small quantities, such as specifically staining cells present in a fixed tissue sample or cells isolated through the use of fluorescence-activated cell sorting, Dr. Hung says. The kit amplifies and labels cRNA for hybridization to microarrays from picogram quantities of RNA, employing as few as 20 cells. It also contains the enzymes and buffer components needed to complete the synthesis of labeled cRNA in a 48-hour period.

    “The technology provides an opportunity to find candidate genes for biomarker discovery rapidly and efficiently,” Dr. Hung concludes.

  • Tracking Genetic Diseases

    Roche NimbleGen recently made available a comparative genomic hybridization (CGH) microarray system for analysis of DNA copy-number variation. The 12 x 135 K format permits simultaneous analysis of 12 independent sample pairs on a single microarray slide, each with 135,000 oligonucleotide probes. This new array format is a research tool designed for rapid and cost-effective analysis of DNA copy-number variation associated with human genetic disorders, cancer, and other complex diseases.

    For researchers interested in targeted analysis of chromosomal regions, genes, or copy-number variants, Roche NimbleGen offers customized arrays for any eukaryotic organism. Custom CGH array designs consisting of either uniform or mixed-density probe spacing can be created for all available array formats (12 x 135 K, 2.1 M, 385 K, 4 x 72 K) and may include whole genomes, single chromosomal regions, or multiple loci of interest.

    According to Burkhard Ziebolz, Ph.D., head of global communications at the Roche Applied Science Group, the high-density arrays of long oligo nucleotide probes provide greater information content and higher data quality revealing the full diversity of genomic and epigenomic variation. The company has developed a technology referred to as Maskless Array Synthesis, which uses digital light processing and rapid, high-yield photochemistry to synthesize long oligonucleotide, high-density DNA microarrays with extreme flexibility.

    The system is a benchtop, solid-state, high-density DNA array fabrication instrument composed of a maskless light projector, a reaction chamber, a personal computer, and a DNA synthesizer.

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