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Sep 1, 2009 (Vol. 29, No. 15)

Next-Gen Presents Array of Opportunities

Researchers Are Finding Myriad Applications for This Rapidly Evolving Technology

  • Single-Molecule Sequencing

    Click Image To Enlarge +
    Helicos BioSciences’ HeliScope Sample Loader is a benchtop instrument used to hybridize samples to precision flow cells in preparation for the sequencing run.

    Patrice M. Milos, Ph.D., vp and CSO, Helicos BioSciences, says her company focuses on scientists who sequence directly. She notes that Helicos takes a different approach to cell biology research because of the lack of PCR, ligations, or gel purification.

    “Genomic DNA is sheared, tailed with poly A, and hybridized to the flow cell surface containing oligo dT for initiating sequencing by synthesis,” says Dr. Milos. “Our technology has been used successfully to sequence an array of bacteria representing the diverse genomic content of microorganisms, C. elegans, and, just recently, a near complete human genome.”

    Dr. Milos explains that the nature of sample preparation has allowed for direct sequencing of nucleic acid from a variety of sample types including formalin-fixed paraffin embedded tissue and archival tissue samples. “We also optimize our sample preparation to allow preparation and sequencing from picogram quantities of nucleic acid,” she continues.

    Helicos addresses what to do with the data, too. “We provide pipelines that help process data. We have SNP Sniffer software for identifying nucleotide variants,” says Dr. Milos. “Other companies’ work allows us to layer our sequence data with their data-visualization tools.”

  • Target Enrichment

    Target enrichment is useful when a researcher is interested in sequencing a particular genome segment. Agilent’s SureSelect platform can capture a subset of exons or other genome targets and wash away the rest of the genome prior to sequencing. SureSelect replaces other labor-intensive methods of targeted re-sequencing such as PCR techniques that cause major bottlenecks in most NGS workflows, according to Dr. Ernani.

    Consequently, Agilent recently introduced the SureSelect DNA Capture Array “as a way to do smaller scale target enrichment,” he says. “This complements Agilent’s in-solution SureSelect Target Enrichment System, designed for a broad range of NGS study sizes including automated high-throughput workflows.”

    The Agilent SureSelect DNA Capture Array was the result of work done in collaboration with the Gregory Hannon lab at Cold Spring Harbor Laboratories. Probes were designed through eArray, Agilent’s web-based design application, and high-fidelity microarrays were then custom synthesized using the SurePrint fabrication platform.

    In addition, Dr. Ernani notes that Agilent acquired Velocity 11, now called Agilent Automation Systems, and is integrating these new capabilities into the next-generation workflow, particularly the BRAVO system. Agilent also provides tools for quality control of samples using the microfluidic 2100 Bioanalyzer with its High Sensitivity DNA Kit.

    “This combination allows our customers to use less PCR in their target enrichment strategy, thus reducing potential for sequencing bias,” explains Dr. Ernani.

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