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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

  • DNA Library Preparation

    Click Image To Enlarge +
    Nextera technology is a transposon-based, single-tube method for preparing fragmental and tagged DNA libraries in less than eight hours, according to Epicentre Biotechnologies.

    Nicholas Caruccio, Ph.D., director of market development at Epicentre Biotechnologies, points out that DNA library preparation is a common entry point for NGS. The company’s Nextera technology is a single-tube method for preparing fragmented and tagged DNA libraries in less than eight hours. This technique can generate libraries for multiple NGS platforms, whole-genome amplification, and related applications, explains Dr. Caruccio.

    “Our core competency is molecular biology,” continues Dr. Caruccio. “We’ve primarily dealt with cloning and manipulation of genomes and RNA, so we’re a good fit with the library preparation market. Researchers performing Sanger sequencing used our transposon technology to get coverage across large fragments. Recently, we realized we could exploit this method and modify the transposons; we ended up creating an NGS Library.”

    Library preparation currently has three distinct steps: fragment the DNA, repair the ends, and ligate on adaptors. “We combine these steps into one transposon fragmentation and tagging reaction. The end result is a flexible library that is compatible with either Illumina or 454 sequencing,” notes Dr. Caruccio.

  • Genomic Loci Enrichment

    Click Image To Enlarge +
    The Primary library production process at RainDance Technologies includes four steps

    RainDance Technologies’ platform was designed to enable PCR for high-throughput amplification of targeted regions of the genome, according to James Brayer, manager of commercial scientific applications.

    “The RainDance Sequence Enrichment Solution allows researchers to generate targeted resequencing data necessary for the characterization of rare variants associated with human health and disease,” he says.

    RainDance launched its first commercial application earlier this year, leveraging the company’s RainStorm™ microdroplet-based technology. “This application facilitates the follow-up of genome-wide association studies and the resequencing of candidate genes and certain pathways of interest,” he notes.

    “Because we use PCR, we can target those genome areas that are of interest to researchers—areas that are often inaccessible using alternative enrichment methods due to repetitive sequence or regions of high homology. The droplets produced are uniform, resulting in consistent amplification of the greater than one million droplets generated per sample. Consequently, targeted regions are uniformly represented. The process is scalable.

    “Researchers apply this technology to accurately identify rare variants, which is critical to understand the genetic basis of disease. Via collaboration with Expression Analysis, we work with eight researchers in the cancer community, each with a slightly different target in mind, to analyze genome content.”

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