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January 01, 2010 (Vol. 30, No. 1)

DNA Sequencing Applications Expanding

Systems Poised to Break Out of Research Labs into Pharma Industry and Clinical Settings

  • Click Image To Enlarge +
    Completely sequenced genomes in Genomes On-Line Database (GOLD) and Integrated Microbial Genomes (IMG)

    There has long been interest in sequencing DNA, but until a few years ago there was not much to say about the competitive dynamics of the market for equipment used to perform that sequencing. Mid-decade, the market declined somewhat as most of the potential customers had already invested in high-end sequencers. That changed in 2006 when new technology in the form of second-generation systems reinvigorated competition.

    Driving near-term sales of sequencers  now is the arrival of third-generation systems, a multiplication of sequenced genomes, and government funding from the stimulus bill. In the long-term, as yet untapped clinical markets also presage a bright future for these systems.

    The scientific usefulness of DNA sequencing continues to be proven, and the number of sequenced and catalogued genomes has grown more than five times from where it was at the middle of the decade. Some of these sequencing projects currently under way are quite ambitious and aim to sequence thousands of individuals, tumors, or other unique samples.

  • Increased NIH Funding

    The annual budgets for sequencing projects at the NIH and DOE have risen at unprecedented rates in the last few years. NIH is still the key funding agency and funds more than one-third of the projects in the Genomes On-Line Database. This year, new funds have been added as a result of the stimulus bill. In addition to the funding for sequencing projects, the National Human Genome Research Institute has been providing millions of dollars per year to a large number of groups for their development of “$100,000 Genome” and “$1,000 Genome” sequencers.

    All of this funding has generated significant momentum in the industry. The last two years have seen fairly significant technology improvements—paired-end techniques, multiplexing, and increasing read-lengths. These advances have resulted in a growth of applications for DNA sequencers and also increased sequencers’ output per hour.

    Most of the second-generation sequencers have read-lengths in the range of 25 bases to 75 bases. This would be a severe limitation if the companies were not offering paired-end reads, which allow the fragments to be mapped more easily. All of the sequencing companies are now offering paired-end reads. These have been developed with long inserts of thousands of kilobases. Companies have also been increasing the systems’ read-lengths and adding multiplexing capabilities.

    New techniques have definitely amplified the usefulness of second-generation systems. Applications are now shifting away from whole-genome studies and toward more targeted resequencing experiments with fewer genes in larger numbers of samples.