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Apr 15, 2009 (Vol. 29, No. 8)

Novel Systems Zero In on the $100 Genome

Technology under Development Is Being Counted on to Provide Rapid and Affordable Sequencing

  • Moving Sequencing Forward

    Click Image To Enlarge +
    Parallel analysis of hybridization reactions with a nanopore array

    “We have developed a method to rapidly sequence DNA known as HANS or hybridization-assisted nanopore sequencing,” stated John Oliver, Ph.D., vp for research at NABsys. It combines two sequencing strategies—direct nanopore sequencing and sequencing by hybridization. “In brief, the genome is fragmented into pieces of 100 kb or longer, which are made single stranded and then hybridized with a short oligonucleotide probe. When these fragments are driven through a nanopore by a potential, they create changes in the current-versus-time profile, which indicates the binding positions of the probes.”

    According to Dr. Oliver, nanopore sequencing differs radically from sequencing approaches that use fluorescent compounds. “With our platform, we don’t need to label the molecule,” Dr. Oliver explained. “When the single-stranded DNA enters the pore, it changes the resistance because the chip is mounted between two chambers with a buffer solution bathing the chip.”

    The nanopores are constructed by perforating a silicon chip with a focused beam from a transmission electron microscope. Prototype wafers are built by hand, but in the future they will be printed robotically. With these devices the size of the DNA molecule or the distance between two probes can be determined with an error range of 7%. The process can now be expanded, providing a genome-length probe map for each genomic fragment, and this can be accomplished in parallel for the entire library of probes.

    The second phase of the process is to reconstruct the sequence from the probe-hybridization data by a process known as “moving window sequencing by hybridization.” The result is a complete genome sequence. “We are still in the early stages of development,” Dr. Oliver added, “but we are moving ahead to perfect a rapid and inexpensive approach to genome sequencing.”

    From the early days of the human genome project, a vast amount of sequence data has been generated, not only for humans, but for many other species as well. Yet the traditional Sanger method is too expensive, cumbersome, and slow to accommodate the demands of large-scale sequencing of many genomes. These barriers must be overcome to satisfy the demands of clinical medicine.

    Several of the companies interviewed for this article are not yet offering their technology to the public, but will do so within the next few months. In addition, other radical technologies, including nanoknife edge sequencing are in the research stage. The technologies that are now being pursued will no doubt bring the $100 genome to reality within the next few years.

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