Low-Cost, Ultra-Fast DNA Sequencing Technology Developed

Sequencing DNA could get a lot faster and less expensive--and thus closer to routine use in clinical diagnostics--due to a new method developed by US researchers. The team has demonstrated the first use of solid-state nanopores (tiny holes in silicon chips that detect DNA molecules as they pass through the pore) to read the identity of the four nucleotides that encode each DNA molecule. Moreover, the researchers have shown the viability of an innovative, more efficient method to detect single DNA molecules in nanopores.

"We have employed, for the first time, an optically-based method for DNA sequence readout combined with the nanopore system,” said Boston University biomedical engineer Dr. Amit Meller, who collaborated with other researchers at Boston University (MA, USA), and at the University of Massachusetts Medical School (Worcester, MA, USA). "This allows us to probe multiple pores simultaneously using a single fast digital camera. Thus, our method can be scaled up vastly, allowing us to obtain unprecedented DNA sequencing throughput.”

The research was published online May 11, 2010, in the journal Nano Letters. The U.S. National Institutes of Health (Bethesda, MD, USA) are currently considering a four-year grant application to further advance Dr. Meller's nanopore sequencing project.

This low-cost, ultra-fast DNA sequencing could transform both healthcare and biomedical research, and lead to major advances in drug development, preventative medicine, and personalized medicine. By gaining access to the entire sequence of a patient's genome, a physician could determine the probability of that patient developing a specific genetic disease.

The researcher's findings show that nanopores, which can analyze extremely long DNA molecules with superior accuracy, are uniquely positioned to compete with current, third-generation DNA sequencing methods for cost, speed, and precision. Unlike those applications, the new nanopore method does not rely on enzymes whose activity limits the rate at which DNA sequences can be read.

"This puts us in the unique advantageous position of being able to claim that our sequencing method is as fast as the rapidly evolving photographic technologies,” said Dr. Meller. "We currently have the capability of reading out about 200 bases per second, which is already much faster than other commercial third-generation methods. This is only the starting point for us, and we expect to increase this rate by up to a factor of four in the next year.”

Licensing intellectual property from Boston University and Harvard University (Cambridge, MA, USA), Dr. Meller and his collaborators recently founded NobleGen Biosciences to develop and commercialize nanopore sequencing based on the new method. "I believe that it will take three to five years to bring cheap DNA sequencing to the medical marketplace, assuming an aggressive research and development program is in place,” said Dr. Meller.

Related Links:
Boston University
University of Massachusetts Medical School