New method to make DNA sequencing faster and cheaper

Boston University biomedical engineers have developed a new method to make DNA sequencing a lot faster and cheaper - and thus closer to routine use in clinical diagnostics.

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.

"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 Amit Meller, who collaborated with other researchers at Boston University, and at the University of Massachusetts Medical School in Worcester. "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 discovery could lead to major advances in drug development, preventative medicine and personalized medicine.

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 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."

"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 Meller.

The research is detailed in Nano Letters.