Low-cost, ultra-fast DNA sequencing brings diagnostic use closer

May 19, 2010, Boston University College of Engineering

Sequencing DNA could get a lot faster and cheaper -- and thus closer to routine use in clinical diagnostics - thanks to a new method developed by a research team based at Boston University. 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. In addition, the researchers have shown the viability of a novel, 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 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 research is detailed in . The National Institutes of Health are currently considering a four-year grant application to further advance Meller's nanopore sequencing project.

This low-cost, ultra-fast DNA sequencing could revolutionize 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 team's findings show that nanopores, which can analyze extremely long DNA molecules with superior precision, are uniquely positioned to compete with current, third-generation DNA sequencing methods for cost, speed and accuracy. Unlike those approaches, the new nanopore method does not rely on enzymes whose activity limits the rate at which 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."
Licensing intellectual property from Boston University and Harvard University, 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 Meller.

Explore further: Faster, cheaper DNA sequencing method developed

More information: Research paper: http://pubs.acs.org/doi/abs/10.1021/nl1012147

Related Stories

Faster, cheaper DNA sequencing method developed

December 20, 2009

(PhysOrg.com) -- Boston University biomedical engineers have devised a method for making future genome sequencing faster and cheaper by dramatically reducing the amount of DNA required, thus eliminating the expensive, time-consuming ...

Nanopore Sequencing Could Slash DNA Analysis Costs

March 27, 2009

(PhysOrg.com) -- Over the past 5 years, researchers have been exploring the use of nanoscale pores as nucleic acid sequencing tools. In theory, such pores should generate a unique response characteristic of each of the four ...

Rapid, Inexpensive DNA Sequencing Moves Closer to Reality

February 19, 2010

As efforts such as The Cancer Genome Atlas and others generate vast quantities of information about the genetic makeup of different types of cancer, it is becoming increasingly clear that such information has great potential ...

Scientists to explore nano advancements in DNA sequencing

October 1, 2007

UC Irvine’s Henry Samueli School of Engineering has been awarded $2.18 million to blend traditional DNA sequencing techniques with cutting-edge nanotechnology to develop a faster and less costly method of analysis. The ...

New cheaper method for mapping disease genes

May 27, 2008

Scientists at the Swedish medical university Karolinska Institutet have developed a new DNA-sequencing method that is much cheaper than those currently in use in laboratories. They hope that this new method will make it possible ...

Recommended for you

Single-celled architects inspire new nanotechnology

July 16, 2018

Diatoms are tiny, unicellular creatures, inhabiting oceans, lakes, rivers, and soils. Through their respiration, they produce close to a quarter of the oxygen on earth, nearly as much as the world's tropical forests. In addition ...

X-ray triggered nano-bubbles to target cancer

July 16, 2018

Innovative drug filled nano-bubbles, able to be successfully triggered in the body by X-rays, have been developed by researchers, paving the way for a new range of cancer treatments for patients.

Smart window controls light and heat, kills microorganisms

July 13, 2018

A new smart window offers more than just a nice view—it also controls the transmittance of sunlight, heats the interiors of buildings by converting solar radiation into heat, and virtually eliminates E. coli bacteria living ...


Adjust slider to filter visible comments by rank

Display comments: newest first

not rated yet May 19, 2010

At 3,000,000,000 base pairs in human dna it would take about 6 months to sequence one persons dna.
not rated yet May 20, 2010
this method is not optimal and will not be practical to sequence dna. they use molecular beacon technology, which only allows them to hybridize to stretches of sequence, not individual base pairs. therefore, in a controlled setting like what they utilize, they are able to sequence stretches of A/T/G/or C. This in no way advances the field, and will not lead to cheaper dna sequencing technology. The authors comment on nanopore's are enzymes in their intro which can discriminate single base, and this system could sequence an entire dna strand. The whole point of using enzymes is to see the translocation event of the polymerase as it grabs the dna and slides one bp at a time.
not rated yet May 20, 2010
At 3,000,000,000 base pairs in human dna it would take about 6 months to sequence one persons dna.

I get about a week if you sequence the 46 chromosomes in parallel. Start reading each chromosome from both ends, add the factor of four speedup, and you are at under a day.

Current methods cut chromosomes into lots of pieces, sequence those, and then solve the puzzle to find the original sequence. You cut two or more sets of chromosomes at different specific sequences then work back and forth to find which piece goes next. With computers, that doesn't take much effort, but you need to sequence thousands of fragments in parallel.

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.