Ion Proton sequencer decodes DNA fast and on the cheap
By Jan Belezina
January 12, 2012
The mapping of the human genome, announced at the White House back in 2000, had immense impact on biomedical research. It allowed us to gain insights into how biological information is encoded in the genome, helped us understand the biological mechanisms behind cancer and hereditary diseases and enabled us to look much deeper into the history of our own species. These are milestone achievements for humanity as a whole, but they have little or no direct impact on everyday medical treatment. That could be about to change, however, as Life Technologies introduces the Benchtop Ion Proton Sequencer - a machine that may finally deliver the power of genetics into the hands of ordinary doctors.
Until recently, DNA decoding machines - fitting in the US$500,000 to $750,000 price range - would take weeks or even months to sequence a human genome, and the whole procedure would cost $5,000 to $10,000. The Ion Proton is priced at $149,000 and is capable of decoding a human genome in one day at a cost of $1,000. These enormous improvements could have a game-changing significance.
Older, optical-based sequencers normally worked on batches of six or more genomes. Processing the huge resultant data sets required expensive IT infrastructure. In contrast, The Ion Proton Sequencer uses analysis software called Ion Reporter to analyze the data of a single genome on a single server. This speeds up the process considerably and removes the IT-related bottlenecks. However, the most important factor in reducing the sequencing speed so dramatically is the introduction of the next generation of Ion Torrent semiconductor chip technology.
"Just six months after our first semiconductor sequencing chip was released, people used it to solve the German E. coli outbreak, sequencing the toxic strain in just a couple of hours," said Dr. Jonathan M. Rothberg, the Founder and CEO of the Ion Torrent division. "Now, six months later we're developing a chip that's 1,000 times more powerful than that to sequence an entire human genome in about the same amount of time. That's the power that semiconductors bring to sequencing."
Although the impact of this technology on medicine is likely to be immense, it is not going to be immediate ... at least, not until doctors learn how to interpret the results and make the right decisions on that basis. To address this challenge, Life Technologies turned to Carnegie Mellon University. Together, they are working on developing open-source software to help ordinary practitioners understand genetic data and put this knowledge to good use. The company is also working with Yale Medical School to establish standards for performing genome sequencing in a clinical setting.
The first Ion Proton machines equipped with the Ion Proton I chip, capable of sequencing exomes - parts of DNA that code for protein - are going to be made available half way through 2012. The Ion Proton II chips that can handle a full human genome are to be introduced half a year later. It may not be until 2013 that the first group of patients receive their DNA-specific medical treatments, but it is 2012 that's likely to go down in history (or at least in medical textbooks) as the year when DNA sequencing hit the mainstream.