Photo: Oxford Nanopore
Ever since the human genome was first sequenced in 2003, researchers have been striving to make this laborious task cheaper and easier.Genomes, and the DNA they are made of, are critically important to every piece of life on Earth. Differences in the sequence of DNA letters that make up an organism’s genome are what makes a fir tree a fir tree and not a platypus. These DNA letters form genes — which are translated by cellular machinery to make proteins and other products that make up the majority of structures in a cell, and therefore the majority of things in a person, animal, plant or even bacteria.
Studying how different DNA codes translate to different proteins is important in clinical settings, as well as in research laboratories in almost every different sector of scientific research.
A company called Oxford Nanopore Technologies is about to release a set of technologies that could make reading this code quicker and easier. They are called the GridION and MinION systems, and could herald in a next generation of DNA sequencing on the cheap. [SEE HOW OXFORD NANOPORE’S DNA SEQUENCER WORKS]
The technology is based on special protein pores. These pores make holes in a special membrane, allowing charged particles in the solution around it to pass through to the other side. On the other side of the membrane, special electrodes can sense this ion flow. When a molecule like a DNA nucleotide passes through the pore, the amount of ions flowing through the pore changes.
The two new products by Oxford Nanopore were announced at the Advances in Genome Biology and Technology meeting in Marco Island, Fl., in February of 2012.
“It sent shock waves through this meeting,” Chad Nusbaum of the Broad Institute, told Matthew Herper of Forbes. “No one is talking about much else right now.”
The nanopore technology will come in a cartridge with all of the chemicals needed to process a DNA sample. It will come in two different setups: A larger desktop version, which takes a cartridge holding about 2,000 nanopores and a smaller USB stick which will have 512 nanopores.
“The USB stick is an absolute game changer,” Oxford Nanopore Chief Executive Officer Gordon Sanghera in a telephone interview with Bloomberg. “It’s plug-and-play, on-the-go DNA sequencing.” [SEE HOW CHEAP GENOME SEQUENCING WILL CHANGE MEDICINE]
The GridION system works with any kind of DNA sample, and the group is also working on systems to analyse RNA or protein samples. The system was first tested on the DNA of a virus, called Phi X phage, which is 5.4 kilobases long. The system was able to sequence the entire DNA strand in one shot.
One of the larger machines, called the GridION “node” will read DNA sequences at roughly 600 million base pairs per hour, which equates to around 14 giga base pairs a day. To read a whole human genome with industry-standard coverage rate of 30 reads would take just under 6 days. When multiple nodes are connected together, the cores can process a complete human genome in 15 minutes.
The ION systems are able to read longer stretches of DNA than other sequencers, which means there are fewer errors when the computer tries to stitch together the resulting fragments of code. The error rate also doesn’t increase with longer reads, making the results more reliable.
The professional-level GridION systems take up much less room than the sequencers many labs use now, and they use much less power (about the amount a typical light bulb takes to run). The system is completely customisable — an academic research lab could work with one node, or hundreds can be run in parallel.
The company has varied pricing schemes. The smaller MinION stick will cost about $900, with the cost of software on top of that. Labs can set up a GridION system by either paying a lot up front for the node and getting a reduced price on the cartridges, or by paying less for the node and more for the cartridges.
“GridION and MinION are poised to deliver a completely new range of benefits to researchers and clinicians,” said Dr. Gordon Sanghera, CEO of Oxford Nanopore. “Our toolbox is customer-ready and we will continue to develop improved nanopore devices over many years, including ongoing work in solid state devices.”
During the announcement, the company said that it is planning to make these sequencers available to the public in the second half of 2012.
“Things are progressing nicely here as we move toward commercialization of GridION and MinION,” Oxford’s business development director Kristen Stoops told us in an email. “We haven’t announced a launch date for the products but will be providing updates to the sequencing community when the time approaches.”
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