For years, the cutting edge technology for DNA sequencing has involved mincing DNA up into tiny pieces. Even as sequencing has gotten faster and cheaper, each new process has relied on chopping the DNA up to be analyzed, because, although this process can introduce errors in the readout and can be expensive, it was still the best we had. Now, technology unveiled at a recent conference in Florida could mean that the age of slicing and dicing is over, thanks to something called a nanopore.
A nanopore is a ring of proteins, made by a bacterium, through which DNA can be threaded, like a string through a bead. In the method of DNA sequencing just debuted by Oxford Nanopore Technologies, long, intact strands of DNA are shunted through nanopores on a chip, and the electrical conductivity of each nucleic acid as it comes through the pore lets scientists tell which DNA “letter” it is—A, T, G, or C. A long strand of DNA analyzed this way, importantly, isn’t destroyed, so it can be reanalyzed, and errors introduced in processes that use chopping are also avoided. Using such basic physical laws to deduce a DNA sequence is a simple, elegant solution to a tough problem. That’s perhaps why nanopore sequencing methods have attracted some significant investment in recent years: the UN National Human Genome Research Institute had, by 2008, given $40 million to groups pursuing nanopore sequencing.
Oxford Nanopore’s presentation featured two devices they hope to start selling later this year: the GridION, which is a heavy-duty lab device that could theoretically sequence a human genome in 15 minutes and which they used to produce a sample viral genome sequence, and the MiniION, which is the size of a USB stick, will cost $900, and should be able to sequence a human genome in 6 hours and tiny viral and bacterial genomes in seconds. That’s very, very fast and very cheap—cheap enough that even curious hobbyists might be able to indulge. An important caveat: Though these devices promise to eliminate the errors brought about by chopping DNA up for analysis, they still currently have an error rate that is four times that of current techniques, perhaps because they still aren’t quite sensitive enough to fulfill nanopore sequencing’s promise, though the coverage of the company’s presentation doesn’t go into detail. But the company plans to have the error rate down to an acceptable level by the time the devices go to market. If Oxford Nanopore can bring accuracy up, and maintain it as they try to sequence larger and larger genomes, DNA sequencing companies with more expensive techniques may be looking at some serious competition.
Scientists are genuinely, if cautiously, excited by what they’ve seen of Oxford Nanopore’s work. “I think it is all credible,” Chad Nusbaum, co-director of the Genome Sequencing and Analysis Program at the Broad Institute in Cambridge, Massachusetts, told Nature News. “I would bet they are even underplaying it because they don’t want to risk overpromising.” For scientists talking about biotech, that’s pretty hopeful phrasing.