It’s been nearly a year since the first portable DNA sequencers were shipped to giddy researchers waiting to be untethered from the refrigerator-sized machines in their labs. Now a desktop version by the same maker, Oxford Nanopore, is heading their way, with the first shipments to be sent by the end of this month.
The devices themselves have generated a ton of excitement and press, but less discussed is the company’s grand, long-term vision: to build an “internet of living things.”
The vision looks like this: researchers, consumers, government employees—everyone—will be reading the DNA of their own bodies and the living things around them, and streaming that data on the internet. DNA-reading sensors would be integrated into food production equipment, polluted waters, farms and phones. They would track the presence and movement of food pathogens and deadly viruses. Individuals could, with a drop of blood from a finger prick, track changes in their DNA—a dream for the most serious self-quantifiers.
To promulgate the vision, Oxford Nanopore, based in Oxford, UK, has spun out a data analytics company called Metrichor that will provide bioinformatics services—software tools that tell you more than just the sequence of the DNA—that will be packaged with the sequencing devices. So far Metrichor provides just a couple of kinds of analyses through a cloud-based system. One of those is called “What’s in My Pot?” It tells users what species of microbes they’ve got by matching their DNA reads to the DNA sequences of known species in its database.
With or without analytics, researchers say the portable sequencer, called MinION, is a game changer. It can fit in a coat pocket, costs about $1000, and connects to a laptop computer via a standard USB port. “It’s phenomenal,” says Yaniv Erlich, a computer scientist at Columbia University who has been teaching his students to use MinION. “You can even use it in zero gravity.” Scientists have toted MinION to rural locations to study Ebola outbreaks and antibiotic resistance and exotic animals. The desktop version, called PromethION, isn’t designed to be carried around, but can handle multiple DNA samples at once at a fraction of the size of traditional sequencers.
Before the portable sequencer can leap from scientists to consumers, Oxford Nanopore will have to overcome some challenges, starting, perhaps, with a better way to prep the DNA samples. A video from Metrichor depicts a person dropping a bit of blood from his finger onto a mini sequencing device. But it’s not that simple. DNA must be extracted from tissue or blood samples and prepared—a multi-step process that requires expertise and lab equipment. “They have to make it simple. Like coffee-maker-simple: put in the material and press a button,” says Erlich. To that end, the company is developing a portable sample prepping device called VolTRAX.
MinION and PromethION are based on nanopore sequencing technology. An electrical potential is applied, causing ions to flow through nanopores. As individual strands of DNA pass through the pores, its presence causes specific changes in the currents. Software quickly translates the sequence of currents into the corresponding DNA components: nucleic acids represented by the letters A, T, G and C. The sequence of the four letters comprises the unique genetic code for every living thing.
The devices differ from their predecessors not only in cost, size and portability, but also in function. The devices can read long strands of DNA in real time—something not possible with any other sequencer. The reads are not quite as accurate as those of traditional sequencers, such as those made by San Diego-based Illumina, but they are good enough for many applications, says Erlich. And in nanopore sequencing the direction in which the DNA strand flows through the pores can be changed on the fly. If it contains something of interest it can be examined further, and if not it can be ejected so that the seequencer can move on to another section.
Going from traditional sequencers to mini versions has been like going from mainframe computers to mobile phones. It decentralizes science. But getting from devices to Oxford Nanopore’s grand vision of an internet of living things will take more of a communal effort. People will have to be willing to share data, figure out ways to interpret one another’s data, and work out some serious privacy ground rules. Oxford Nanopore’s chief tech officer, Clive Brown, has likened it to the early days of digitizing the stock market. “If you get million of people collecting data and thousands of people looking at it, you’ll figure it out as you go,” he said in a talk last year.