Portable DNA Sequencer MinION Helps Build the Internet of Living Things

The device that will realize Oxford Nanopore's grand vision to read the world in DNA

3 min read
Portable DNA Sequencer MinION Helps Build the Internet of Living Things

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.

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This CAD Program Can Design New Organisms

Genetic engineers have a powerful new tool to write and edit DNA code

11 min read
A photo showing machinery in a lab

Foundries such as the Edinburgh Genome Foundry assemble fragments of synthetic DNA and send them to labs for testing in cells.

Edinburgh Genome Foundry, University of Edinburgh

In the next decade, medical science may finally advance cures for some of the most complex diseases that plague humanity. Many diseases are caused by mutations in the human genome, which can either be inherited from our parents (such as in cystic fibrosis), or acquired during life, such as most types of cancer. For some of these conditions, medical researchers have identified the exact mutations that lead to disease; but in many more, they're still seeking answers. And without understanding the cause of a problem, it's pretty tough to find a cure.

We believe that a key enabling technology in this quest is a computer-aided design (CAD) program for genome editing, which our organization is launching this week at the Genome Project-write (GP-write) conference.

With this CAD program, medical researchers will be able to quickly design hundreds of different genomes with any combination of mutations and send the genetic code to a company that manufactures strings of DNA. Those fragments of synthesized DNA can then be sent to a foundry for assembly, and finally to a lab where the designed genomes can be tested in cells. Based on how the cells grow, researchers can use the CAD program to iterate with a new batch of redesigned genomes, sharing data for collaborative efforts. Enabling fast redesign of thousands of variants can only be achieved through automation; at that scale, researchers just might identify the combinations of mutations that are causing genetic diseases. This is the first critical R&D step toward finding cures.

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