Since the introduction of the MinION of Oxford Nanopore Technologies, it is possible to read DNA very quickly and relatively easily. And the device fits your pocket too. “This could just be the iPod of the DNA world."
It took thirteen years and $ 3 billion to completely sequence the human DNA. In recent years, next generation sequencing (NGS) techniques made it possible to analyze more data in less time, mainly using the sequencers of Illumina and Pacific Biosciences. But these technologies still require a lot of efforts for sample preparation and the devices are still enormous. A few years ago, a small device with the size of a smartphone challenged the status quo and makes reading genetic material quick and easy. This device is the MinION of the British company Oxford Nanopore Technologies. It almost sounds too good to be true. "But it's an impressive device, at least at first glance," says Dr. Adalberto Costessi, Product Manager NGS at BaseClear.
BaseClear, based in the Leiden BioScience Park, has been performing DNA tests for companies and academics for the past 23 years, mainly in the area of microbiology. BaseClear identifies fungi, bacteria and other small organisms and maps their genetic code. Every day Dr. Costessi works with the next generation sequencing and Sanger sequencing instruments, which copy endlessly small pieces of DNA and finally gives information about a particular part of the genome. “That works flawlessly. The Sanger sequencing technology has been around for 40 years and next generation sequencing for 10 years now. We know how to handle it, making it affordable and easy. We prepare the DNA, load it on the instrument and come back the next day to retrieve a large amount of data.”
But for some applications these methods are old-fashioned and no longer meet the customers’ needs. Think of people who want to figure out their entire genetic code in search for diseases or want to investigate microorganisms. “For example, cheese bacteria make different things depending on their DNA content. You can only fully understand this if you analyze their entire genome, but not when you focus on just one piece. Furthermore, speed is a major issue nowadays. In crisis situations such as food poisoning or a letter possibly containing Anthrax, results need to become available as quick as possible. This is difficult for the classic sequencers, although we have recently analyzed Salmonella strains within 48 hours with our Illumina sequencers. But, in some cases, this is still too slow.” There is a need for something that reads long stretches of DNA. And of course quickly and cheaply. The MinION, which can read theoretically infinitely long strings of genetic material, makes this possible.
Reliability and accuracy compared to traditional machines need to be tested further. But the potential is huge.
The MinION succeeds thanks to its nanopores, holes that are so small that only a single DNA strand can pass through. By installing such a pore on a microchip and applying a voltage, the nanopore turns into a sensor that detects everything that runs through it. If you then let a DNA molecule move through the pore, the changes in current reveal which of the four bases are flowing through the pore (DNA consists of long combinations of nucleobases: molecule ends that have the letters C, G, A and T). In this way, a computer quickly and easily reads the whole DNA string. The numbers do not lie: last October, Oxford Nanopore Technologies announced that the latest MinION can read 450 bases per second.
This technology sounds easier than the sophisticated sequencing that Costessi and his laboratory colleagues are using now. In their method, DNA pieces must first be copied many times and each base has to get a color tag for identification later on. “The MinION technology is indeed much simpler and therefore extremely convenient”, concludes Costessi. “If we have to analyze bacteria, we must now first chop the DNA into small pieces of three hundred base pairs. That is the maximum read length of current Illumina devices. To unravel the entire genome, you have to find millions of those three hundred bases long pieces together, which is time consuming and has limitations. Sticking these pieces together is a puzzle that you do not have to solve with the MinION.”
This does not mean that there are no problems at all. “This technology requires a higher sample quality. The DNA strands must be as intact as possible to make sure that you do not make too many measurement errors. And although the portability of the device is impressive, practical applications are limited at this moment. In specific cases, portability may be useful. During the Ebola outbreak in Sierra Leona the device helped to map the spread of different Ebola strains. But there is a big problem: DNA must first be isolated and prepared for MinION analysis. You cannot just use a drop of blood or saliva and discover your genetic pattern. For the isolation of DNA, no handy and portable kits exist yet; that's still laboratory work.” For the time being, the use of the MinION outside the lab is limited. “However,” says Costessi, as he grabs one of the MinIons on the workbench, “it's a great device that can do things none of the other sequencers can. The question is only how to use it.”
This is also a challenge for BaseClear. The MinION devices that the company now has are used for research and development projects. Reliability and accuracy compared to traditional machines need to be tested further. “I see all kinds of challenges and these need to be solved first. But the potential is huge. This could just be the iPod of the DNA world.”
Although it is not yet easy to isolate high quality DNA, this may change in the future. Oxford Nanopore Technologies is working on a preparation method that takes just ten minutes instead of half a day. “Then DNA reading suddenly becomes something a family doctor can perform in their office. That could save huge amounts of time and money for hospitals.” And if it becomes so easy, are traditional DNA technicians still needed? “It can definitely change our work, because generating DNA patterns from genetic material becomes easier,” adds Costessi. “But the analysis of DNA patterns is still largely work for specialists. For example, we built our own analysis programs and this requires specific knowledge.” Moreover, Oxford Nanopore Technologies also has a kind of super-MinION that has the throughput of 48 MinION DNA readers in one. “Such a device would help us to remain important, thanks to cheap and fast analyses.”
The last thing Oxford Nanopore Technologies is working on is a smartphone module, allowing anyone to analyze DNA anywhere. Oxford Nanopore aims to have this module in store by the end of 2017. Will this become a game changer? Costessi frowns: “I find it challenging to foresee its applications. But, initially the iPod was not seen as a very useful device, until it turned out that so many people were waiting for it. Maybe the same applies here.” And then everyone can suddenly unravel the entire human genome within a half hour, something that took scientists about thirteen years at the start of this century.
This blog is an edit and translation from the article as published in 'De ingenieur', February 2017.