Advanced MinION Mini Sequencer
MinION – portable DNA sequencer has received an upgrade
Andrey Vasilkov, "Computerra"Oxford Nanopore has introduced a new version of the MinION DNA analyzer.
Its dimensions are only ten centimeters in length, and the power consumption does not exceed two and a half watts, which allows the device to receive power from the USB port.
In 1989, biophysicist David Deamer made a sketch of a conceptually new technique for decoding DNA, which was ahead of its time. Literally the next year after the invention of the Dimer, the most ambitious project of modern genetics began, in which completely different approaches were used. The international program "Human Genome" took thirteen years. Six countries have spent over $3 billion to implement it.
Only twenty-three years after the idea was sketched, Oxford Nanopore was able to implement it in the form of a portable MinION device. With all the obvious advantages, its accuracy did not exceed 80%, which did not allow the device to be used in clinical practice without repeated rechecks.
MinION DNA Analyzer (photo: tgac.ac.uk ).
The development of compact analyzers has been carried out for ten years. During this time, the firm has attracted investments worth about $292 million. After two years of refinement of the device, its accuracy and speed have significantly increased. It is still smaller than that of certified laboratory installations the size of a cabinet, but it is already quite suitable for many practical applications.
A portable sequencer can be useful for screening biomaterials taken from a crime scene or identifying strains in the midst of an epidemic. The new MinION will become not just another, but the smallest and most accurate among all such devices. A more productive version of PromethION is already being developed with hundreds of thousands of nanopores through which the multiplied DNA will simultaneously pass.
Today, laboratories are coping with the task of complete genome sequencing within a day. To do this, different methods are used, differing in speed, cost and percentage of errors. However, in general, expensive installations of impressive size and a variety of reagents are used. Therefore, a complete DNA analysis is hardly a popular service, and personalized medicine remains a dream of a bright future.
Portable DNA analyzer MinION (photo: mqgenomics.blogspot.com ).
Unlike these bulky devices, MinION was created according to the concept of "laboratory-on-a-chip". Recognition of nucleotides in it is carried out directly. As the nucleic acid molecule passes through the nanopores of the membrane, its potential and electrical resistance change. As a first approximation, we can say that the magnitude of their changes correspond to which nucleotide is in the pore now, and which was before it.
The idea of passing DNA through the smallest pores to determine the sequence of nucleotides originated with Dimer while working on artificial cells. He told her colleagues, explaining that the nucleotides will change the electrical state of the membrane, which can be read.
"A lot of smart people said then that it was technically impossible," recalls Jeffrey Schloss, head of the genomics department at the National Human Genome Institute of Maryland. – As we see now, they were wrong. Now the whole question is how to improve the methodology for use in practice."
Beta version of the MinKNOW program for the MinION DNA sequencer (photo: mqgenomics.blogspot.com ).
Thanks to the improved technique of nanopore sequencing, today the determination of the sequence of nucleotides in DNA or RNA can be performed on a personal device smaller than a smartphone. Decoding of viral genomes occurs on it almost instantly. It takes about a minute to analyze the prokaryotic genome, and the human genome is sequenced for several hours.
This fall, Oxford Nanopore sent out five hundred test copies of the device to partner organizations and affiliated laboratories. According to Mark Akeson, who worked on the creation of the sequencer together with Dimer, the speed of its completion was enormous. The first reviews came in June. Over the past two and a half months, the company has made two new versions of the prototype.
One of them was tested at the Roslin Institute, where in 1997 Jan Wilmut cloned Dolly the sheep. A researcher at the bioinformatics laboratory, Mick Watson, highly appreciated the prospects of the method: "Nanopore sequencing has the necessary potential to become a revolutionary technology that will dominate the market for many years," he wrote in the comments to the review.
A prototype of the MinION DNA analyzer at Lancaster University (photo: Nikki Copeland).
Now there is a rapid increase in demand for high-speed DNA analyzers. In addition to research laboratories, they are used in medical centers and private companies. At the same time, almost everywhere there is equipment from the same company – Illumina. This company from San Diego has brought its market share to 90% this year, and it will be extremely difficult to move it off the pedestal.
The current accuracy of Illumina sequencers is estimated at 99.9%. Errors occur due to the use of short DNA fragments in the SBS (sequencing by synthesis) method - up to three hundred base pairs per reading. Data about each site is combined with a common database, and the original DNA sequence is restored due to data redundancy as a huge puzzle. Some parts of this mosaic sometimes fall out, which makes the overall picture incomplete. At the same time, the accuracy of the SBS method is considered very high, and its cost is the lowest – only ten cents for every million base pairs.
One of the most popular sequencing systems is HiSeq 2500 (photo: illumina.com ).
The approach used in portable analyzers is based on reading long DNA sequences. In this technique, the length of fragments reaches seventy-nine thousand pairs of nucleotides, which can be considered a kind of record. Calculations of the cost of costs for it have not yet been published, but they will clearly be the lowest. Indeed, in this case, reagents, manual manipulations and even preliminary preparation of nucleic acids are not required for analysis.
Placing the test sample in the minION sequencer (photo: technologyreview.com ).
A couple of years ago, the Swiss pharmaceutical company Hoffmann-La Roche unsuccessfully tried to acquire Illumina when it was just beginning its rapid growth.
Now the Roche Diagnostics division has abandoned this idea and is betting on alternative technologies. It invests in firms involved in the development of nanopore sequencing – such as Stratos Genomics and the biotech division of Hitachi.
Small startups working in this direction are more profitable to buy. The latest acquisition was Genia Technologies, the value of which ($ 125 million), according to analysts, will return a hundredfold in the coming years.
Oxford Nanopore has no plans to sell its assets yet and is preparing a real revolution. Its main trump card will be the price of the device and its compactness. "In terms of dimensions, this is no longer a closet or even a drawer. We can quickly ship thousands of such devices via FedEx anywhere," Exxon comments.
The price of the device will be another surprise. It has not been officially announced yet, but a researcher from the University of Birmingham, Nick Loman, said that his laboratory paid about a thousand dollars for each prototype. For comparison, the HiSeq 2500 analyzer from Illumina costs about a million dollars.
Portal "Eternal youth" http://vechnayamolodost.ru18.09.2014