A British company named Oxford Nanopore Technologies has manufactured the first pocket-sized, portable DNA sequencing device. This USB device, called minION, is smaller than a regular phone and connects to a conventional laptop to sequence long strands of DNA. minION has already been used to sequence the human genome and has also been able to fill in some of the known gaps in the data.
minION works on what is called nanopore technology. There is a pore inside a protein molecule embedded in a synthetic membrane and submerged in a liquid. When a voltage is applied across the membrane, ions flow through the pore and an electric current can be measured. The obstruction of the pore by any other molecule, like DNA, leads to a drop in the measured current.
The DNA molecule is made up of four different types of bases: adenine (A), thymine (T), guanine (G) and cytosine (C). Each of these bases alter the current across the pore to different levels. Thus, by measuring the current, the four different bases can be picked up. And by doing this repeatedly, minION can ‘read’ the sequence of A, T, G and C on DNA strands.
Tested in space
The minION sequencer is much faster than other sequencing machines, such as those produced by Pacific Biosciences and Illumina, the dominant players in the sequencing market, according to Bloomberg BNA. minION works with longer DNA strands, around 882,000 base pairs in length, compared to a shorter read length of 100-200 base pairs that is accepted by other sequencing machines. minION is also priced more competitively: at $1000, it is cheaper than existing sequencing devices, the cheapest of which is priced at a whopping $19,900.
Extant sequencing technologies require shearing of DNA – breaking it into smaller pieces, amplifying the copy numbers of these pieces, sequencing them and then reassembling the reads to get a complete genome. minION works on a different principle that completely skips the amplification part.
DNA samples are directly loaded on to the flow cell in the device, which then threads the DNA strand through the pore so that it can be sequenced. A distinct advantage of this method is that it allows for certain epigenetic modulations, like methylation, to be preserved. On the other hand, the amplification step in existing methods leads to a loss of this information, as Ars Technica reported.
But it’s not all peachy. The main disadvantage of the minION system is that its error rate of 1 in 100 bases is much higher than other sequencing technologies, although this can be somewhat offset by repeated measurements. Matthew Loose, an author of the Nature paper that detailed the use of minION to read the human genome, told Gizmodo that they are not sure if these errors are due to sensitivity issues or if the machines are reading structural deformations in the DNA molecules.
Nonetheless, owing to its size and cost, minION is ideal for probing the existence of DNA-based life forms in extraterrestrial environments. Researchers have already conducted studies on an island 560 miles off the North Pole, where environmental conditions are similar to that on Mars, and found microbial life in some perennial cold springs.
Researchers have also gone the extra mile: the first sequencing in space was performed aboard the International Space Station (ISS) using a minION device, NASA has said. Unto discerning the identity of extraterrestrial microbes on the ISS, NASA astronaut Peggy Whitson collected samples from different locations on the station and performed the first ever sample transfer and gene sequencing in space under the guidance of a ground team in Houston. The sequence thus obtained was verified on ground when Whitson brought the samples back on her return from the ISS, and identified the same critters that Houston had. This proved that minION was reliable. According to INQUISTR, a minION device could be installed on the ExoMars 2020 rover to keep
an eye a pore out on the presence of DNA-based life on Mars.
Rocky road ahead
Additionally, scientists’ inability to tackle viral outbreaks, like ebola in 2014, can find a potential solution in devices like minION. Its technology could allow scientists to sequence viral genomes quickly and find potential defences. The Atlantic had reported that the remoteness of the outbreak’s epicentres and difficulties in bringing samples from the field to the lab had slowed down researchers trying to develop diagnostic tests and vaccines.
In fact, Nick Loman from the University of Birmingham had sent his graduate student, Joshua Quick, to Guinea near the end of the ebola epidemic in 2015. Using minION sequencers, the two were able to sequence 142 ebola genomes – information that was then used to track the disease’s transmission and curb its spread.
But despite its promises, minION does not measure up to giants like Illumina in terms of processing power. While it is well equipped to work with smaller genomes, like those of viruses and bacteria, minION can’t yet take on larger genomes, like those of animals and plants. However, reports suggest that this may change with newer versions, and other devices, that Oxford Nanopore has planned in the future. Speaking on the high error rates of minION, chief technology officer Clive Brown said, “The error rate is now in single figure percentages in our hands, and we’re not at the limit.”
However, the journey forward may not be smooth. According to a Bloomberg BNA report, the Oxford Nanopore has already had lawsuits filed against it by Pacific Biosciences for patent infringement. Rival companies based on similar nanopore technologies may make the competition harder.