Nature: The handheld sequencer performs amazingly

Release date: 2015-05-08

In April of this year, Joshua Quick of the University of Birmingham installed three sequencers (MinION) in the baggage and boarded the plane to Guinea. This was unimaginable in the past, as most of the sequencers were big and heavy. In Guinea, Quick sequenced the viral genome of 14 Ebola patients in just 12 days, and the results were obtained 48 hours after the sample was collected.

This is an unprecedented opportunity for epidemiologists. Researchers have set up a dedicated MinION lab in the treatment center in Guinea to analyze the patient's DNA and trace the source of the virus infection. "This is the democratization of sequencing," Quick said. “We no longer rely on expensive facilities and instruments.”

MinION is a handheld sequencer from Oxford Nanopore Technologies, which is easy to carry and cheap. It can read longer gene fragments, which helps to understand the complex regions of the genome. MinION can also be plugged into the laptop's USB port to display the data generation process on the screen.

Oxford Nanopore Technologies launched MinION's early experience program last spring, providing researchers with sequencing equipment and a one-time flow cell for a $1,000 deposit. Users will share their experiences and data analysis programs written by themselves on May 14th and 15th. For example, David Deamer, a biochemist at the University of California, uses MinION to detect nucleic acids and study the origins of life on Earth.

Initially, MinION did not reach the speed of propaganda, and it also produced a lot of mistakes. However, with the improvement of technology, recently published research shows that MinION is quite practical. It accurately sequences small genomes (such as bacterial and yeast genomes), distinguishes closely related bacteria and viruses, reads complex regions of the human genome, and more.

MinION sequencing blossoms everywhere

Many biologists began using MinION for field sequencing. On May 4th, Italian biologists brought MinION to the rainforests of southern Tanzania to sequence a local frog. Karen James of the MDI Biology Laboratory intends to send MinION to folk research enthusiasts to study the biodiversity of Acadia National Park. Michael Schatz, a computational biologist at Cold Spring Harbor Laboratory, also wrote an app for MinION. NASA scientists even plan to send MinION to the International Space Station to allow astronauts to test under microgravity conditions. If all goes well, space biologist Aaron Burton suggests sending the sequencer to Mars to look for signs of life at the molecular level.

At present, there are some limitations in MinION. This kind of sequencer is not suitable for large genomes, and the error rate is higher than that of large-scale sequencers. It is also difficult to read long repeat sequences. However, this situation is gradually improving, for example, bioinformatics experts have developed error correction methods.

Biologists want MinION to be faster and more accurate, and it's best not to sample directly for sequencing. They expect Oxford Nanopore Technologies to release new technological improvements at its May meeting. In addition, the price of MinION is still unknown, and low price is one of the most attractive selling points of this device.

Source: Biopass

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