A disruptive sequencing technology
Every new generation, a new concept is born and can completely reshape the landscape of biomedical research. Nanopore sequencing technology, although still at its infancy, is beginning to look like a “game-changer.” It’s a revolutionary concept in sequencing in which strands of nucleic acids are fed through a tiny pore (nanopore) made of either protein or synthetic material, such as graphene, embedded on a membrane, which blocks out all the electric current on both sides. Then, a constant stream of current can be fed through the membrane. Changes in electrical current as each nucleotide passes through the pore generate a unique signature that the machine deciphers to discern the nucleotide sequence.
In 1989, a biophysicist, named David Deamer, conceived the idea of nanopore sequencing. He called it an “intuitive” concept. Yet, it took more than two decades and an incredible amount of research and development for the commercialization of this technology to gain foothold. There were two major challenges. How do you tell the nucleotides apart? The distance between each nucleotide base is only about half a nanometer. That is more than a million times smaller than the width of a human hair! In addition, how do you guide or pull a strand of coiled-coiled DNA through a molecular size nanopore? These obstacles have finally been overcome and nanopore sequencing might finally be ready for primetime. This technology could potentially take genome sequencing to the next-level, as they started rolling out testing programs with different academic labs across the world.
Nanopore Sequencing Technology vs. Traditional Next Gen Sequencing
Why is Nanopore sequencing technology such a “disruptive” technology? Comparing it to all current DNA sequencing technologies, one of the most important differences is that nanopore sequencing requires no amplification of DNA. Direct sequencing eliminates a number of problems. First, it eliminates the use of color probes that represent different bases. This would certainly reduce the reagent cost and the number of steps required for sequencing. Second, it eliminates the use of stationary PCR machines for amplification. Imagine a pocket-sized nano sequencer that you can bring to any places. This scenario would not be part of the scientific novel anymore. Third the data can potentially be analyzed in real time as the DNA runs through the nanopore, compared to having to wait until the reaction is finished. Currently it is capable of sequencing up to approximately 8kb of continuous DNA strand in real time!
Since this technology is still at its infancy, it will only get better. For example, the current array chips by Oxford Nanopore consist of protein nanopores embedded on an electrically resistant polymer material. It allows multiple experiments to be run in parallel in one chip. However, the development of a “solid-state” nanopore made of cutting-edge material, such as graphene, is currently underway. This would allow the customization of the pore-size and permit scientists to sequence a wide array of molecules besides DNA, such as RNA and protein. As of now, a consortium of institutions around the globe has been conducting genome sequencing research using the Oxford Nanopore’s MinIon. The initial opinion of the pundits is that this device has the potential to deliver a vast amount of sequencing data in a short amount of time and in any research environment. Already, researchers have sequenced the DNA genomes of bacteria and viruses (1). Even more exciting news came recently as a team of researchers at UConn was able to demonstrate RNA sequencing on the MinIon (2).
The next development for Oxford Nanopore will be even more critical. It needs to improve upon the current technology to decrease the reading error rate and maximize the ability to read even longer stretch of DNA in a continuous fashion. Our futures will all benefit from such technology and I can’t wait to watch what happens next.
- “International Consortium Provides Standard Protocol for Using Oxford Nanopore’s DNA-Sequencing Device.” News-Medical.net. Accessed November 12, 2015. http://www.news-medical.net/news/20151016/International-consortium-provides-standard-protocol-for-using-Oxford-Nanopores-DNA-sequencing-device.aspx.
- “UConn Team Demonstrates RNA Sequencing on MinIon; Plans to Sequence Whole Transcriptomes.” GenomeWeb. Accessed November 12, 2015. https://www.genomeweb.com/sequencing-technology/uconn-team-demonstrates-rna-sequencing-minion-plans-sequence-whole.
- Ammar, Ron, Tara A. Paton, Dax Torti, Adam Shlien, and Gary D. Bader. “Long Read Nanopore Sequencing for Detection of HLA and CYP2D6 Variants and Haplotypes.” F1000Research 4 (2015): 17. doi:10.12688/f1000research.6037.1.
- Loman, Nicholas J., Joshua Quick, and Jared T. Simpson. “A Complete Bacterial Genome Assembled de Novo Using Only Nanopore Sequencing Data.” Nature Methods 12, no. 8 (August 2015): 733–35. doi:10.1038/nmeth.3444.
- “Oxford Nanopore Researchers Assemble Bacterial Genomes from Environmental Sample.” GenomeWeb. Accessed October 13, 2015. https://www.genomeweb.com/sequencing-technology/oxford-nanopore-researchers-assemble-bacterial-genomes-environmental-sample.
- “Oxford Researchers Lay Out Path to High-Throughput Nanopore Sequencing With Optical Detection.” GenomeWeb. Accessed October 13, 2015. https://www.genomeweb.com/sequencing-technology/oxford-researchers-lay-out-path-high-throughput-nanopore-sequencing-optical.