Nanopore sequencing: What would you sequence? -

Gene-sequencing is a technology which has the potential to revolutionise many scientific disciplines, from medicine to climate science and conservation. In this article, former St John’s student Julia Eales describes just a few of these many applications and the ways in which they are being used by scientists around the world.

Sequencing is the process of identifying the order of bases (or sequences) making up the DNA or RNA present in living things. The specific sequences in the genome of an organism determine the proteins it synthesises which, in combination with environmental factors, are responsible for the characteristics of that organism. This makes studying these sequences crucial across fields spanning from developing new medicines, to understanding evolutionary processes, to fighting climate change. The technology used to do this has developed at a very rapid pace, enabling scientists to use it in ways that weren’t possible just a few years ago.

I’m a member of Oxford Nanopore Technologies, a company that makes sequencing technology using a method called nanopore sequencing. A nanopore is essentially a tiny channel made of protein, with a hole running through the middle. When embedded in a membrane, this acts as a gateway, through which an electrical current can be passed. If a strand of DNA or RNA is passed through a nanopore – like thread being pulled through a bead – it disrupts the electrical current flowing through it. The electrical signal this disruption produces depends on the specific sequence of the molecule in the nanopore. This means that, by measuring changes in electrical current, it’s possible to determine the sequence of DNA or RNA passing through the nanopore. Using this method across hundreds or thousands of nanopores at once any DNA or RNA of interest from any organism can be sequenced.

Everything that’s needed for nanopore sequencing can be packaged into very small electronic devices – the smallest is about the size of a chocolate bar and can be run from a laptop. This means that, while traditional sequencing requires samples to be transported to a laboratory and then analysed, researchers can now take the sequencer to the sample and perform their experiments in the field.

Many scientists are taking advantage of this to sequence in environments where it wasn’t previously possible. One team took a nanopore sequencer (by sledge) on a trek to an ice cap in Iceland¹. Sequencing the DNA of microbes in a sample taken from a hot spring gorge, using only solar power, they found unknown sequences that could belong to previously uncharacterised species. Going further afield, nanopore technology has become the first sequencing technology to be used in space². On board the International Space Station, scientists demonstrated that it was possible to sequence microbes in micro-gravity conditions, showing the future potential to identify an infectious pathogen in a crew member without having to return to earth³.

Crucially, this portability means that the sequencing technology can be quickly deployed where and when it’s needed, including in low-resource settings where there may not be access to a laboratory. Nanopore sequencing has been used to rapidly sequence viruses in outbreaks around the world – including Ebola⁴, Zika⁵ and, most recently, COVID-19^6-8. By sequencing SARS-CoV-2 virus genomes and rapidly sharing their data online, scientists have been able to monitor COVID-19 transmission routes, and identify variants that could affect features including how easily the virus spreads.

Many scientists are also using nanopore sequencing to study the human genome. Using nanopore technology, it’s possible to sequence very long, unbroken molecules of DNA, producing very long ‘reads’. This makes it much simpler to study large or complex mutations in the human genome, which can be associated with rare or inherited diseases, potentially providing information critical to developing new tests or treatments.

Other researchers are using nanopore sequencing to characterise biodiversity and help conserve species at risk of extinction. In New Zealand, for example, the technology is being used to track the extremely endangered kākāpō parrot – by sequencing the traces of DNA they leave in the soil, causing no harm to the birds⁹. Sequencing plant genomes, meanwhile, can help scientists develop strategies to preserve rare and unusual species, and could help identify genes that give important crops resistance to disease and the changing climate.

Even with so much research into the genomes of different organisms, there is still so much left to discover. In fact, the first truly complete human genome sequence was only just published in May 2021¹⁰, and of all known plant species, only around 0.1% have had their genomes sequenced^11,12.

What would you sequence?

Julia Eales studied Biological Sciences at St John’s College, and currently works for Oxford Nanopore

References

Gowers, G-O. et al. (2019). Entirely Off-Grid and Solar-Powered DNA Sequencing of Microbial Communities during an Ice Cap Traverse Expedition. Genes 2019, 10(11), 902; https://doi.org/10.3390/genes10110902
Castro-Wallace, S.L. et al. (2017). Nanopore DNA Sequencing and Genome Assembly on the International Space Station. Sci Rep 7, 18022. https://doi.org/10.1038/s41598-017-18364-0
Burton, A.S. et al. (2020). Off Earth Identification of Bacterial Populations Using 16S rDNA Nanopore Sequencing. Genes 2020, 11(1), 76. https://doi.org/10.3390/genes11010076
Quick, J. et al. (2016). Real-time, portable genome sequencing for Ebola surveillance. Nature. 530(7589):228-232.
Faria, N. R. et al. Mobile real-time surveillance of Zika virus in Brazil. Genome Med. 8(1):97 (2016).
Zhu, N. et al. (2020). A novel Coronavirus from patients with pneumonia in China, 2019. N Engl J Med. 382;8. DOI: 10.1056/NEJMoa2001017
Lu, J. et al. (2020). Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China. Cell 2020 May 28;181(5):997-1003.e9. doi: 10.1016/j.cell.2020.04.023.
Fauver, J.R. et al. Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States. Cell. 2020 May 28;181(5):990-996.e5. DOI: 10.1016/j.cell.2020.04.021.
Urban, L. Leveraging adaptive sampling of environmental DNA for monitoring the critically endangered kākāpō. Presentation. Available at: https://nanoporetech.com/resource-centre/video/lc21/leveraging-adaptive-sampling-of-environmental-dna-for-monitoring-the-critically-endangered-kakapo
Nurk, S. et al. (2021). The complete sequence of a human genome. bioRxiv. https://doi.org/10.1101/2021.05.26.445798
NCBI National Center for Biotechnology Information. Genomes information by organism. Available at: https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/
Royal Botanic Gardens Kew. 2017. State of the world’s plants. Available online: https://stateoftheworldsplants.com/2017/report/SOTWP_2017.pdf

Challenge

What would you sequence?

Plants, animals, fungi, bacteria, viruses – what would you sequence, and why?

Imagine that you’re writing to a member of your team as you plan your own nanopore sequencing experiment. In your letter, describe your method, what you’re hoping to investigate, why you feel it’s an important area of research, and the impact your results could have.

As you plan your experiment, consider:

What organism, or organisms, would you like to sequence? Why did you choose these in particular?
What samples would you extract your DNA or RNA from, and where would you find them?
Would you perform your sequencing in the lab or in the field, and why?
Once you have sequenced your organism(s) of interest, what do you plan to find out from the data?
How might your findings be used?

You can also use the resources on this page to help you develop your answer: https://sjcinspire.com/wp-content/uploads/2021/01/Inspire-Y10-11-Class-1-Biology-and-Darwinian-evolution.pdf

Your letter should be 500 words or less.

CLICK HERE TO SUBMIT YOUR WORK!