Last week I was invited to virtually attend and present a poster at London Calling 2022, Oxford Nanopore’s largest conference, where scientists who are using nanopore sequencing technology share their research and experience together. The speakers covered a broad range of research topics including epigenomics, epigenetics and human disease, single cell, transcriptomics, cancer and bioinformatics, featuring a board agenda of 88 talks.
The conference provided an insight of what it’s like to work with scientific technology, translational research, and future healthcare applications, but almost more importantly, it showcased the Oxford Nanopore, which has entirely revolutionised how sequencing can be done almost anytime, anywhere in the world.
As someone who works at openCELL, who’s mission is to lower the barriers to biotechnoogy, I loved being able to hear about the acceleration of research and innovation, as well as the real-life impact that increasing access to science has on our understanding of the world around us (and the many tiny worlds within us).
- Turning 5387 words into a poster is as hard as it sounds, but it’s worth it!
I was asked to present a poster based on our latest published research named rapid genome surveillance of SARS-CoV-2 and study of risk factors using shipping container laboratories and portable DNA sequencing technology (you can read all about it and even see a video at the openCELL blog). I used the poster to cover an introduction on SARS-CoV-2, the pipeline (Artic protocol based on Josh Quick's SARS-COV-2 nanopore sequencing protocol) used to carry out the experiment.
Turning a whole research paper (all 5387 words of it!) into a one-page poster is as hard as it sounds but actually when you think about it as a way of making your research more accessible by creating a clear narrative that people can take in within one glance, it really makes it more rewarding. Posters are a great way of distilling science that can be very long, dense, full of jargon or even behind paywalls. By being given the chance to show the amazing work we did on a poster, people who normally wouldn’t come across it were able to quickly see and engage with our amazing work on SARS-CoV-2 research work in Jersey.
- Flexible labs are the future
Even though we’re building labs of the future (have you heard about our amazing bioHOTEL?) It was so nice to see people still interested in openCELL’s first iteration, the shipping container labs. I spoke to so many people at London Calling about our work on SARS-CoV-2 sequencing in our mobile, shipping container laboratory using nanopore sequencing technology, explaining how it was not only a great experience for me, but also for the 100+ biotech startups that had shipping container bio labs in the Old Laundry Yard at Shepherd’ Bush Market. These labs were not only affordable, meaning that more startups were able to access them and create new and exciting innovations in biotechnology, they’re also highly contained (no pun intended) which means that you can do all your work in one place (not like in a university department where you might be running between labs or even buildings!), making it so quick and efficient to do your work. This flexible, adaptable model for bio labs is actually so great to work in for something like PCR testing and it’s what we’re really trying to achieve with the bioHOTEL, to create small, daisy-chained labs that are linked that you can move through in a one-way system.
- You never know where you’ll meet a Guinness World Record holder!
This was one of my favourite talks from the whole conference, really showing the power of the nanopore technology and how it’s really opened up a whole new world of science: Euan Ashley is a professor of medicine, of genetics and of biomedical data science at Stanford University AND he’s also a Guinness world record holder, having sequenced entire human genome in five hours and two minutes.
He and his team developed a whole genome nanopore sequencing approach that can characterise genetic disease much faster than any previously published approach, enabling faster detection of variants that cause genetic disease. This can make a huge difference in prognosis during time-critical situations, such as identifying suspected pathogenic variants in critically ill patients. Ultimately, this could mean that scientists will be able to work out if a critically ill patient is sick because of a genetic disease or pathogen, making a huge difference in how quickly and effectively they can be treated.
- You can take the oxford nanopore literally anywhere!
This is one of my favourite things about the Oxford Nanopore, it has really lowered the barriers to entry and innovation in terms of sequencing. Previously, sequencing was only done in the lab, but now people can literally put the sequencer machine in their pockets and take them anywhere in the world. This has really revolutionized and expanded our ideas about what can be sequenced, where in the world it can happen and who can do science! I was particularly inspired by a talk on an educational, field-based sequencing lab facilitating biodiversity research in the Ecuadorian tropical andes delivered by Zane Libke.
He explained how the traditional sequencing technologies have not been accessible and students lack practical molecular biology experience. So, he established practical, experiential-based courses and research experiences, which have allowed over 70 Ecuadorian students and professionals to experience field-adapted molecular biology and nanopore sequencing techniques. The participants have been working with amphibian communities, discovering several species new to science and informing conservation plans. This on-site, low-overhead nanopore sequencing laboratory will not only accelerate biodiversity research (and help us discover cool new frogs!), it also empowers new communities and local researchers to fight the biodiversity crisis.
- Nanopore technology is working FAST to fight cancer
Another one of my favourite talks was delivered by Micheal Dean about understanding cancer epigenetics, immunogenetics, and energetics. He explained the complexitiblity of cancer with an epigenetic component which is currently poorly understood. A major emerging theme is how nanopore sequencing is enabling the most comprehensive understanding of diseases such as cancer research, allowing for the sequencing of native DNA fragments of any length.
The previous sequencing methodology only allowed the short read (DNA broken into short fragments), however next generation sequencing such as nanopore made it possible to sequence long reads, with the significant increase in capacity to sequence read length of DNA in one single read. The benefits of long read sequencing are eliminating amplification bias and improving accuracy of genome assembly, detection of structural variants, thereby requiring less reads to cover the same gene.
Dr. Dean and his team have used nanopore sequencing for deeper understanding of cancer pathogenesis, such as HPV virus through direct cDNA and RNA sequencing and epigenetic components of cancer through methylation sequencing. They have found that they are able to receive bias-free transcriptomic data and identify RNA modifications in the MYC oncogene. This sounds like a lot but what it really means is that for something like cancer diagnosis and treatment, we might be able to better understand individual cases and develop personalised treatments to improve treatment survival rates and reduce costs sooner than we ever imagined.
Overall, it was such an inspiring experience. It really showed that there are so many researchers and scientists working on amazing projects and the impact technology like the oxford nanopore can make in terms of opening up science to more people and places, and ultimately the effect that will have on the future of patient experience and treatment, cancer diagnosis, and the preservation of our planet’s biodiversity (and frogs!).