Nanopore sequencing has become an indispensable tool for scientists exploring the genomic landscape to make groundbreaking research discoveries in microbiology, cancer, animal, environmental, infectious disease, and large-scale genome analysis programs. Oxford Nanopore Technologies has partnered with Tecan to automate nanopore sequencing workflows, making the technology more accessible to a diverse user community and helping to drive the transition from academia to production genomics.
Oxford Nanopore Technologies was spun out from the University of Oxford in 2005 with the aim of developing a disruptive, electronic, single-molecule sensing system based on nanopore science. In the years since then, it has launched a range of nanopore sequencing products that provide rapid, scalable, and affordable access to rich genomic insights both in the field and on the lab bench.
Nanopore sequencing is currently the only sequencing technology to offer real-time analysis. It enables the analysis of native DNA and RNA, allowing the sequencing of fragments of any length, delivering short to ultra-long reads. Stephanie Wilbraham, Director of Automation Product Management at Oxford Nanopore, explained how automation is helping to widen access to the technology and expand the user community: “Automation is very much about lowering the barrier to entry, and has grown in importance as sequencing has entered into more general use rather than being a specialist lab technique. It allows us to remove a lot of manual steps to make nanopore sequencing much easier, especially for users who are not molecular biology specialists.”
Stephanie continued: “As our product line matured, we found ourselves expanding into new markets, such as biopharma and other applied markets, as well as production genomics, where automation would be particularly beneficial. Our sequencers are very compact and don't have lasers, which means that they can be integrated with a liquid handling platform much more easily than a lot of other devices. All of these factors came together and it felt like the right time to invest in an automated product, and that is how Project TurBOT – which delivered the ElysION™ device – was born.”
“We knew from the outset that we would need to complement our sequencing expertise with that of an OEM partner with liquid handling knowhow and a track record of building and manufacturing automated platforms, as well as the ability to provide support services at customers’ sites. Compliance with ISO 13485 is also becoming more and more important, especially in good manufacturing practice and clinical environments, so expertise in this area was one of the main reasons that we chose Tecan as that partner. The company has a deep understanding of these markets, backed by a long pedigree of OEM projects in that space. It also has a well-established service business, with a large global team of field service engineers.”
The challenge for Oxford Nanopore and Tecan was to integrate the MinION™ Mk1D sequencer onto a liquid handling platform without major modifications to the workstation or a redesign of the flow cell, to ensure pricing remained affordable. “Initially, we worked with a small team from Tecan to integrate the sequencers onto a Cavro® Magni Flex liquid handling platform, driven by MAPlinx™ software that is integrated with our sequencing software to provide a single end-user interface. Within a year of completing the proof-of-concept stage, we had displayed our first device at a conference and were able to bring the product to market quite quickly after that.”
ElysION was the result of a large, complex integration project, and Tecan was very accommodating, flexible and easy to work with, making the process remarkably straightforward.
ElysION was developed as an automated, sample-to-answer sequencing solution that could accommodate a variety of workflows and use cases. “We’ve created a completely new interface aimed at production genomics environments where users might not have the expertise to develop their own workflow in house. The entire workflow can be automated – extraction of DNA or RNA, library preparation and loading onto the flow cell for sequencing, and then data analysis – or users can perform library preparation and sequencing only. Pre-installed, plug-and-play workflows are provided, so operators just have to choose the most appropriate run for their application, with options for some parameters, such as PCR cycling or bead clean-up ratios, to be customized.”
The logistics of shipping larger devices and after sales support were also key considerations when evaluating potential partners. “Tecan’s service business and the footprint of its staff has been important for us. Our other products are physically much smaller than liquid handling workstations, and we’ve leaned on Tecan’s expertise to help manage the logistics of shipping the much larger ElysION automated device. To make life as easy as possible for our customers, we are the first point of contact whenever support is needed. We coordinate everything, whether it is a hardware issue that requires a visit from a Tecan field service engineer, or software or applications queries that we handle in house.”
“Finding a partner that could work flexibly with us was vital,” said Stephanie. “We’re a very agile, technology led company. Tecan was very adaptable to working in different ways that suited our approach to product development. It's really important to us to get a product to market as early as possible, to get it into people's hands and have user feedback before finalizing the design. There is a very strict process to follow to bring an ISO 13485 product to market, and the idea of doing that while simultaneously working in a very agile way is not something that every company can do. Partnering with Tecan allowed us to get ElysION into the field for beta testing at an early stage and incorporate the feedback into the end-product design.”
“Our current focus is on infectious disease and biopharma applications but, in the longer term, the aim is to move into human genomics projects. We are currently further developing ElysION by integrating a higher output sequencer – PromethION™ 2 Solo – and expanding the menu to address additional customer needs. Our goal is to launch an ISO 13485 IVD-compliant device and move into more regulated markets, and Tecan’s expertise will be crucial to this. ElysION was the result of a large, complex integration project, and Tecan was very accommodating, flexible and easy to work with, making the process remarkably straightforward,” Stephanie concluded.
For research use only. Not for use in clinical diagnostics.
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