Oxford Nanopore Technologies was spun out from the University of Oxford in 2005. Until May 2008, the company was named Oxford NanoLabs Ltd. Oxford Nanopore employs a team of more than 300 people including scientists, engineers, informaticians, manufacturing and commercial specialists. Headquartered in Oxford, UK, the Company also has employees in Cambridge (UK), New York and Boston.
The company was founded by Dr Gordon Sanghera, Dr Spike Willcocks and Professor Hagan Bayley, who is currently Professor of Chemical Biology at the University of Oxford, with seed funding from IP Group plc. Since 2008 the Company has also been working with collaborators at Harvard, Boston University and the University of California Santa Cruz and now includes a broad intellectual property position for the use of nanopores in molecular analysis and specifically DNA sequencing.
In 2005, Dr Gordon Sanghera joined Oxford Nanopore as CEO. Gordon brings his experience of combining biological and electronic technologies; he previously delivered blood glucose-sensing products to the market, a technology that has transformed the lives of diabetes patients worldwide. Gordon now leads an experienced management team towards the development and commercialisation of a new gold-standard in DNA-sequencing products.
In July 2009, the Company relocated to the Oxford Science Park. Our premises at Edmund Cartwright House were inaugurated by the UK Science and Innovation Minister, Lord Drayson. In 2011, an additional 7,000 square feet on the Oxford Science Park was opened and a new Cambridge office was also opened as an informatics outstation.
In February 2012 at the AGBT conference, Oxford Nanopore presented a variety of nanopore DNA 'strand sequencing' and protein-analysis data, and an overview of the hardware and software behind the GridION and MinION systems. These data included small genomes that had been sequenced using the Company's technology over the sense and antisense strands, showing tens of kilobases in single reads. This was the first nanopore sequence data to be shown worldwide since the technique was first theoretically proposed in 1996.
In spring 2014, the MinION Access Programme (MAP) was commenced; early access users were invited to contribute a refundable $1,000 deposit to use the MinION in its earliest stages of release. Over the subsequent months, performance and processes were improved and publications on the technology started to emerge.
In October 2014, at the ASHG conference, the PromethION was presented for the first time. PromethION is a tablet-sized benchtop instrument giving users the choice of the number of samples and the number of nanopores being used for a particular experiment, ranging from individual samples at a time to multiple samples in parallel. Specifications of the device can be found here.
In May 2015, the first nanopore sensing conference was convened (London Calling) where users of MinION technology gathered to hear from 20 speakers and additional abstracts from numerous other MAP participants across a range of applications. MinION became commercially available at this time and the MinION Access Programme became the Nanopore community.
In July 2015, the PromethION Access Programme was opened for registration.
In November 2015, Professor Hagan Bayley retired from the Board.
In November 2015, MinION users gathered at the first Nanopore Community Meeting in New York.
In May 2016, the second London Calling conference was convened. A series of announcements were made including the full availability of the new R9 nanopore with improved performance. The mobile phone compatible, pipeline product SmidgION was announced.
In September 2016, Oxford Nanopore held a technical update, announcing new product upgrades to the MinION.
In October 2016, Oxford Nanopore announced that the early queue for the PromethION Early Access Programme was now full and announced transition to a more mature phase of the programme.
In October 2016, registration for the VolTRAX Introduction Programme was announced, for shipping in December 2016
In December 2016, the second Nanopore Community Meeting was held. During this meeting, three groups presented or released the first human genomes to be sequenced on the handheld MinION.
MinION progress so far
Continuous integration for continuous performance improvement
MinION was launched into the MinION Access Programme in Spring 2014 and made commercially available in May 2015. The Nanopore Community has grown around the two phases of MinION availability.
Oxford Nanopore delivers continual improvement where all parts of the technology are shipped, improved and developed. The format of the hardware, software and chemistry changes on a regular basis (often over weeks rather than months). This iterative improvement process will continue throughout the lifetime of all Oxford Nanopore products.
Updates across different parts of the technology can combine to produce specific, measurable improvements. This has been achieved through a combination of software updates, changes in the library preparation kits and protocols, changes in the flow cell design and changes in the flow cell chemistries.
Examples of developments to date include:
Library preparation kits
- These have been updated several times during the Nanopore Community, and additional kits and protocols have been introduced to enable new applications, for example cDNA sequencing and barcoding of genomic DNA and amplicons. Changes have also contributed towards improving the accuracy of sequence data.
- We have also made several changes to our library preparation kits to improve the user experience. These include reducing the number of steps and consequently the time taken, and improving robustness and performance. The newest Rapid Sequencing kit prepares a library in five minutes.
- VolTRAX, an automated library preparation device, will be introduced in late 2016 through the VolTRAX Introduction Programme.
MinION flow cells, containing the bespoke nanopore sensor and associated chemistries
- Three new versions of these flow cells have been delivered to date that increase yield by delivering more working nanopores per flow cell.
- In the summer of 2016, 'R9' was released to supercede the previous R7. This is designed to improve accuracy of both 1D (read one strand of the DNA) and 2D (read both template and complement strands) sequencing. Running at speeds of 250+ bases per second per nanopore it is designed to increase the speed of data generation and therefore yield of a flow cell.
- In October 2016, new flow cells containing R9.4 were shipped, increasing sequencing speeds to 450 bases per second and enabling 10Gb DNA sequencing data to be obtained from a MinION Flow Cell.
The MinION device
- In May 2015 the second version of the device, the MinION MkI was introduced. The MinION MkI was a full production device featuring improvements of performance and ease of use.
- In May 2016, the MinION Mk 1B was introduced. Preparing for future iterations of nanopore chemistry it included improvements such as greater temperature control of the flow cell.
Speed of individual nanopore processing
Faster processing speed results in greater yield of data per unit of time. Speed is affected by multiple factors including buffers, temperature and the motor enzyme deployed
- During the first year of the Nanopore Community, Oxford Nanopore recommended a speed of around 30 bases per second per nanopore
- By 2015 users could run at 70bps.
- With the introduction of R9 in the summer of 2016, DNA was passed through the nanopore at 250+bps
- In October 2016, processing speed can now by 450 bases per second
Flow cells: Duration of use
- The MinION does not have a fixed run time; users may run the instrument for as long as it takes to accumulate sufficient data for their needs. The total available life time of a flow cell does not need to be consumed in a single experiment. In the Nanopore Community, later releases of flow cells have been run for longer periods of time resulting in increased overall yields.
The instrument control software (MinKNOW)
- New versions of MinKNOW have been released to improve MinION performance for all applications. For example, adjusting the frequency of data sampling can improve yield and accuracy.
- Most recently, MinKNOW now allows local basecalling.
- Oxford Nanopore provides signal processing and base-calling tools, but file formats are documented and participants can write their own data analysis tools or modify the scripts provided in the GitHub repository. Sources for any software are provided on an ‘as-is’ and ‘without warranties’ basis
- Oxford Nanopore currently provides basecalling in the cloud and in the future anticipates that this will be available locally. The cloud based analysis service Metrichor will evolve for more comprehensive analyses and services.
- New and evolved analysis algorithms and other updates have been made to Metrichor, improving data quality and speed of analysis
- Nanopore Community participants have developed a variety of tools for nanopore data analysis
Knowledge and support
We provide the latest information on how to use the products via the Nanopore community website, which also serves as a forum for MinION users to share information.