Oxford Nanopore Technologies

Oxford Nanopore Technologies

Industry	Nanopore sequencing
Founded	2005
Founder	Hagan Bayley Gordon Sanghera Spike Willcocks
Headquarters	Oxford Science Park, Oxford, United Kingdom
Key people	Hagan Bagley [1] Clive G. Brown (CTO) Jim McDonald (CFO) John Milton (CSO) Gordon Sanghera (CEO) Spike Willcocks (VP)
Website	nanoporetech.com

Oxford Nanopore Technologies Limited, also known as the MinION technology, is a U.K.-based company which is developing and selling nanopore sequencing products for the direct, electronic analysis of single molecules.^[2][3][4][5]

History

The company was founded in 2005 as a spin-out from the University of Oxford by Hagan Bayley, Gordon Sanghera, and Spike Willcocks, with seed funding from the IP Group.^[6][7] As of 2014 the company had raised over £250 million in investment.^[6]

Products

The main products of Oxford Nanopore are:

• MinION:^[3][8][9] this portable protein nanopore sequencing USB device has been commercially available since May 2015^[10] after having been launched initially through an early access programme, the MiniON Access Programme (MAP).^[11] An editorial describes the rapid pace of development during the MAP: “for the MAP participants it has been a white-knuckle ride. We have had three “pore” changes (R6, which was only around for about a month, R7 and the current version R7.35). This was coupled with six chemistry changes and a software update seemingly every few weeks. For some it has been too much change, but early access programmes are not for everyone”. Publications from this programme outline its use in rapid identification of viral pathogens,^[12] monitoring ebola,^[13] environmental monitoring,^[14] food safety monitoring,^[15] monitoring of antibiotic resistance,^[16] analysis of structural variants in cancer,^[17] haplotyping,^[18] analysis of fetal DNA,^[19][20] and other applications.^[21]
• PromethION: this desktop, high throughput device will be available through an access programme^[22] that opened for registration in July 2015. The device contains channels for 144,000 nanopores (in comparison to MinION’s 500.^[23]
• VolTRAX: this device, currently in development, is designed for automated sample preparation so that users do not need a laboratory or lab skills to run the device.^[24]
• Metrichor: This spinout company from Oxford Nanopore was set up to provide cloud-based analysis of real time DNA sequencing data streaming.^[25]
• GridION

These products are intended to be used for the analysis of DNA, RNA, proteins and small molecules with a range of applications in personalized medicine, crop science, and scientific research.^[3][26]

As of late 2015, MinION is being used by over 1,000 researchers.^[27] PromethION and GridION have not yet been brought to market. In a paper published in November 2014, one of the MAP participants wrote, "The MinION is an exciting step in a new direction for single-molecule sequencing, though it will require dramatic decreases in error rates before it lives up to its promise.".^[3] In July 2015, a group published on nanopore sequencing of an influenza genome, noting “A complete influenza virus genome was obtained that shared greater than 99% identity with sequence data obtained from the Illumina Miseq and traditional Sanger-sequencing. The laboratory infrastructure and computing resources used to perform this experiment on the MinION nanopore sequencer would be available in most molecular laboratories around the world. Using this system, the concept of portability, and thus sequencing influenza viruses in the clinic or field is now tenable.“ In a paper and accompanying editorial ^[28] published in October 2015,^[29] a group of MinION users wrote, “At the time of this writing, around a dozen reports have emerged recounting utility of the MinION for de novo sequencing of viral, bacterial, and eukaryotic genomes.”

Internet of Living Things

Oxford Nanopore has worked to establish the concept of an 'Internet of Living Things', originally conceived as an 'Internet of DNA' by a bioinformatician based at UCSC ^[30] In an article in Wired in 2015, Clive Brown, CTO of Oxford Nanopore noted that "future nanopore sensing devices linked to cloud based analyses could run anywhere on anything.".^[25]

The concept of an Internet of Living Things was referenced in a 2015 paper by Yaniv Erlich^[31] describing a future of ubiquitous genomics. Erlich noted that "multiple appliances could benefit from integration with sequencing sensors, including air conditioning or the main water supply to monitor harmful pathogens. However, of all possible options, toilets may offer the best integration point.”.^[32] For health-related applications he noted that "rapid sequencing at airport checkpoints might be useful to control pathogen outbreaks and offer medical assistance to affected passengers. Similarly, a portable sequencer will enable physicians to provide more accurate diagnoses in the field during humanitarian crises or in the clinic without the need to waste time by sending samples to a lab.”

References

1. BAYLEY, Prof. (John) Hagan (Pryce). Who's Who 2015 (online edition via Oxford University Press ed.). A & C Black, an imprint of Bloomsbury Publishing plc. (subscription required)
2. Eisenstein, M. (2012). "Oxford Nanopore announcement sets sequencing sector abuzz". Nature Biotechnology 30 (4): 295. doi:10.1038/nbt0412-295. PMID 22491260.
3. Mikheyev, A. S.; Tin, M. M. Y. (2014). "A first look at the Oxford Nanopore MinION sequencer". Molecular Ecology Resources 14 (6): 1097–102. doi:10.1111/1755-0998.12324. PMID 25187008.
4. Loman, N. J.; Quinlan, A. R. (2014). "Poretools: A toolkit for analyzing nanopore sequence data". Bioinformatics 30 (23): 3399–401. doi:10.1093/bioinformatics/btu555. PMID 25143291.
5. Oxford Nanopore on Twitter
6. "Company history". Oxford Nanopore Technologies.
7. "DNA sequencing: The hole story". The Economist (London). 2008-10-16. Retrieved 2014-10-19.
8. Check Hayden, E. (2014). "Data from pocket-sized genome sequencer unveiled". Nature. doi:10.1038/nature.2014.14724.
9. Check Hayden, E. (2015). "Pint-sized DNA sequencer impresses first users". Nature 521 (7550): 15. doi:10.1038/521015a.
10. "Archived copy". Archived from the original on November 21, 2015. Retrieved November 20, 2015.
11. Loman, Nicholas J; Watson, Mick (2015). "Successful test launch for nanopore sequencing". Nature Methods 12 (4): 303–304. doi:10.1038/nmeth.3327. ISSN 1548-7091.
12. Greninger, Alexander L.; Naccache, Samia N.; Federman, Scot; Yu, Guixia; Mbala, Placide; Bres, Vanessa; Stryke, Doug; Bouquet, Jerome; Somasekar, Sneha; Linnen, Jeffrey M.; Dodd, Roger; Mulembakani, Prime; Schneider, Bradley S.; Muyembe-Tamfum, Jean-Jacques; Stramer, Susan L.; Chiu, Charles Y. (2015). "Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis". Genome Medicine 7 (1). doi:10.1186/s13073-015-0220-9. ISSN 1756-994X.
13. Nick Loman (15 May 2015). "How a small backpack for fast genomic sequencing is helping combat Ebola". The Conversation.
14. "TGAC's take on the first portable DNA sequencing 'laboratory'". EurekAlert!. 19 March 2015.
16. "Real-time strain typing and analysis of antibiotic resistance potential using Nanopore MinION sequencing".
17. Norris, Alexis L.; Workman, Rachael E.; Fan, Yunfan; Eshleman, James R.; Timp, Winston (2016). "Nanopore sequencing detects structural variants in cancer". Cancer Biology & Therapy: 1–8. doi:10.1080/15384047.2016.1139236. ISSN 1538-4047.
18. Ammar, Ron; Paton, Tara A.; Torti, Dax; Shlien, Adam; Bader, Gary D. (2015). "Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes". F1000Research. doi:10.12688/f1000research.6037.2. ISSN 2046-1402.
19. Cheng, S. H.; Jiang, P.; Sun, K.; Cheng, Y. K. Y.; Chan, K. C. A.; Leung, T. Y.; Chiu, R. W. K.; Lo, Y. M. D. (2015). "Noninvasive Prenatal Testing by Nanopore Sequencing of Maternal Plasma DNA: Feasibility Assessment". Clinical Chemistry 61 (10): 1305–1306. doi:10.1373/clinchem.2015.245076. ISSN 0009-9147.
20. Wei, S.; Williams, Z. (2015). "Rapid Short-Read Sequencing and Aneuploidy Detection Using MinION Nanopore Technology". Genetics 202 (1): 37–44. doi:10.1534/genetics.115.182311. ISSN 0016-6731.
21. "Publications and more from the MAP community". Publications and more from the MAP community. Archived from the original on June 26, 2015.
22. "Community - Oxford Nanopore Technologies".
23. "Specifications - Community - Oxford Nanopore Technologies".
24. "Oxford Nanopore CTO Clive Brown’s Talk at London Calling: MinION ASIC, volTRAX, promethION". Next Gen Seek.
25. "Oxford Nanopore: we want to create the internet of living things". Wired UK.
26. Check Hayden, Erika (2012). "Nanopore genome sequencer makes its debut". Nature. doi:10.1038/nature.2012.10051. ISSN 1744-7933.
27. "Genes genie: Oxford Nanopore’s Gordon Sanghera". Financial Times.
28. "A disruptive sequencer meets disruptive publishing - F1000Research".
29. "Mini DNA sequencer tests true". EMBL.
30. http://www.technologyreview.com/featuredstory/535016/internet-of- dna/.
31. Check Hayden, Erika (2013). "Privacy protections: The genome hacker". Nature 497 (7448): 172–174. doi:10.1038/497172a. ISSN 0028-0836.
32. Erlich, Yaniv (2015). "A vision for ubiquitous sequencing". Genome Research 25 (10): 1411–1416. doi:10.1101/gr.191692.115. ISSN 1088-9051.