Products
The main products of Oxford Nanopore are:
- MinION:[3][8][9] this harmonica-sized portable protein nanopore sequencing USB device has been commercially available since May 2015[10] after having been launched initially through an early access program, the MinION Access Program (MAP).[11] An editorial describes the rapid pace of development during the MAP: “We have had three 'pore' changes, six chemistry changes, and a software update seemingly every few weeks.”. Publications from this program 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] Publications indicate a read rate of 90 nucleotides per second per nanopore[22] with an error rate of 30% during the early phase of its release around 2014.[23] With the latest R9 release in 2016 raw error rates have been reduced to between 2-13% for various types of DNA sequencing ('1D' vs '2D', described below).[24][25][26][27] In October 2016 R9.4 was released running at 450 bases per second per nanopore for 10 Gb data per MinION Flow Cell.[28] More recently, the R10 pore has been developed and with a different aperture, it has different read out characteristics, early data from ONT show that the R10 pores can overcome homopolymer sequences.[29]
- GridION X5: this desktop device has been commercially available since March 2017.[30] The device processes up to five MinION Flow Cells and enables generation of up to 100 Gb of data per run.[31]
- PromethION: this desktop, high throughput device will be available through an access program[32] that opened for registration in July 2015. The device contains channels for 144,000 nanopores (in comparison to MinION’s 512).[33]
- 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.[34] Registration for the early access program was opened in October 2016.[35]
- Metrichor: this spinout company from Oxford Nanopore was set up to provide end to end solutions for biological analyses, using nanopore sensing technologies.[36][37]
- SmidgION: a mobile phone sequencer announced in May 2016, currently in development.[38]
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][39]
As of October 2016, over 3,000 MinIONs have been shipped.[40] PromethION has started to ship in early access.[28] 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] By August 2016, bioinformatician Jared Simpson noted that 99.96% consensus accuracy was generated using the nanopolish tool after raw accuracy had been improved with the new R9 nanopore.[41]
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 [42] published in October 2015,[43] 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.”.
In March 2016 the company announced a chemistry upgrade to ‘R9’, using the protein nanopore CsgG in collaboration with the lab of Han Remaut (VIB/Vrije Universiteit Brussel).[44] The Company stated in a webcast that R9 is designed to improve error rates and yield.[45] In late May 2016, the R9 nanopore was launched and users have reported high performance levels with the upgraded flow cells.[24] Early reports on social media report high levels of '1D' accuracy (sequencing one strand of the duplex DNA),[25] '2D' accuracy (sequencing both the template and complement strand)[26] and assembled accuracy.[27]
