February 18, 2012

Oxford Nanopore is commercializing a USB-sized sequencing machine

Oxford Nanopore Technologies is developing the GridION system, a new generation of electronic molecular analysis system for use in scientific research, personalised medicine, crop science, security/defence and more. The platform technology uses nanopores to analyse single molecules including DNA/RNA and proteins.

New generation of sequencing technology uses nanopores to deliver ultra long read length single molecule sequence data, at competitive accuracy, on scalable electronic GridION platform. Miniaturised version of technology, MinION, will make nanopore sequencing universally accessible. Oxford Nanopore intends to commercialise GridION and MinION directly to customers within 2012.

Technology Review - Oxford Nanopore says it will begin selling by the end of the year a disposable DNA sequencer about the size of a USB memory stick that can be plugged directly into a laptop or desktop computer and used to perform a single-molecule sensing experiment. The device is expected to sell for $900,

At the Advances in Genome Biology and Technology conference (AGBT), FL, US, Oxford Nanopore presented:

A novel method of DNA 'strand sequencing' that uses an array of proprietary protein nanopores embedded in a robust polymer membrane. Each nanopore sequences multiple strands of DNA from solution in succession, as individual strands are passed through the nanopore by a proprietary processive enzyme. Base calling is performed by identifying characteristic electronic signals (disruptions in current through the nanopore), created by unique combinations of DNA bases as they pass through a specially engineered region inside the nanopore.DNA and enzyme are mixed in solution, engage with the nanopore for sequencing and once the strand has been completed a new strand is loaded into the nanopore for sequencing.

Genomes that have been sequenced as contiguous reads comprising both complementary strands of the entire genome. An example was shown of lamda, a 48kb genome, sequenced as complete fragments, whose sense and antisense strand total 100 kilobases. Read lengths mirror fragment sizes in the sample with no exponential loss of processivity.

Accuracy levels competitive with existing market-leading systems were shown. No deterioration of accuracy is seen throughout the sequencing of individual strands. A development pathway was presented that is expected to achieve accuracy exceeding current market-leading platforms through further design iteration of Oxford Nanopore's custom-made nanopores.

Oxford Nanopore's GridION platform was presented, consisting of a scalable network device - a node - designed for use with a consumable cartridge. Each cartridge is initially designed for real-time sequencing by 2,000 individual nanopores at any one time. Alternative configurations with more processing cores will become available in early 2013 containing over 8,000 nanopores.

Nodes may be clustered in a similar way to computing devices, allowing users to increase the number of nanopore experiments being conducted at any one time if a faster time-to-result is required. For example, a 20-node installation using an 8,000 nanopore configuration would be expected to deliver a complete human genome in 15 minutes.

A variety of sample preparation options were presented. No sample amplification is required and any user-derived sample preparation resulting in double stranded DNA (dsDNA) in solution is compatible with the system. With nanopores embedded in robust polymer membranes, dsDNA can be sensed directly from blood and in some cases with no sample preparation.

Oxford Nanopore's disruptive "Run Until..." informatics workflow: Nanopores allow the analysis of data in real time, as the experiment happens. Each GridION node contains all the computing hardware and control software required for primary analysis of data as it is streamed from each nanopore, resulting in full length real-time delivery of complete reads so that the user can perform secondary analyses as the experiment progresses. This allows the user to pre-determine an experimental question and continue the sequencing experiment until sufficient data have been accumulated to answer the question and move on to the next experiment.

Oxford Nanopore intends to introduce a new pricing model for its GridION sequencing system, which moves away from the traditional instrument price and consumable price. This is designed as a series of packages that allow the user to tailor a scheme to their budget structure, whether more flexible with capital or consumable expenditure. Transparent pricing schemes are designed for online ordering and fulfilment, with discounts applying to larger packages. Overall the schemes are designed to deliver a competitive 'price per base' compared to other systems on the market based on like-for-like user settings.

Nanopore Sensing

Intro to nanopore sensing

A nanopore is, essentially, a nano-scale hole. This hole may be:
• Biological: formed by a pore-forming protein in a membrane such as a lipid bilayer
• Solid-state: formed in synthetic materials such as silicon nitride or graphene
• Hybrid: formed by a pore-forming protein set in synthetic material

GridION part 1: nanopore sensing and an introduction to the GridION system from Oxford Nanopore on Vimeo.

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