Title: Development of a novel nanotechnology DNA sequencing technology to integrate into a hand-held or bench-top device.
Funder: Department of Health (England)

Abstract: Research Plan An IP landscape review has been conducted by two independent search reports Knobbe Martens Olsen & Bear LLP, IP attorneys, USA and Spoor Fisher, South Africa and found no prior teachings for QuantuMDx's sequencing technologies, as excerpts from the reports show below; 1. Following a patentability search relating to QuantuMDx's methods and devices for DNA sequencing, performed on October 30th, 2008, Knobbe Martens Olsen & Bear LLP stated: “It is our initial impression, based solely on a review of the above-summarized third party references, that none of the references teach QuantuMDx's method of sequencing by synthesis in which a change in charge mass is detected using a nanowire, and none of the references teach a handheld device configured to carry out QuantuMDx's method.” 2. Following a patentability search relating to QuantuMDx's patents, US 2009/055892, US 2009/055843, US 2009/055898, performed on February 5th, 2009, Spoor Fisher stated: “Based on our understanding of the QuantuMDx Q-POC technology describes above, it appears that none of the identified prior art references anticipates each of the aspects of the Q-POC technology” The full search reports are presented in Annex 5, section 6.0. As QuantuMDx's technology is positioned in a `virginal' field, there is immense scope to develop and exploit IP. Aims The project's aimDevelop an optics-free, cost effective DNA sequencing device, capable of providing high quality clinical DNA sequence data at a price point that enables routine molecular & genetic testing. To be deployed as a benchtop pathology DNA sequencer & a handheld device for rapid POC testing. Research question: can a cost effective sequencing device be developed to address the requirements of a modern clinical genetics & molecular diagnostics service? Methodology SummaryThis project is a highly collaborative & integrative project & as such the project plan has been carefully designed to take a holistic approach to the development of the final device. The development has been split into 5 work packages (WP), with each WP constitutively collaborating via an online project management package & at regular meetings. The device design (WP1) & iteration will be run in parallel with both the chemistry (WP2) & molecular biology development (WP3). Furthermore, instrument development electronics (WP4) will be developed once the output signal specifications have been defined. Constant WP collaboration will be driven throughout the project & guided at all times by end user & patient input (WP5) to deliver a low cost sequencing device. Work Packages -Annex 2 & 3 for further detailsWP1.0 Devices Inventive step - Novel nanowire FET biosensors (See Annex 5, section 4 for pilot study data)The work package will develop a cost effective, scalable method for the fabrication of nanowire FET devices using a combination of standard lithography techniques to form an array of nanowires on the device layer of a silicon on insulator (SOI) wafer.Detailed optimisation and characterisation of the basic device structure will be carried out in order to understand the relationship between structure and function. Specific device designs, to meet the requirements of multiple sequencing approaches, will be determined and first version devices will be fabricated.Mi1.1: Successful wet test & characterisation of nanowire FETDO1: (M9) First iteration of LRL and SHG devicesPrototype nanowire devices for long read out length (LRL) sequencing will encompass a train track of nanowires, fabricated within a shallow microfluidic channel to promote extension of the DNA. Devices for shot gun sequencing (SHG) will require clusters of nanowires within a defined well. The technical challenges are expected to be the empirical optimisation of the nanowire layout, formation of appropriate flow cells for sample handling, formation of an integrated well structure on the SHG device and definition of electrical connections to reduce the device footprint.Mi1.2: Successful wet testing & characterisation of both prototypes DO4: (M18) Prototype LRL and SHG sequencing devicesThroughout integration with surface chemistry, molecular biology and electronics will take place.Finally, the device technology will be validated in a fully integrated system encompassing clinically relevant protocols for detection.Mi1.3 Successful wet test & characterisation of integrated prototypeD06 (M24) Fully integrated LRL and SHG devicesTechnical risk: Biosensor sensitivity. The nanowire FET biosensors are sensitive to fluctuations of the charge mass at the surface of the nanowire, caused by micro concentrations in the buffer, some vibrations & light. The use of high charged moieties on the nucleotides, novel electronic signal processing and shielding strategies will mitigate these risks. Furthermore, the project will be investigating a range of different surface chemistries to improve the sensitivity and specificity of the biosensor. WP2.0 Chemistry Inventive step - novel synthetic nucleotides & sensor surface chemistryThis work package will develop the surface fuctionalisation of the biosensor & the synthesis of supercharged nucleotides.The project will develop novel nucleotides to which have a high charge/mass reporter moiety attached via a cleavable linker. These nucleotides will be used wherein DNA, or more specifically, the nucleotides are detected during the sequencing reaction (WP3.0) using biosensors produced in WP1.0, with the signal amplified by the charged moiety.Mi2.1 Synthesis of supercharged analogues of dTTP, with a range of linker lengths & moiety charge sizesThe charged moieties will be attached to the 3'-position, or to the base group of a nucleotide, via a linker that can be removed under the same conditions as a 3'-blocking group. DO2 (M9) Synthesis of super charged analogues of T, C, G and A nucleotidesThe surface chemistry will be developed to maximise the effect of the supercharged nucleotides on the nanowire, optimising the sensitivity of the wire to the different charged groups. The reproducibility of this surface layer will be investigated along with the resulting stability and lifetime of the biosensors.DO3 (M12) A thin Benefit As identified previously, existing diagnostic technologies for complex testing are expensive, time consuming, not truly portable and can result in delays to treatment or inappropriate and ineffective treatment. Offering complex diagnostics on a handheld device offers a plethora of patient healthcare benefits as follows. The patient benefit offered by QuantuMDx's technology is that in one consultation the patient can have their underlying condition diagnosed or their pre-disposition to a particular disease identified or advised of their prognosis, be prescribed the correct treatment, be fully informed about their condition, can receive the appropriate education and advice and have the opportunity to question their diagnosis and treatment to improve their understanding. This will not only reduce patient anxiety from having to wait days for test results but also ensure the patient has the best chance of optimal recovery. As the device will include connectivity, further patient benefits are obtained when a patient's results are immediately uploaded into the hospital's central medical records and therefore available immediately within the patient's electronic medical record. Results can be shared instantaneously with all members of the multi-disciplinary team including other health professionals such as the patient's GP. This facility offers the ability to deliver a seamless care pathway as well as enables rapid access to past medical history, vital in directing appropriate interventions and therapies during future medical episodes. It is well documented that a reduction in morbidity and mortality has been associated with goal-directed therapy techniques when used in conjunction with point of care results. Potential operational benefits of the point of care device which impact on patient care and therefore patient healthcare benefits include more rapid decision making and triage, reducing operating times, reducing high-dependency, postoperative care time, reducing A&E room time, reducing the number of outpatient clinic visits, reducing the number of hospital beds required, and ensuring optimal use of professional time. Lastly, to demonstrate the technology's potential in saving patient lives and the financial and economic cost benefit of saving lives the following is an example using a potential swine flu pandemic: According to the `Market Oracle', a swine flu pandemic similar to the `Spanish Flu' pandemic that killed 50 million people in 1918, may cause global economic losses of as much as $2 trillion, as estimated by the World Bank. Worst case scenarios suggest as many as 145 million people could die globally with the cost to the world economy as high as $5 trillions. Even a mild out break could kill some 2 million with an economic cost to the world of $400 billions.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: GENERIC HEALTH RELEVANCE;CANCER AND NEOPLASMS