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Denmark-Copenhagen: Miscellaneous evaluation or testing instruments
Voluntary ex ante transparency notice
Section I: Contracting authority/entity
Main address: www.KU.dk
Section II: Object
Acquisition of a GridION Mk1
University of Copenhagen Department of Food Science and Fermentation is in need of third generation nucleic acids sequencing platform allowing sequencing of DNA and RNA without PCR or reverse-transcription steps during library preparation.
University of Copenhagen Department of Food Science and Fermentation is in need of third generation nucleic acids sequencing platform allowing sequencing of DNA and RNA without PCR or reverse-transcription steps during library preparation. The platform is essential to generate ultra-long reads necessary for recovering whole genomes and transcriptomes of bacteria, yeast and viruses. Generated data will at the same time allow to study DNA modifications. Oxford Nanopore Technologies (ONT) is currently the sole producer of nanopore based nucleic acids sequencing platforms.
Section IV: Procedure
Oxford Nanopore’s sequencing platform is the only technology that offers real-time analysis (for rapid insights), in fully scalable formats from pocket to population scale, that can analyze native DNA or RNA and sequence any length of fragment to achieve short to ultra-long read lengths.
Oxford Nanopore has a broad patent portfolio, through in-house development and licensing agreements with third parties. Oxford Nanopore has an intellectual property portfolio of more than 650 issued patents and patent applications, in over 200 patent families. These cover all aspects of nanopore sensing including fundamental patents for nanopore sensing, and patents relating to DNA-sequencing.
List of patents:
The following themes are included in Oxford Nanopore's patent portfolio:
• DNA base identification using a biological nanopore;
• addition of adapters to nanopores for sensing;
• modified nanopores for sensing;
• use of molecular motors in combination with nanopores;
• localising polymerases to a surface, including pore-bound localisation;
• use of solid-state nanopores for detecting labelled ssDNA and dsDNA;
• use of solid-state devices to control movement of polymers;
• detection and positional measurement of probes on a DNA strand as the strand passes through a nanoscale detector;
• methods of fabricating solid-state nanopores including multi-layered devices;
• the use of functionalised solid-state nanopores for molecular characterisation, including graphene, tunnelling currents and nanotubes;
• time-based multiplexed nanopore measurements on a single chip, including the incorporation of 96 well plate;
• use of voltage to control DNA under feedback;
• measurement of DNA interacting with a limited volume, such as a polymerase on a surface;
• array chip for parallel sensing from multiple channels;
• sequencing by means of detection of products of enzymatic action on DNA/RNA using a nanopore;
• the use of multiple 'nodes' to analyse samples in a federated/clustered manner to reduce the time to result, and improve operating efficiencies;
• methods and algorithms for nanopore signal analysis;
• nanopore arrays/nanopore array structures;
• direct RNA sequencing;
• protein characterisation using nanopores;
• chip/array architecture;
• methods of sensitivity enhancement.
For our research it is critical to use PCR free, long-read nucleic acids sequencing technology. ONT is for the time being the sole provider of nanopore technology allowing ultra-long reads sequencing and is about 7 times cheaper regarding equipment cost compare to alternative solutions. It is at the same time one of the cheapest solution in terms of data generation on the market.
Section V: Award of contract/concession
Internet address: https://nanoporetech.com
Section VI: Complementary information
Internet address: www.KLFU.dk