Patents Assigned to Illumina Cambridge Limited
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Publication number: 20240150508Abstract: In some examples, novel photochemically-reversible hydrogels and nanogel particles are described comprising copolymer chains including at least one reactive alkene or reactive 1,4-diene end group capable of [2+2] or [2+2+2+2] photodimerization, respectively, at wavelengths >270 nm. In various examples, the photochemically-reversible hydrogels comprise copolymer chains including at least one —N3, —C?CH or —CO2H end group for dual functionality and/or pH responsiveness. For nucleic acid sequencing, amplification primers are grafted to photochemically-reversible hydrogels or nanogel particles reversibly bound to surfaces within a flow cell. After sequencing is complete, the photochemically-reversible hydrogel or nanogel particles is/are removable from the flow cell surfaces by irradiation, enabling the flow cell to be reusable.Type: ApplicationFiled: October 6, 2023Publication date: May 9, 2024Applicants: Illumina, Inc., Illumina Cambridge Limited, Illumina Singapore Pte. Ltd.Inventors: Nam Nguyen, Xavier von Hatten, Wayne George, Gianluca Artioli, Brian Mather, Johan Basuki, Shima Gholizadeh
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Patent number: 11975478Abstract: An example of a flow cell includes a substrate and a cured, patterned resin on the substrate. The cured, patterned resin has nano-depressions separated by interstitial regions. Each nano-depression has a largest opening dimension ranging from about 10 nm to about 1000 nm. The cured, patterned resin also includes an interpenetrating polymer network. The interpenetrating polymer network of the cured, patterned resin includes an epoxy-based polymer and a (meth)acryloyl-based polymer.Type: GrantFiled: April 20, 2021Date of Patent: May 7, 2024Assignee: Illumina Cambridge LimitedInventor: Alexandre Richez
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Patent number: 11975328Abstract: The assembly includes a docking console and a manifold. The docking console includes a cartridge support surface having a first end and a second end. The manifold has one or more wells defined therein. The docking console further includes a manifold retention bracket to releasably hold the manifold against a fluid cartridge supported on the cartridge support surface at an interface position such that the one or more wells are in fluid communication with the fluid cartridge and a biased seal bar to press the fluid cartridge against the manifold held by the manifold retention bracket. A hydrophilic porous frit disposed within at least one of the wells and is to permit liquid to flow through the outlet aperture but prevent gas from passing through the outlet aperture.Type: GrantFiled: October 21, 2021Date of Patent: May 7, 2024Assignees: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITEDInventors: Bradley Kent Drews, Gudrun Stengel, James Christopher Blake, Mohammed Kafeel Ahamed, Michael Steven Becker, Michael Dangelo, Mark J. Nibbe, Daniel L. Fuller, Oliver Jon Miller
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Patent number: 11970695Abstract: Presented are methods and compositions for using immobilized transposase and a transposon end for generating an immobilized library of 5?-tagged double-stranded target DNA on a surface. The methods are useful for generating 5?- and 3?-tagged DNA fragments for use in a variety of processes, including massively parallel DNA sequencing.Type: GrantFiled: March 10, 2021Date of Patent: April 30, 2024Assignee: Illumina Cambridge LimitedInventors: Niall Gormley, Geoffrey Paul Smith
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Publication number: 20240124916Abstract: The present disclosure relates to a nanoparticle including a first layer including a first polymer and a first plurality of accessory oligonucleotides, a second layer including a second polymer and a single template site for bonding a template polynucleotide, and a third layer including a third polymer and a second plurality of accessory oligonucleotides. Also described herein is a method of making said nanoparticle, including “dip-coating,” e.g., successively dipping a surface with wettable nanodomains in different polymer solutions. Further described herein is a method of making the nanoparticles by forming them in nanowells and subsequently releasing them from the nanowells. Also described herein is a method of attaching the nanoparticle to a substrate and amplifying the template polynucleotide using a polymerase.Type: ApplicationFiled: September 15, 2023Publication date: April 18, 2024Applicant: ILLUMINA CAMBRIDGE LIMITEDInventors: Alexandra SZEMJONOV, Angelo LA ROSA, Gianluca ARTIOLI, Xavier VON HATTEN, Alexandre RICHEZ
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Patent number: 11959138Abstract: Embodiments of the present disclosure relate to nucleotides labeled with photoswitchable compounds. Also provided herein are methods and kits of using these labeled nucleotides for sequencing applications.Type: GrantFiled: July 18, 2022Date of Patent: April 16, 2024Assignee: Illumina Cambridge LimitedInventors: Wayne N. George, Andrew A. Brown
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Publication number: 20240117426Abstract: In some examples, novel nanogel particles are described having dual functionality, temperature responsiveness and pH responsiveness. For nucleic acid sequencing, amplification primers are grafted to nanogel particles to form primer-grafted nanogel particles, and the primer-grafted nanogel particles are captured onto surfaces within a flow cell. Within flow cells such as used in SBS nucleic acid sequencing, each primer-grafted nanogel particle functions as a nano-well in the flow cell, thus eliminating the need for nano-wells in some examples.Type: ApplicationFiled: September 18, 2023Publication date: April 11, 2024Applicants: Illumina, Inc., Illumina Cambridge LimitedInventors: Nam Nguyen, Xavier von Hatten, Will Tovey, Andrew Brown, Wayne George, Eric Brustad, Gianluca Artioli
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Publication number: 20240117409Abstract: Provided herein is a method of using transposition to improve methods of sequencing RNA molecules. Provided herein is a method of tagging nucleic acid duplexes, such as DNA:RNA duplexes or DNA:DNA duplexes. The method includes the steps of providing a transposase and a transposon composition, providing one or more nucleic acid duplexes immobilized on a support, and contacting the transposase and transposon composition with the one or more nucleic acid duplexes under conditions wherein the one or more nucleic acid duplexes and transposon composition undergo a transposition reaction to produce one or more tagged nucleic acid duplexes, wherein the transposon composition comprises a double stranded nucleic acid molecule comprising a transferred strand and a non-transferred strand.Type: ApplicationFiled: October 23, 2023Publication date: April 11, 2024Applicant: Illumina Cambridge LimitedInventors: Niall Anthony Gormley, Louise Fraser, Paula Kokko-Gonzales
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Patent number: 11946096Abstract: The present invention relates to methods of imaging template hybridisation for estimating cluster numbers prior to solid phase amplification and sequencing. More particularly, an initial round of imaging is carried out at the single molecule template hybridisation stage which allows a general estimation of cluster numbers prior to clusters being formed. Amplification of the signal allows single molecule imaging to be carried out using standard sequencing imaging apparatus.Type: GrantFiled: June 14, 2021Date of Patent: April 2, 2024Assignee: ILLUMINA CAMBRIDGE LIMITEDInventors: Isabelle Marie Julia Rasolonjatovo, Jonathan Mark Boutell, Vincent Peter Smith, Roberto Rigatti
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Patent number: 11938475Abstract: In an example of the method, a functionalized coating layer is applied in depressions of a patterned flow cell substrate. The depressions are separated by interstitial regions. A primer is grafted to the functionalized coating layer to form a grafted functionalized coating layer in the depressions. A hydrogel is applied on at least the grafted functionalized coating layer.Type: GrantFiled: December 7, 2020Date of Patent: March 26, 2024Assignees: Ilumina, Inc., Illumina Cambridge LimitedInventors: Hongji Ren, Jonathan Mark Boutell, John A. Moon, M. Shane Bowen, Alex Nemiroski, Gary Mark Skinner, Kenny Chen
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Patent number: 11932900Abstract: An example of an array includes a support, a cross-linked epoxy polyhedral oligomeric silsesquioxane (POSS) resin film on a surface of the support, and a patterned hydrophobic polymer layer on the cross-linked epoxy POSS resin film. The patterned hydrophobic polymer layer defines exposed discrete areas of the cross-linked epoxy POSS resin film, and a polymer coating is attached to the exposed discrete areas. Another example of an array includes a support, a modified epoxy POSS resin film on a surface of the support, and a patterned hydrophobic polymer layer on the modified epoxy POSS resin film. The modified epoxy POSS resin film includes a polymer growth initiation site, and the patterned hydrophobic polymer layer defines exposed discrete areas of the modified epoxy POSS resin film. A polymer brush is attached to the polymer growth initiation site in the exposed discrete areas.Type: GrantFiled: October 25, 2022Date of Patent: March 19, 2024Assignees: Illumina, Inc., Illumina Cambridge LimitedInventors: Wayne N. George, Alexandre Richez, M. Shane Bowen, Andrew A. Brown, Dajun Yuan, Audrey Rose Zak, Sean M. Ramirez, Raymond Campos
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Patent number: 11933728Abstract: Techniques are described for reducing the number of angles needed in structured illumination imaging of biological samples through the use of patterned flowcells, where nanowells of the patterned flowcells are arranged in, e.g., a square array, or an asymmetrical array. Accordingly, the number of images needed to resolve details of the biological samples is reduced. Techniques are also described for combining structured illumination imaging with line scanning using the patterned flowcells.Type: GrantFiled: January 13, 2023Date of Patent: March 19, 2024Assignees: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITEDInventors: Gary Skinner, Geraint Evans, Stanley Hong
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Publication number: 20240084379Abstract: Polynucleotide sequencing methods include incubating unlabeled nucleotides with a cluster of template polynucleotide strands having the same sequence when the identity of the previously added labeled nucleotide is being detected. The detection step provides time for the addition of the unlabeled nucleotides to be incorporated into the copy strands in which the previously added labeled nucleotide did not get incorporated. Thus, at the end of the detection step, all or most of the copy strands will be in phase and ready to incorporate the appropriate labeled nucleotide in the subsequence incorporate step.Type: ApplicationFiled: August 9, 2023Publication date: March 14, 2024Applicant: ILLUMINA CAMBRIDGE LIMITEDInventors: Pietro Gatti-Lafranconi, Philip Balding
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Publication number: 20240076322Abstract: Barriers including crosslinked amphiphilic molecules, and methods of making the same, are provided herein. In some examples, a barrier between first and second fluids includes at least one layer comprising a plurality of amphiphilic molecules. Amphiphilic molecules of the plurality of amphiphilic molecules are crosslinked to one another.Type: ApplicationFiled: March 30, 2023Publication date: March 7, 2024Applicant: ILLUMINA CAMBRIDGE LIMITEDInventors: Antonio Conde-Gonzalez, Charlotte Vacogne, Istvan Kocsis, Alexandre Richez, Oliver Uttley, Miguel Angel Aleman Garcia, Yuliia Vyborna
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Patent number: 11913067Abstract: A composition for amplifying a polynucleotide is provided that includes a substrate comprising a first region and a second region. A first plurality of capture primers is coupled to the first region of the substrate. A second plurality of capture primers is coupled to the second region of the substrate. The capture primers of the second plurality of capture primers are longer than the capture primers of the first plurality of capture primers. A first plurality of orthogonal capture primers are coupled to the first region of the substrate. A second plurality of orthogonal capture primers are coupled to the second region of the substrate. The orthogonal capture primers of the second plurality of orthogonal capture primers are shorter than the orthogonal capture primers of the first plurality of orthogonal capture primers.Type: GrantFiled: August 27, 2021Date of Patent: February 27, 2024Assignees: Illumina, Inc., Illumina Cambridge LimitedInventors: Jeffrey Fisher, Jason Betley
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Patent number: 11884976Abstract: An example of a resin composition includes a free radical curable resin matrix including an acrylate and a siloxane, and a free radical photoinitiator. When cured, the resin composition has low or no autofluorescence when exposed to blue excitation wavelengths ranging from about 380 nm to about 480 nm or green excitation wavelengths ranging from about 510 nm to about 560 nm.Type: GrantFiled: July 18, 2019Date of Patent: January 30, 2024Assignees: Illumina, Inc., Illumina Cambridge LimitedInventors: Timothy J. Merkel, Wayne N. George, Andrew A. Brown, Audrey Zak, Gianluca Andrea Artioli, Julia Morrison, Nikolai Romanov, Lorenzo Berti, Graham Boud
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Patent number: 11884825Abstract: The present application relates to exocyclic amine-substituted coumarin derivatives and their uses as fluorescent labels. These compounds may be used as fluorescent labels for nucleotides in nucleic acid sequencing applications.Type: GrantFiled: July 1, 2022Date of Patent: January 30, 2024Assignee: Illumina Cambridge LimitedInventors: Nikolai Nikolaevich Romanov, Carole Anastasi, Patrick McCauley
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Publication number: 20240026348Abstract: Materials and methods for preparing nucleic acid libraries for next-generation sequencing are described herein. A variety of approaches are described relating to the use of unique molecular identifiers with transposon-based technology in the preparation of sequencing libraries. Also described herein are sequencing materials and methods for identifying and correcting amplification and sequencing errors.Type: ApplicationFiled: September 28, 2023Publication date: January 25, 2024Applicants: Illumina, Inc., Illumina Cambridge LimitedInventors: Susan C. Verity, Robert Scott Kuersten, Niall Anthony Gormley, Andrew B. Kennedy, Sarah E. Shultzaberger, Andrew Slatter, Emma Bell, Sebastien Georg Gabriel Ricoult, Grace DeSantis, Fiona Kaper, Han-Yu Chuang, Oliver Jon Miller, Jason Richard Betley, Stephen M. Gross, Mats Ekstrand
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Patent number: 11873480Abstract: Embodiments provided herein relate to methods and compositions for preparing an immobilized library of barcoded DNA fragments of a target nucleic acid, identifying genomic variants, determining the contiguity information, phasing information, and methylation status of the target nucleic acid.Type: GrantFiled: October 16, 2015Date of Patent: January 16, 2024Assignee: ILLUMINA CAMBRIDGE LIMITEDInventors: Frank J. Steemers, Kevin L. Gunderson, Fan Zhang, Jason Richard Betley, Niall Anthony Gormley, Wouter Meuleman, Jacqueline Weir, Avgousta Ioannou, Gareth Jenkins, Rosamond Jackson, Natalie Morrell, Dmitry K. Pokholok, Steven J. Norberg, Molly He, Amirali Kia, Igor Goryshin, Rigo Pantoja
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Publication number: 20240011014Abstract: A method may be implemented for in-tip flow-through magnetic bead processing. A biological solution may include a plurality of magnetic beads suspended therein. The biological solution may be introduced to a tube via an opening in a tip portion of the tube. The tip portion of the tube may include a magnetizable material arranged in a flow path of the biological solution. The magnetizable material may include a ferromagnetic matrix or a wire within the tip portion. A magnetic field may be applied proximate to the tip portion of the tube using an electromagnetic coil. The electromagnetic coil may be wound around the tip portion. The biological solution may be removed from the tube, for example, via the opening in the tip portion. The plurality of magnetic beads may be captured within the magnetizable material in the tip portion using the magnetic field.Type: ApplicationFiled: June 30, 2023Publication date: January 11, 2024Applicants: Illumina, Inc., Illumina Cambridge LimitedInventors: Gianluca Artioli, Brian Mather, Dave Jones