Patents Assigned to Illumina Cambridge Limited
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Patent number: 12043637Abstract: The present application relates to substituted dyes containing bis-boron fused heterocycles and their uses as fluorescent labels. These compounds may be used as fluorescent labels for nucleotides in nucleic acid sequencing applications.Type: GrantFiled: May 4, 2022Date of Patent: July 23, 2024Assignee: Illumina Cambridge LimitedInventors: Michael Callingham, Nikolai Nikolaevich Romanov, Xiaohai Liu, Justyna Piekos
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Publication number: 20240240243Abstract: 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: ApplicationFiled: January 22, 2024Publication date: July 18, 2024Applicants: Illumina, Inc., Illumina Cambridge LimitedInventors: Jeffrey Fisher, Jason Betley
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Patent number: 12031178Abstract: Embodiments of the present disclosure relate to cyclooctatetraene containing dyes and their uses as fluorescent labels. Also provided are composition containing cyclooctatetraene. The dyes and compositions may be used in various biological applications, such as nucleic acid sequencing.Type: GrantFiled: February 14, 2023Date of Patent: July 9, 2024Assignee: Illumina Cambridge LimitedInventors: Xiaolin Wu, Xiaohai Liu, Nikolai Nikolaevich Romanov, Antoine Francais, Patrick McCauley, Michael Callingham, Carole Anastasi
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Patent number: 12018103Abstract: An example of a flow cell includes a substrate and a pattern of two different silanes on at least a portion of a surface of the substrate. A first polymer is attached to a first of the two different silanes and a second polymer is attached to a second of the two different silanes. The first and second polymers respectively include a first functional group and a second functional group of a functional group pair, the functional group pair being selected from the group consisting of an activated ester functional group and an azide functional group, a tetrazine functional group and an activated ester functional group, and a tetrazine functional group and an azide functional group. A first primer set is grafted to the first polymer and a second primer set is grafted to the second polymer. The first and second primer sets are different.Type: GrantFiled: April 26, 2022Date of Patent: June 25, 2024Assignee: Illumina Cambridge LimitedInventors: Wayne N. George, Andrew A. Brown
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Patent number: 12013330Abstract: An example of a resin composition includes an epoxy resin matrix, a free radical photoinitiator selected from the group consisting of 2-ethyl-9,10-dimethoxyanthracene, 2,2-dimethoxy-2-phenylacetophenone, 2-ethoxy-2-phenylacetophenone, and a phosphine oxide, and a photoacid generator. 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: June 18, 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: 11999696Abstract: Described herein are heterocyclic azide-containing monomer units, copolymers comprising such heterocyclic azide-containing monomer units, substrate-bound copolymers, and oligonucleotide-bound copolymers, methods for making such copolymers and reacting them with a substrate and/or oligonucleotide, and methods of using such copolymers for immobilization of oligonucleotides to a substrate, for example for use in DNA sequencing or other diagnostic applications.Type: GrantFiled: December 9, 2019Date of Patent: June 4, 2024Assignee: Illumina Cambridge LimitedInventors: Wayne N. George, Xiaolin Wu, Andrew A. Brown, Donald Wellings
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Patent number: 11988957Abstract: An example of a flow cell includes a substrate; a first primer set attached to a first region on the substrate, the first primer set including an un-cleavable first primer and a cleavable second primer; and a second primer set attached to a second region on the substrate, the second primer set including a cleavable first primer and an un-cleavable second primer.Type: GrantFiled: May 15, 2023Date of Patent: May 21, 2024Assignees: Illumina, Inc., Illumina Cambridge LimitedInventors: Jeffrey S. Fisher, Brian D. Mather, Maria Candelaria Rogert Bacigalupo, Justin Fullerton, Ludovic Vincent, Lewis J. Kraft, Sahngki Hong, Boyan Boyanov, M. Shane Bowen, Sang Park, Wayne N. George, Andrew A. Brown
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Patent number: 11981955Abstract: The present disclosure relates to new compounds and their use as fluorescent labels. The compounds may be used as fluorescent labels for nucleotides in nucleic acid sequencing applications.Type: GrantFiled: December 6, 2022Date of Patent: May 14, 2024Assignee: Illumina Cambridge LimitedInventors: Antoine Francais, Xiaohai Liu
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Patent number: 11981964Abstract: The present application relates to 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 26, 2021Date of Patent: May 14, 2024Assignee: Illumina Cambridge LimitedInventors: Nikolai Nikolaevich Romanov, Michael Callingham, Carole Anastasi, Patrick Mccauley, Niall Hynes, Natasha Crake, Xiaolin Wu, Xiaohai Liu
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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: 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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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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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