Patents Assigned to Illumina Cambridge Limited
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Publication number: 20220090187Abstract: 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: August 27, 2021Publication date: March 24, 2022Applicants: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITEDInventors: Jeffrey Fisher, Jason Betley
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Patent number: 11279975Abstract: Provided herein is a method for sequencing a polynucleotide molecules. The method includes the steps of providing a plurality of polynucleotide molecules attached to a surface, wherein a first portion of each polynucleotide molecule is attached to a first location of the surface and a second portion of each polynucleotide molecule is attached to a second location of the surface, the relative proximity of the first and second locations being correlated with the probability that the first and second portions are paired, separating the first and second portions of the polynucleotide molecules on the surface, determining the sequences of the first and second portions of the polynucleotide molecules and comparing the relative proximities and the sequences to determine which first and second portions are paired and to determine the sequence of the target polynucleotide molecules.Type: GrantFiled: June 10, 2019Date of Patent: March 22, 2022Assignee: Illumina Cambridge LimitedInventors: Roberto Rigatti, Niall Anthony Gormley, Jonathan Mark Boutell
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Patent number: 11257568Abstract: The present disclosure provides methods and systems for determining and/or characterizing one or more haplotypes and/or phasing of haplotypes in a nucleic acid sample. In particular, the disclosure provides methods for determining a haplotype and/or phasing of haplotypes in a nucleic acid sample by incorporating synthetic polymorphisms into fragments of a nucleic acid sample and utilizing the synthetic polymorphisms in determining one or more haplotypes and/or phasing of haplotypes.Type: GrantFiled: May 11, 2018Date of Patent: February 22, 2022Assignee: Illumina Cambridge LimitedInventors: Roberto Rigatti, Jonathan Mark Boutell
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Publication number: 20220040690Abstract: 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: ApplicationFiled: October 21, 2021Publication date: February 10, 2022Applicants: 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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Publication number: 20220025342Abstract: The invention relates to modified polymerase enzymes which exhibit improved incorporation of nucleotide analogues bearing substituents at the 3? position of the sugar moiety that are larger in size than the naturally occurring 3? hydroxyl group. Also described are methods of using the polymerases to incorporate nucleotides into polynucleotides, particularly in the context of DNA sequencing.Type: ApplicationFiled: August 24, 2021Publication date: January 27, 2022Applicant: Illumina Cambridge LimitedInventors: Geoffrey Paul Smith, David Mark Dunstan Bailey, Raquel Maria Sanches-Kuiper, Harold Swerdlow, David James Earnshaw
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Patent number: 11230734Abstract: Some embodiments of the present application relate to novel modified nucleotide linkers for increasing the efficiency of nucleotide incorporation in Sequencing by Synthesis applications. Methods of preparing these modified nucleotide linkers are also provided herewith.Type: GrantFiled: January 25, 2019Date of Patent: January 25, 2022Assignee: Illumina Cambridge LimitedInventors: Xiaolin Wu, Xiaohai Liu
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Patent number: 11226475Abstract: The disclosure provides for structured illumination microscopy (SIM) imaging systems. In one set of implementations, a SIM imaging system may be implemented as a multi-arm SIM imaging system, whereby each arm of the system includes a light emitter and a beam splitter (e.g., a transmissive diffraction grating) having a specific, fixed orientation with respect to the system's optical axis. In a second set of implementations, a SIM imaging system may be implemented as a multiple beam splitter slide SIM imaging system, where one linear motion stage is mounted with multiple beam splitters having a corresponding, fixed orientation with respect to the system's optical axis. In a third set of implementations, a SIM imaging system may be implemented as a pattern angle spatial selection SIM imaging system, whereby a fixed two-dimensional diffraction grating is used in combination with a spatial filter wheel to project one-dimensional fringe patterns on a sample.Type: GrantFiled: January 14, 2019Date of Patent: January 18, 2022Assignees: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITEDInventors: Peter Clarke Newman, Danilo Condello, Shaoping Lu, Simon Prince, Merek C. Siu, Stanley S. Hong, Aaron Liu, Gary Mark Skinner, Geraint Wyn Evans
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Publication number: 20220010290Abstract: The invention relates to modified polymerase enzymes which exhibit improved incorporation of nucleotide analogues bearing substituents at the 3? position of the sugar moiety that are larger in size than the naturally occurring 3?hydroxyl group. Also described are methods of using the polymerases to incorporate nucleotides into polynucleotides, particularly in the context of DNA sequencing.Type: ApplicationFiled: September 24, 2021Publication date: January 13, 2022Applicant: Illumina Cambridge LimitedInventors: Geoffrey Paul Smith, David Mark Dunstan Bailey, Raquel Maria Sanches-Kuiper, Harold Swerdlow, David James Earnshaw
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Publication number: 20220002711Abstract: Provided is a method, including stretching a polynucleotide over a substrate including a plurality of equally spaced cleavage regions including a plurality of transposases, cleaving the polynucleotide with two or more of the plurality of transposases to form a plurality of polynucleotide fragments, and separating, within the plurality of polynucleotide fragments, a population of longer polynucleotide fragments from a population of shorter polynucleotide fragments. Also provided is a method including stretching a polynucleotide over a substrate including a plurality of equally spaced cleavage regions including a plurality of transposases, cleaving the polynucleotide with two or more of the plurality of transposases to form a plurality of polynucleotide fragments, and separating, within the plurality of polynucleotide fragments, a population of longer polynucleotide fragments from a population of shorter polynucleotide fragments.Type: ApplicationFiled: June 25, 2021Publication date: January 6, 2022Applicants: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITEDInventors: Maria Candelaria Rogert BACIGALUPO, Frank STEEMERS, Jeffrey FISHER, Andrew SLATTER, Lewis KRAFT, Niall GORMLEY, M. Shane BOWEN
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Patent number: 11213976Abstract: An imprinting apparatus includes a silicon master having a plurality of nanofeatures defined therein. An anti-stick layer coats the silicon master, the anti-stick layer including a molecule having a cyclosiloxane with at least one silane functional group. A method includes forming a master template by: depositing a formulation on a silicon master including a plurality of nanofeatures defined therein, the formulation including a solvent and a molecule having a cyclosiloxane with at least one silane functional group; and curing the formulation, thereby forming an anti-stick layer on the silicon master, the anti-stick layer including the molecule. The method further includes depositing a silicon-based working stamp material on the anti-stick layer of the master template; curing the silicon-based working stamp material to form a working stamp including a negative replica of the plurality of nanofeatures; and releasing the working stamp from the master template.Type: GrantFiled: December 19, 2017Date of Patent: January 4, 2022Assignees: Illumina, Inc., Illumina Cambridge LimitedInventors: Alexandre Richez, Andrew A. Brown, Julia Morrison, Wayne N. George, Timothy J. Merkel, Audrey Rose Zak
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Patent number: 11199540Abstract: Some examples described herein relate to a substrate comprising a silane functionalized surface for reversibly immobilizing a biological molecule of interest, such as oligonucleotides, polynucleotides, or protein. Methods for immobilizing the biological molecule and the use in DNA sequencing and other diagnostic applications are also disclosed.Type: GrantFiled: June 3, 2020Date of Patent: December 14, 2021Assignee: Illumina Cambridge LimitedInventors: Xavier von Hatten, Wayne N. George, Alexandre Richez, Anne-Cecile Dingwall, Andrew A. Brown
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Publication number: 20210380972Abstract: The present disclosure is concerned with compositions, methods, and kits for preparing a sequencing library. In one embodiment, methods include producing a library of target nucleic acids having the same adapter at each end and then switching the identity of one adapter to result in target nucleic acids flanked by distinct adapters.Type: ApplicationFiled: June 10, 2021Publication date: December 9, 2021Applicants: Illumina, Inc., Illumina Cambridge Limited, Oregon Health & Science UniversityInventors: Andrew C. Adey, Ryan Mulqueen, Frank Steemers, Dmitry K Pokholok, Fan Zhang, Esther Musgrave-Brown
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Patent number: 11179724Abstract: 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: September 11, 2018Date of Patent: November 23, 2021Assignees: 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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Publication number: 20210348141Abstract: Presented herein are altered polymerase enzymes for improved incorporation of nucleotides and nucleotide analogues, in particular altered polymerases that maintain high fidelity under reduced incorporation times, as well as methods and kits using the same.Type: ApplicationFiled: April 9, 2021Publication date: November 11, 2021Applicants: Illumina, Inc., Illumina Cambridge Limited, Illumina Singapore Pte. Ltd.Inventors: Kay Klausing, Hamed Tabatabaei Ghomi, Misha Golynskiy, Saurabh Nirantar, Seth McDonald, Sergio Peisajovich
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Patent number: 11150455Abstract: 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 22, 2019Date of Patent: October 19, 2021Assignees: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITEDInventors: Gary Mark Skinner, Geraint Wyn Evans, Stanley S. Hong
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Patent number: 11142789Abstract: The present invention relates to a method for preparing a library of template polynucleotides and use thereof in methods of solid-phase nucleic acid amplification. More specifically, the invention relates to a method for preparing a library of template polynucleotides that have common sequences at their 5? ends and at their 3? ends.Type: GrantFiled: April 2, 2019Date of Patent: October 12, 2021Assignee: Illumina Cambridge LimitedInventors: Niall Anthony Gormley, Geoffrey Paul Smith, David Bentley, Roberto Rigatti, Shujun Luo
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Patent number: 11136564Abstract: The invention relates to modified polymerase enzymes which exhibit improved incorporation of nucleotide analogues bearing substituents at the 3? position of the sugar moiety that are larger in size than the naturally occurring 3? hydroxyl group. Also described are methods of using the polymerases to incorporate nucleotides into polynucleotides, particularly in the context of DNA sequencing.Type: GrantFiled: June 26, 2018Date of Patent: October 5, 2021Assignee: Illumina Cambridge LimitedInventors: Geoffrey Paul Smith, David Mark Dunstan Bailey, Raquel Maria Sanches-Kuiper, Harold Swerdlow, David James Earnshaw
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Patent number: 11124829Abstract: 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: June 7, 2019Date of Patent: September 21, 2021Assignees: 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, Dajun Yuan
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Patent number: 11112591Abstract: 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 22, 2019Date of Patent: September 7, 2021Assignees: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITEDInventors: Gary Mark Skinner, Geraint Wyn Evans, Stanley S. Hong
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Patent number: 11111533Abstract: A method of sequencing a plurality of polynucleotides includes: attaching a single DNA template molecule to each of a plurality of attachment elements on a sample container, wherein the average distance between adjacent elements is less than Abbe's limit; applying a stochastic photo-switching chemistry to all of the molecules at the same time to cause the attached molecules to fluoresce in on and off events in up to four different colors by stochastic photo-switching; and imaging the on and off events in a color channel for each color in real-time as the on and off events are occurring for the attached molecules.Type: GrantFiled: March 6, 2019Date of Patent: September 7, 2021Assignees: ILLUMINA CAMBRIDGE LIMITED, ILLUMINA, INC.Inventors: Gary Mark Skinner, Geraint Wyn Evans, Stanley S. Hong