Patents Assigned to Illumina
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Patent number: 11761035Abstract: The disclosed embodiments concern methods, apparatus, systems and computer program products for determining sequences of interest using unique molecular index sequences that are uniquely associable with individual polynucleotide fragments, including sequences with low allele frequencies and long sequence length. In some implementations, the unique molecular index sequences include variable-length nonrandom sequences. In some implementations, the unique molecular index sequences are associated with the individual polynucleotide fragments based on alignment scores indicating similarity between the unique molecular index sequences and subsequences of sequence reads obtained from the individual polynucleotide fragments. System, apparatus, and computer program products are also provided for determining a sequence of interest implementing the methods disclosed.Type: GrantFiled: October 16, 2020Date of Patent: September 19, 2023Assignee: Illumina, Inc.Inventors: Kevin Wu, Chen Zhao, Han-Yu Chuang, Alex So, Stephen Tanner, Stephen M. Gross
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Patent number: 11760994Abstract: 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: GrantFiled: June 25, 2021Date of Patent: September 19, 2023Assignees: 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: 11760772Abstract: Embodiments of the present disclosure include methods and compositions for functionalizing molecules, such as oligonucleotides, with functional groups, including polyhistidine tags useful in affinity methods. Some embodiments include methods for modifying and purifying complex mixtures of molecules by exchange of functional tags.Type: GrantFiled: May 26, 2021Date of Patent: September 19, 2023Assignee: Illumina, Inc.Inventors: Frank J. Steemers, Kevin L. Gunderson, Kerri York, Ryan Christopher Smith
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Publication number: 20230287476Abstract: Degradable polyester bead are described comprising a plurality of transposome complexes immobilized to the surface thereof, wherein each transposome complex comprises a transposase bound to a first polynucleotide and a second polynucleotide, wherein the first polynucleotide comprises a 3? portion comprising a transposon end sequence and a tag, and the second polynucleotide comprises a 5? portion that is complementary to and hybridized to the transposon end sequence, and wherein the polyester bead has a melting point of from 50° C. to 65° C. Flow cells and methods related to these polyester beads are described. Also described herein are compositions comprising a bead and at least one nanoparticle and methods of use of such compositions comprising transposome complexes immobilized to nanoparticles.Type: ApplicationFiled: January 6, 2023Publication date: September 14, 2023Applicant: Illumina, Inc.Inventors: Yir-Shyuan Wu, Tarun Kumar Khurana, Elisabet Rosàs-Canyelles, Fei Shen, Jeffrey Brodin, Lena Storms, Jeffrey S. Fisher
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Patent number: 11753685Abstract: The present invention includes methods and materials for use in the detection preeclampsia and/or determining an increased risk for preeclampsia in a pregnant female, the method including identifying in a biosample obtained from the pregnant women a plurality of circulating RNA (C-RNA) molecules.Type: GrantFiled: November 20, 2020Date of Patent: September 12, 2023Assignee: ILLUMINA, INC.Inventors: Sarah E. Shultzaberger, Fiona Kaper, Sarah Kinnings, Suzanne Rohrback, Carlo Randise-Hinchliff
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Publication number: 20230279385Abstract: A variety of different types of targeted transposome complexes are described herein that may be used to mediate sequence-specific targeted transposition of nucleic acids.Type: ApplicationFiled: February 16, 2023Publication date: September 7, 2023Applicants: Illumina, Inc., Illumina Cambridge LimitedInventors: Frank J. STEEMERS, Jonathan Mark BOUTELL, Pietro GATTI LAFRANCONI, Oliver Jon MILLER, Emma BELL, Sebastien Georg Gabriel RICOULT, Niall Anthony GORMLEY, Kim SCHNEIDER
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Patent number: 11747263Abstract: Flow cells and corresponding methods are provided. The flow cells may include a support frame with top and back sides, and at least one cavity extending from the top side. The flow cells may include at least one light detection device with an active area disposed within the at least one cavity. The flow cells may include a support material disposed within the at least one cavity between the support frame and the periphery of the at least one light detection device coupling them together. The flow cells may include a lid extending over the at least one light detection device and coupled to the support frame about the periphery of the at least one light detection device. The lid and at least a top surface of the at least one light detection device form a flow channel therebetween.Type: GrantFiled: July 11, 2022Date of Patent: September 5, 2023Assignee: Illumina, Inc.Inventors: Arnaud Rival, Ali Agah, Tracy H. Fung, Dietrich Dehlinger, Poorya Sabounchi, Tarun Khurana, Craig M. Ciesla, M. Shane Bowen
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Patent number: 11749380Abstract: The technology disclosed relates to artificial intelligence-based base calling. The technology disclosed relates to accessing a progression of per-cycle analyte channel sets generated for sequencing cycles of a sequencing run, processing, through a neural network-based base caller (NNBC), windows of per-cycle analyte channel sets in the progression for the windows of sequencing cycles of the sequencing run such that the NNBC processes a subject window of per-cycle analyte channel sets in the progression for the subject window of sequencing cycles of the sequencing run and generates provisional base call predictions for three or more sequencing cycles in the subject window of sequencing cycles, from multiple windows in which a particular sequencing cycle appeared at different positions, using the NNBC to generate provisional base call predictions for the particular sequencing cycle, and determining a base call for the particular sequencing cycle based on the plurality of base call predictions.Type: GrantFiled: February 19, 2021Date of Patent: September 5, 2023Assignee: Illumina, Inc.Inventors: Anindita Dutta, Gery Vessere, Dorna Kashefhaghighi, Kishore Jaganathan, Amirali Kia
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Patent number: 11740255Abstract: A system includes a droplet actuator having a droplet-operation gap between top and bottom substrates, a reservoir(s) external to and coupled to the droplet actuator, the reservoir(s) sized for a large-volume fluid, and pressure source(s) external to the droplet actuator and coupled to the at least one reservoir. Operation of the system includes filling the reservoir(s) with a large volume of fluid(s), dispensing droplet(s) of the fluid(s) to the droplet-operation gap using the pressure source(s) as part of performing a droplet operation(s). Movement of the droplet(s) may be effectuated by activating the droplet actuator.Type: GrantFiled: November 9, 2018Date of Patent: August 29, 2023Assignee: ILLUMINA, INC.Inventors: Jennifer Olivia Foley, Darren Segale, Cyril Delattre
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Patent number: 11739372Abstract: A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.Type: GrantFiled: February 9, 2023Date of Patent: August 29, 2023Assignees: Spatial Transcriptomics AB, Illumina, Inc.Inventors: Jonas Frisen, Patrik Stahl, Joakim Lundeberg, Gordon M. Cann, Leila Bazargan, Alex Aravanis
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Patent number: 11732301Abstract: The disclosure provides detection apparatus having one or more nanopores, methods for making apparatus having one or more nanopore and methods for using apparatus having one or more nanopores. Uses include, but are not limited to detection and sequencing of nucleic acids.Type: GrantFiled: March 1, 2021Date of Patent: August 22, 2023Assignee: Illumina, Inc.Inventors: Boyan Boyanov, Jeffrey G Mandell, Kevin L Gunderson, Jingwei Bai, Liangliang Qiang, Bradley Baas
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Patent number: 11733147Abstract: In an example, a flow cell includes a substrate, a selectively removable porous molecular network on the substrate and defining exposed substrate regions, and sequencing surface chemistry on at least some of the exposed regions. The sequencing surface chemistry is selected from the group consisting of i) an activated pad, a polymer layer attached to the activated pad, and a primer attached to the polymer layer; or ii) a nanostructure and an enzyme attached to the nanostructure.Type: GrantFiled: July 25, 2019Date of Patent: August 22, 2023Assignee: Illumina Cambridge LimitedInventor: Xavier von Hatten
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Publication number: 20230260096Abstract: Artificial intelligence driven enhancement of motion blurred sequencing images enables enhanced sequencing that determines a sequence of bases in genetic material with any one or more of: improved performance, improved accuracy, and/or reduced cost. A training set of images taken after unreduced and reduced movement settling times during sequencing is used to train a neural network to enable the neural network to recover enhanced images, as if taken after the unreduced movement settling time, from unenhanced images taken after the reduced movement settling time.Type: ApplicationFiled: February 17, 2023Publication date: August 17, 2023Applicants: Illumina, Inc., Illumina Software, Inc.Inventors: Simon Prince, Stanley Hong, Michael Gallaspy, Merek Siu, Jeffrey Gau, Anindita Dutta, Aathavan Karunakaran, Yina Wang, Rishi Verma
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Patent number: 11724258Abstract: A method includes engaging a well of a cartridge with a flow sensor of an instrument. The cartridge includes: a rotary valve including a rotatable port and a center port; the well in fluid communication with a channel, the channel including a channel port that the rotatable port is to align to in order to receive fluid from the well; and a flowcell including an inlet gasket in fluid communication with the center port. A source of pressurized air is connected to the flow sensor in order to establish a mass flow of air through a flow path. The flow path extends through one of the flow sensor, the channel, the rotary valve, and the flowcell. The mass flow of air through the flow path is measured with the flow sensor. It is determined if there is one of an air leak and an air blockage within the flow path.Type: GrantFiled: May 23, 2022Date of Patent: August 15, 2023Assignee: ILLUMINA, INC.Inventors: Sz-Chin Steven Lin, Richard Lemoine, Rajagopal Panchapakesan, Wesley A. Cox-Muranami, Darren Segale
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Patent number: 11719637Abstract: Biosensor including a device base having a sensor array of light sensors and a guide array of light guides. The light guides have input regions that are configured to receive excitation light and light emissions generated by biological or chemical substances. The light guides extend into the device base toward corresponding light sensors and have a filter material. The device base includes device circuitry electrically coupled to the light sensors and configured to transmit data signals. A passivation layer extends over the device base and forms an array of reaction recesses above the light guides. The biosensor also includes peripheral crosstalk shields that at least partially surround corresponding light guides of the guide array to reduce optical crosstalk between adjacent light sensors.Type: GrantFiled: August 18, 2021Date of Patent: August 8, 2023Assignee: ILLUMINA, INC.Inventors: Cheng Frank Zhong, Hod Finkelstein, Boyan Boyanov, Dietrich Dehlinger, Darren Segale
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Publication number: 20230242982Abstract: A polynucleotide sequencing method comprises (i) removing a label and a blocking moiety from a blocked, labeled nucleotide incorporated into a copy polynucleotide strand that is complementary to at least a portion of a template polynucleotide strand; and (ii) washing the removed label and blocking moiety away from the copy strand with a wash solution comprising a first buffer comprising a scavenger compound. Removing the label and blocking moieties may comprise chemically removing the moieties. The first buffer may also comprise an antioxidant and may be used in a scanning buffer used during a nucleotide detection step.Type: ApplicationFiled: February 6, 2023Publication date: August 3, 2023Applicant: ILLUMINA CAMBRIDGE LIMITEDInventors: Pietro Gatti-Lafranconi, Helen Sansom, Matthew Hancock
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Publication number: 20230245724Abstract: Provided is a computer-implemented method, including inputting to a trained machine learning classifier genomic information of a non-training subject that includes features from a tumor sample, wherein the trained machine learning classifier trained on features of tumor samples obtained from training subjects and their a responsiveness to checkpoint inhibition treatment and the machine-learning classifier is trained to predict responsiveness to the treatment, and generating a checkpoint inhibition responsiveness classification predictive of the subject's responding to the checkpoint inhibition with the trained machine-learning classifier, and reporting the checkpoint inhibition responsiveness classification using a graphical user interface. Also provided are a computer system for performing the method and a machine learning classifier trained by the method.Type: ApplicationFiled: December 3, 2018Publication date: August 3, 2023Applicant: ILLUMINA, INC.Inventors: Shile Zhang, Mengchi Wang, Aaron Wise, Han Kang, Vitor Ferreira Onuchic, Kristina Kruglyak
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Patent number: D998709Type: GrantFiled: May 13, 2022Date of Patent: September 12, 2023Assignee: Illumina, Inc.Inventors: Christopher Morgan Dye, Gi Youn Lee, Max Warren Pollock, Vincent Russell Derama, Nahida Lebbos, Raymond Lawrence Oyung, Madeline Uebelhor, Jack Godfrey Wood, John Tate Sager, Jacob Dessau
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Patent number: D998710Type: GrantFiled: May 13, 2022Date of Patent: September 12, 2023Assignee: Illumina, Inc.Inventors: Christopher Morgan Dye, Gi Youn Lee, Max Warren Pollock, Vincent Russell Derama, Nahida Lebbos, Raymond Lawrence Oyung, Madeline Uebelhor, Jack Godfrey Wood, John Tate Sager, Jacob Dessau
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Patent number: D999425Type: GrantFiled: November 25, 2019Date of Patent: September 19, 2023Assignee: Illumina, Inc.Inventors: Jay Taylor, James Osmus, Philip Paik, Jack Godfrey Wood, Max Pollock