Patents Assigned to Illumina, Inc.
  • Patent number: 11827932
    Abstract: The present disclosure provides methods and systems for detecting multiple different nucleotides in a sample. In particular, the disclosure provides for detection of multiple different nucleotides in a sample utilizing fewer detection moieties than the number of nucleotides being detected and/or fewer imaging events than the number of nucleotides being detected.
    Type: Grant
    Filed: January 20, 2021
    Date of Patent: November 28, 2023
    Assignee: Illumina, Inc.
    Inventors: Robert C. Kain, Xiaohai Liu, Wenyi Feng, Bernard Hirschbein, Helmy A. Eltoukhy, Xiaolin Wu, Geoffrey Paul Smith, Jonathan Mark Boutell, Thomas Joseph, Randall Smith, Min-Jui Richard Shen, Carolyn Tregidgo, Kay Klausing
  • Patent number: 11828924
    Abstract: The technology disclosed relates to structured illumination microscopy (SIM). In particular, the technology disclosed relates to capturing and processing, in real time, numerous image tiles across a large image plane, dividing them into subtiles, efficiently processing the subtiles, and producing enhanced resolution images from the subtiles. The enhanced resolution images can be combined into enhanced images and can be used in subsequent analysis steps.
    Type: Grant
    Filed: November 21, 2022
    Date of Patent: November 28, 2023
    Assignee: Illumina, Inc.
    Inventors: Bo Lu, Robert Ezra Langlois, Andrew James Young, Andrew Dodge Heiberg
  • Publication number: 20230379316
    Abstract: Flexible authentication technologies customized to particular tenants of a data center network can be implemented. For example, an administrator can specify a primary authentication server and specify at which data centers different applications are to be hosted for a given tenant. End users can be shielded from the complexities of implementing such configuration details. For example, single sign-on authentication can be implemented, even when applications are configured to be hosted in different data centers. Enterprise tenants can thus control where applications are hosted and enforce data containment scenarios without encumbering users with additional tasks. Collaboration and application-to-application authentication can be achieved.
    Type: Application
    Filed: May 22, 2023
    Publication date: November 23, 2023
    Applicant: Illumina, Inc.
    Inventors: Milan Karangutkar, Prabhu Palanisamy, Satnam Alag
  • Publication number: 20230374493
    Abstract: Embodiments of the present invention relate to analyzing components of a cell. In some embodiments, the present invention relate to analyzing components of a single cell. In some embodiments, the methods and compositions relate to sequencing nucleic acids. In some embodiments, the methods and compositions relate to identifying and/or quantitiating nucleic acid, proteins, organelles, and/or cellular metabolites.
    Type: Application
    Filed: February 27, 2023
    Publication date: November 23, 2023
    Applicant: ILLUMINA, INC.
    Inventors: Kevin L. Gunderson, Frank J. Steemers, Jeffrey S. Fisher, Roberto Rigatti
  • Patent number: 11819843
    Abstract: An example of a flow cell includes a substrate, which includes nano-depressions defined in a surface of the substrate, and interstitial regions separating the nano-depressions. A hydrophobic material layer has a surface that is at least substantially co-planar with the interstitial regions and is positioned to define a hydrophobic barrier around respective sub-sets of the nano-depressions.
    Type: Grant
    Filed: April 26, 2022
    Date of Patent: November 21, 2023
    Assignee: Illumina, Inc.
    Inventors: Tarun Kumar Khurana, Arnaud Rival, Lewis J. Kraft, Steven Barnard, M. Shane Bowen, Xi-Jun Chen, Yir-Shyuan Wu, Jeffrey S. Fisher, Dajun Yuan
  • Patent number: 11821411
    Abstract: Actuation systems and methods are disclosed. An apparatus includes a system including a flow cell receptacle and a valve drive assembly including a shape memory alloy actuator including a pair of shape memory alloy wires and a flow cell disposable within the flow cell receptacle and having a membrane valve. The system actuates the membrane valve, via the shape memory alloy actuator, by causing a voltage to be applied to a first one of the shape memory alloy wires and the system not applying the voltage to a second one of the shape memory alloy wires.
    Type: Grant
    Filed: December 22, 2022
    Date of Patent: November 21, 2023
    Assignee: ILLUMINA, INC.
    Inventors: Reto Schoch, Xuance Zhou, Tarun Khurana, Chetanya Jain, Gregory Suematsu
  • Patent number: 11815458
    Abstract: A method comprises: directing, using an objective and a first reflective surface, first autofocus light toward a sensor, the first autofocus light reflected from a first surface of a substrate; preventing second autofocus light from reaching the sensor, the second autofocus light reflected from a second surface of the substrate; and directing, using the objective and a second reflective surface, emission light toward the sensor, the emission light originating from a sample at the substrate.
    Type: Grant
    Filed: December 22, 2020
    Date of Patent: November 14, 2023
    Assignee: Illumina, Inc.
    Inventors: Simon Prince, Danilo Condello, Vincent Hsieh, Krysada Phounsiri, John O'Shaughnessy
  • Patent number: 11816816
    Abstract: Techniques are described for dynamically correcting image distortion during imaging of a patterned sample having repeating spots. Different sets of image distortion correction coefficients may be calculated for different regions of a sample during a first imaging cycle of a multicycle imaging run and subsequently applied in real time to image data generated during subsequent cycles. In one implementation, image distortion correction coefficients may be calculated for an image of a patterned sample having repeated spots by: estimating an affine transform of the image; sharpening the image; and iteratively searching for an optimal set of distortion correction coefficients for the sharpened image, where iteratively searching for the optimal set of distortion correction coefficients for the sharpened image includes calculating a mean chastity for spot locations in the image, and where the estimated affine transform is applied during each iteration of the search.
    Type: Grant
    Filed: December 23, 2022
    Date of Patent: November 14, 2023
    Assignee: Illumina, Inc.
    Inventors: Robert Langlois, Paul Belitz
  • Patent number: 11814678
    Abstract: The disclosed embodiments concern index oligonucleotides configured to identify sources of samples of nucleic acids and methods, apparatus, systems and computer program products for identifying and making the index oligonucleotides. In some implementations, the index oligonucleotides include a set of index sequences, a Hamming distance between any two index sequences of the set of index sequences meeting one or more criteria. System, apparatus, and computer program products are also provided for determining a sequence of interest using the index oligonucleotides.
    Type: Grant
    Filed: May 4, 2021
    Date of Patent: November 14, 2023
    Assignee: Illumina, Inc.
    Inventors: Tatjana Singer, Ryan Kelley, Gordon Bean, Eric Vermaas
  • Patent number: 11817182
    Abstract: We propose a neural network-implemented method for base calling analytes. The method includes accessing a sequence of per-cycle image patches for a series of sequencing cycles, where pixels in the image patches contain intensity data for associated analytes, and applying three-dimensional (3D) convolutions on the image patches on a sliding convolution window basis such that, in a convolution window, a 3D convolution filter convolves over a plurality of the image patches and produces at least one output feature. The method further includes beginning with output features produced by the 3D convolutions as starting input, applying further convolutions and producing final output features and processing the final output features through an output layer and producing base calls for one or more of the associated analytes to be base called at each of the sequencing cycles.
    Type: Grant
    Filed: October 19, 2022
    Date of Patent: November 14, 2023
    Assignee: Illumina, Inc.
    Inventor: Emrah Kostem
  • Publication number: 20230357731
    Abstract: 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: Application
    Filed: March 13, 2023
    Publication date: November 9, 2023
    Applicants: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITED, ILLUMINA SINGAPORE PTE. LTD.
    Inventors: Kay Klausing, Hamed Tabatabaei Ghomi, Misha Golynskiy, Saurabh Nirantar, Seth McDonald, Sergio Peisajovich
  • Patent number: 11806836
    Abstract: A composition is provided that comprises a calcium carbonate slurry. The calcium carbonate slurry comprises a plurality of calcium carbonate particles suspended in a solution, where the solution comprises a dispersant and an anionic surfactant. The concentration of the calcium carbonate particles in the calcium carbonate slurry is equal to or less than about 2.0 wt. %.
    Type: Grant
    Filed: December 6, 2021
    Date of Patent: November 7, 2023
    Assignee: Illumina, Inc.
    Inventors: Robert Yang, Samantha K. Brittelle, You-Jung Cheng, Scott William Bailey, James M. Tsay
  • Patent number: 11803554
    Abstract: Methods, systems, and apparatuses, including computer programs for generating and using a hash table configured to improve mapping of reads are disclosed that include obtaining a first seed of K nucleotides from a reference sequence, generating a seed extension tree having a nodes, wherein each node of the nodes corresponds to (i) an extended seed that is an extension of the first seed and has a nucleotide length of K* and (ii) one or more locations, in a seed extension table, that include data describing reference sequence locations that match the extended seed, and for each node: storing interval information at a location of the hash table that corresponds to an index key for the extended seed, wherein the interval information references one or more locations in the seed extension table that include reference sequence locations that match the extended seed associated with the node.
    Type: Grant
    Filed: May 22, 2020
    Date of Patent: October 31, 2023
    Assignee: Illumina, Inc.
    Inventor: Michael Ruehle
  • Patent number: 11798650
    Abstract: The technology disclosed relates to constructing a convolutional neural network-based classifier for variant classification. In particular, it relates to training a convolutional neural network-based classifier on training data using a backpropagation-based gradient update technique that progressively match outputs of the convolutional neural network-based classifier with corresponding ground truth labels. The convolutional neural network-based classifier comprises groups of residual blocks, each group of residual blocks is parameterized by a number of convolution filters in the residual blocks, a convolution window size of the residual blocks, and an atrous convolution rate of the residual blocks, the size of convolution window varies between groups of residual blocks, the atrous convolution rate varies between groups of residual blocks. The training data includes benign training examples and pathogenic training examples of translated sequence pairs generated from benign variants and pathogenic variants.
    Type: Grant
    Filed: October 15, 2018
    Date of Patent: October 24, 2023
    Assignee: Illumina, Inc.
    Inventors: Laksshman Sundaram, Kai-How Farh, Hong Gao, Jeremy Francis McRae
  • Patent number: 11795578
    Abstract: Presented herein are methods and compositions for analyzing rare nucleic acid species. Some methods presented herein use DNA reassociation kinetics following thermal denaturation to define populations of nucleic acid sequences, e.g., highly abundant (e.g., cDNA from rRNA), moderately abundant, and less abundant or rare sequences (e.g., cDNA from mRNA).
    Type: Grant
    Filed: April 25, 2022
    Date of Patent: October 24, 2023
    Assignee: Illumina, Inc.
    Inventors: Scott Kuersten, Agnes Radek, Ramesh Vaidyanathan, Haiying Li Grunenwald
  • Patent number: 11795581
    Abstract: A method of characterizing candidate agents including steps of (a) providing a library of candidate agents attached to nucleic acid tags; (b) contacting the library with a solid support to attach the candidate agents to the solid support, whereby an array of candidate agents is formed; (c) contacting the array with a screening agent, wherein one or more candidate agents in the array react with the screening agent; (d) detecting the array to determine that at least one candidate agent in the array reacts with the screening agent; (e) sequencing the nucleic acid tag to determine the tag sequences attached to candidate agents in the array; and (f) identifying the at least one candidate agent in the array that reacts with the screening agent based on the tag sequence that is attached to the at least one candidate agent.
    Type: Grant
    Filed: October 11, 2018
    Date of Patent: October 24, 2023
    Assignee: Illumina, Inc.
    Inventors: Molly He, Michael Previte, Misha Golynskiy, Matthew William Kellinger, Sergio Peisajovich, Jonathan Mark Boutell
  • Patent number: 11787930
    Abstract: A flow cell includes a support and a heteropolymer attached to the support. The heteropolymer includes an acrylamide monomer including an attachment group to react with a functional group attached to a primer, and a monomer including a stimuli-responsive functional group. The monomer including the stimuli-responsive functional group may be pH-responsive, temperature-responsive, saccharide-responsive, nucleophile-responsive, and/or salt-responsive.
    Type: Grant
    Filed: December 19, 2019
    Date of Patent: October 17, 2023
    Assignees: Illumina Inc., Illumina Cambridge Limited
    Inventors: Wayne N. George, Ludovic Vincent, Andrew A. Brown, Mathieu Lessard-Viger
  • Patent number: 11786898
    Abstract: Systems and methods for conducting designated reactions that include a fluidic network having a sample channel, a reaction chamber, and a reservoir. The sample channel is in flow communication with a sample port. The system also includes a rotary valve that has a flow channel and is configured to rotate between first and second valve positions. The flow channel fluidically couples the reaction chamber and the sample channel when the rotary valve is in the first valve position and fluidically couples the reservoir and the reaction chamber when the rotary valve is in the second valve position. A pump assembly induces a flow of a biological sample toward the reaction chamber when the rotary valve is in the first valve position and induces a flow of a reaction component from the reservoir toward the reaction chamber when the rotary valve is in the second valve position.
    Type: Grant
    Filed: March 13, 2020
    Date of Patent: October 17, 2023
    Assignee: ILLUMINA, INC.
    Inventors: Sebastian Bohm, Alex Aravanis, Alexander Hsiao, Behnam Javanmardi, Tarun Khurana, Hai Quang Tran, Majid Aghababazadeh, M. Shane Bowen, Boyan Boyanov, Dale Buermann
  • Patent number: 11788139
    Abstract: The disclosed embodiments concern index oligonucleotides configured to identify sources of samples of nucleic acids and methods, apparatus, systems and computer program products for identifying and making the index oligonucleotides. In some implementations, the index oligonucleotides include a set of index sequences, a Hamming distance between any two index sequences of the set of index sequences meeting one or more criteria. System, apparatus, and computer program products are also provided for determining a sequence of interest using the index oligonucleotides.
    Type: Grant
    Filed: May 4, 2021
    Date of Patent: October 17, 2023
    Assignee: Illumina, Inc.
    Inventors: Ryan Kelley, Gordon Bean, Eric Vermaas
  • Patent number: D1003452
    Type: Grant
    Filed: July 27, 2022
    Date of Patent: October 31, 2023
    Assignee: Illumina, Inc.
    Inventors: Jay Taylor, Bradley Drews, James Osmus, Philip Paik, Tsukasa Takahashi, Brandon Westerberg, Jack Godfrey Wood, Carlos Dominguez