Patents Assigned to Illumina, Inc.
  • Publication number: 20220243261
    Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.
    Type: Application
    Filed: January 13, 2022
    Publication date: August 4, 2022
    Applicant: Illumina, Inc.
    Inventors: Min-Jui Richard Shen, Jonathan Mark Boutell, Kathryn M. Stephens, Mostafa Ronaghi, Kevin L. Gunderson, Bala Murali Venkatesan, M. Shane Bowen, Kandaswamy Vijayan
  • Publication number: 20220245801
    Abstract: The technology disclosed relates to training a convolutional neural network (CNN) to identify and classify images of sections of an image generating chip resulting in process cycle failures. The technology disclosed includes creating a training data set of images of dimensions M×N using labeled images of sections of image generating chip of dimensions J×K. The technology disclosed can fill the M×N frames using horizontal and vertical reflections along edges of J×K labeled images positioned in M×N frames. A pretrained CNN is further trained using the training data set. Trained CNN can classify a section image as normal or depicting failure. The technology disclosed can train a root cause CNN to classify process cycle images of sections causing process cycle failure. The trained CNN can classify a section image by root cause of process failure among a plurality of failure categories.
    Type: Application
    Filed: January 28, 2022
    Publication date: August 4, 2022
    Applicant: Illumina, Inc.
    Inventors: Kimberly Jean GIETZEN, Jingtao LIU, Yifeng TAO
  • Publication number: 20220245455
    Abstract: The technology disclosed relates to determining tag signals from measured intensities for purposes of base calling in next-generation sequencing. In particular, the measured intensities are collected by light sensors in a sensor array directed to a sample surface including pixel areas and holding a plurality of clusters during a sequence of sampling events. Each light sensor is directed to and measuring intensity from one of the pixel areas during each sampling event. The method includes adjusting the measured intensities from a pixel in the pixel areas for background intensity based on variations in background levels of the light sensors in the sensor array and determining an intensity of a tag signal originating from the pixel based on the adjusted measured intensities of the pixel.
    Type: Application
    Filed: March 24, 2022
    Publication date: August 4, 2022
    Applicant: Illumina, Inc.
    Inventor: Emrah KOSTEM
  • Patent number: 11402358
    Abstract: An apparatus includes a flow cell body, a plurality of electrodes, an imaging assembly, and one or more barrier features. The flow cell body defines one or more flow channels and a plurality of wells defined as recesses in the floor of each flow channel. Each well is fluidically coupled with the corresponding flow channel. The flow cell body further defines interstitial surfaces between adjacent wells. Each well defines a corresponding depth. Each electrode is positioned in a corresponding well of the plurality of wells. The electrodes are to effect writing of polynucleotides in the wells. The imaging assembly is to capture images of polynucleotides written in the wells. The one or more barrier features are positioned in the wells, between the wells, or above the wells. The one or more barrier features contain reactions in each well, reduce diffusion between the wells, or reduce optical cross-talk between the wells.
    Type: Grant
    Filed: September 20, 2021
    Date of Patent: August 2, 2022
    Assignee: ILLUMINA, INC.
    Inventors: Tarun Khurana, Ali Agah, Aathavan Karunakaran, Stanley Hong, Merek Siu, Arvin Emadi, Craig Ciesla
  • Patent number: 11400446
    Abstract: A flow cell including inlet and outlet ports in fluid communication with each other through a flow channel that extends therebetween. The flow channel includes a diffuser region and a field region that is located downstream from the diffuser region. The field region of the flow channel directs fluid along reaction sites where desired reactions occur. The fluid flows through the diffuser region in a first flow direction and through the field region in a second flow direction. The first and second flow directions being substantially perpendicular.
    Type: Grant
    Filed: August 1, 2019
    Date of Patent: August 2, 2022
    Assignee: ILLUMINA, INC.
    Inventors: Helmy A. Eltoukhy, Tarun Khurana, Behnam Javanmardi, Poorya Sabounchi, Majid Aghababazadeh
  • Publication number: 20220237457
    Abstract: The technology disclosed relates to constructing a computer-implemented method for variant classification. In particular, the method includes using a pathogenicity prediction neural network to process as input, (i) a reference protein sequence that has a first chain of amino acids with at least twenty amino acids, (ii) an alternative protein sequence aligned with the reference sequence, where the alternative protein sequence has a second chain of amino acids with at least twenty amino acids, and the first and second chains of amino acids differ by a variant amino acid caused by a nucleotide substitution, and (iii) a primate conservation profile generated using a primate cross-species multiple sequence alignment that aligns the reference protein sequence with other protein sequences from primate species. The method further includes based on the processing of the input by the neural network, generating as output a pathogenicity prediction for the nucleotide substitution.
    Type: Application
    Filed: April 6, 2022
    Publication date: July 28, 2022
    Applicant: Illumina, Inc.
    Inventors: Laksshman Sundaram, Kai-How Farh, Hong Gao, Samskruthi Reddy Padigepati, Jeremy Francis McRae
  • Patent number: 11396985
    Abstract: LED board interconnect schemes for illuminable assemblies are provided. Multiple LED boards may form a partial perimeter along an illuminable assembly. The multiple LED boards and interconnects must fit within a limited width and height of the illuminable assembly. In some implementations, an interconnect board and spring connectors are used to provide a low-profile electrical interconnection while maintaining co-planarity of the LEDs across the LED boards.
    Type: Grant
    Filed: August 27, 2020
    Date of Patent: July 26, 2022
    Assignee: Illumina, Inc.
    Inventors: Brian Elliot Sinofsky, Michael Justin Wright, Lim Peng Huay, Low Hong Yeap, Voon Yeow Seng
  • Patent number: 11397124
    Abstract: A fluid detection system includes a wicking material to draw fluid away from a first location with space limitations and proximate to a fluid device or a fluid interface. The wicking material draws the fluid to a remote fluid indicator at a second location. Contact between fluid and the remote fluid indicator produces a detectable alteration to the remote fluid indicator, and a non-contact optical sensor detects the alteration.
    Type: Grant
    Filed: January 3, 2020
    Date of Patent: July 26, 2022
    Assignee: ILLUMINA, INC.
    Inventors: Gregory L. Holst, Jay Taylor
  • Patent number: 11397889
    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 network 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: July 26, 2022
    Assignee: Illumina, Inc.
    Inventors: Kishore Jaganathan, Kai-How Farh, Sofia Kyriazopoulou Panagiotopoulou, Jeremy Francis McRae
  • Patent number: 11391693
    Abstract: Example devices include a cis well associated with a cis electrode, a trans well associated with a trans electrode, and a field effect transistor (FET) positioned between the cis well and the trans well. Examples of the field effect transistor (FET) include a fluidic system defined therein. The fluidic system includes a first cavity facing the cis well, a second cavity fluidically connected to the trans well, and a through via extending through the field effect transistor from the first cavity. A first nanoscale opening fluidically connects the cis well and the first cavity, the first nanoscale opening having an inner diameter. A second nanoscale opening fluidically connects the through via and the second cavity, the second nanoscale opening having an inner diameter. The second nanoscale opening inner diameter is larger than the first nanoscale opening inner diameter.
    Type: Grant
    Filed: February 13, 2019
    Date of Patent: July 19, 2022
    Assignee: Illumina, Inc.
    Inventors: Boyan Boyanov, Jens Gundlach
  • Patent number: 11390912
    Abstract: 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: Grant
    Filed: March 11, 2022
    Date of Patent: July 19, 2022
    Assignees: Spatial Transcriptomics AB, Illumina, Inc.
    Inventors: Jonas Frisen, Patrik Stahl, Joakim Lundeberg, Gordon M. Cann, Leila Bazargan, Alex Aravanis
  • Patent number: 11390864
    Abstract: In the examples set forth herein, nucleic acid extraction materials are capable of selectively extracting cell free nucleic acids, including cell free DNA, directly from whole blood samples or plasma. Also included are methods of making and using the nucleic acid extraction materials. One example of a nucleic acid extraction material includes a substrate. This example of the nucleic acid extraction material also includes a polycation bonded to at least a portion of a surface of the substrate. In this example, the polycation consists of a polymer of a quaternized monomer selected from the group consisting of a quaternized 1-vinylimidazole monomer and a quaternized dimethylaminoethyl methacrylate monomer, or a copolymer of a neutral monomer and the quaternized monomer.
    Type: Grant
    Filed: June 28, 2018
    Date of Patent: July 19, 2022
    Assignees: Illumina, Inc., Illumina Cambridge Limited
    Inventors: Brian D. Mather, Cyril Delattre, Tarun Kumar Khurana, Yir-Shyuan Wu, Pallavi Daggumati, Behnam Javanmardi, Filiz Gorpe-Yasar, Sebastien Georg Gabriel Ricoult, Xavier von Hatten, Daniel Leonard Fuller
  • Publication number: 20220220242
    Abstract: In one example, an unsaturated cyclic dione is coupled to the substrate, and is reacted with an indole or indazole including a first functional group to form a first adduct coupling the first functional group to the substrate. In another example, an unsaturated cyclic dione is coupled to a substrate and reacted with a diene including a functional group to form an adduct coupling the functional group to the substrate. In another example, an indole or indazole is coupled to a substrate, and is reacted with an unsaturated cyclic dione including an oligonucleotide to form an adduct coupling the oligonucleotide to the substrate. In another example, a diene is coupled to a substrate, and is reacted with an unsaturated cyclic dione including an oligonucleotide to form an adduct coupling the oligonucleotide to the substrate.
    Type: Application
    Filed: December 30, 2021
    Publication date: July 14, 2022
    Applicants: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITED
    Inventors: Randall Smith, Wayne George, Andrew Brown
  • Patent number: 11387269
    Abstract: Disclosed in one example is an apparatus including a substrate, a sensor over the substrate including an active surface and a sensor bond pad, a molding layer over the substrate and covering sides of the sensor, the molding layer having a molding height relative to a top surface of the substrate that is greater than a height of the active surface of the sensor relative to the top surface of the substrate, and a lidding layer over the molding layer and over the active surface. The lidding layer and the molding layer form a space over the active surface of the sensor that defines a flow channel.
    Type: Grant
    Filed: May 20, 2020
    Date of Patent: July 12, 2022
    Assignee: ILLUMINA, INC.
    Inventors: Arvin Emadi, Arnaud Rival, Ali Agah
  • Patent number: 11386603
    Abstract: A method comprises: accessing animation graphics files and a mask graphics file; generating first binary sequences corresponding to the animation graphics files, and generating a second binary sequence corresponding to the mask graphics file; and outputting the first binary sequences and the second binary sequence to hardware controlling an array of electrical components.
    Type: Grant
    Filed: December 1, 2020
    Date of Patent: July 12, 2022
    Assignee: Illumina, Inc.
    Inventors: Brian Sinofsky, Kirkpatrick Norton, Soham Sheth
  • Patent number: 11385162
    Abstract: 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: Grant
    Filed: January 13, 2021
    Date of Patent: July 12, 2022
    Assignee: ILLUMINA, INC.
    Inventors: Arnaud Rival, Ali Agah, Tracy H. Fung, Dietrich Dehlinger, Poorya Sabounchi, Tarun Khurana, Craig M. Ciesla, M. Shane Bowen
  • Patent number: 11384392
    Abstract: 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: Grant
    Filed: December 31, 2020
    Date of Patent: July 12, 2022
    Assignees: Illumina, Inc., Illumina Cambridge Limited
    Inventors: 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
  • Patent number: 11386324
    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: January 27, 2020
    Date of Patent: July 12, 2022
    Assignee: Illumina, Inc.
    Inventors: Hong Gao, Kai-How Farh, Laksshman Sundaram, Jeremy Francis McRae
  • Publication number: 20220216191
    Abstract: Provided herein include various examples of a method for manufacturing aspects of an apparatus, a sensor system. The method may include obtaining a first carrier bonded to an upper surface of the silicon wafer. This wafer includes through silicon vias (TSVs) extended through openings in a passivation stack, with electrical contacts coupled to portions of the TSVs exposed through these openings. The method may include de-bonding the first carrier from the upper surface of the silicon wafer. The method may include dicing the silicon wafer into subsections comprising dies.
    Type: Application
    Filed: September 26, 2020
    Publication date: July 7, 2022
    Applicant: ILLUMINA, INC.
    Inventors: Arvin EMADI, Jon ADAY, Ali AGAH, Arnaud RIVAL
  • Patent number: D959453
    Type: Grant
    Filed: August 5, 2020
    Date of Patent: August 2, 2022
    Assignee: Illumina, Inc.
    Inventors: Eliza Van Gerbig, Igor Freilafert, Jeffrey Pohlmann