Patents Assigned to Illumina
  • Publication number: 20240319224
    Abstract: An apparatus includes a fluidic circuit, a bypass fluidic circuit, a first set of fluid wells, a second set of fluid wells, a first valve, and a second valve. The first valve operatively associated with the first set of fluid wells such that the first selectively fluidly connects any one of the first set of fluid wells to a first valve outlet. The second valve operatively associated with the fluidic circuit, the bypass fluidic circuit, the first valve outlet, and the second set of fluid wells such that the second valve selectively fluidly connects any one of the second set of fluid wells and the first valve outlet to the fluidic circuit or the first valve outlet to the bypass fluidic circuit.
    Type: Application
    Filed: June 3, 2024
    Publication date: September 26, 2024
    Applicant: Illumina, Inc.
    Inventors: Wesley A. COX-MURANAMI, James OSMUS, Paul CRIVELLI, Bradley Kent DREWS
  • Patent number: 12100125
    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: October 5, 2023
    Date of Patent: September 24, 2024
    Assignee: Illumina, Inc.
    Inventors: Robert Langlois, Paul Belitz
  • Patent number: 12100723
    Abstract: An image sensor structure including an image stack disposed over a device stack. The image stack includes a plurality of light detectors. A first optical filter stack is disposed over the image stack. The first optical filter stack includes a light guide layer. Light pipe cavities are disposed in the light guide layer. Each light pipe cavity is associated with a light detector. Each light pipe cavity has an aspect ratio that is greater than about 2.5 to about 1. A nanowell layer is disposed over the first optical filter stack. Nanowells are disposed in the nanowell layer. Each nanowell is associated with a light detector.
    Type: Grant
    Filed: September 29, 2020
    Date of Patent: September 24, 2024
    Assignee: Illumina Inc.
    Inventors: Arvin Emadi, Ali Agah, Xiuyu Cai, Craig Lee Hetherington
  • Patent number: 12097502
    Abstract: A cartridge for use with chemical or biological analysis systems, as well as methods of using the same, is provided. The cartridge may include a floating microfluidic plate that is held in the cartridge using one or more floating support brackets that incorporate gaskets that may seal against fluidic ports on the microfluidic plate. The floating support brackets may include indexing features that may align the microfluidic plate with the seals.
    Type: Grant
    Filed: February 11, 2023
    Date of Patent: September 24, 2024
    Assignee: Illumina, Inc.
    Inventors: David Elliott Kaplan, Anthony John de Ruyter, Richard Alan Kelley, Ashish Kumar
  • Publication number: 20240309423
    Abstract: Automated methods conducted in a sequencing flowcell, and kits for reusing a flowcell, are provided herein. In some examples, an automated method conducted in a sequencing flowcell may include, at a surface of the sequencing flowcell coupled to a first moiety, using a reagent to decouple a first complex from the first moiety. In some examples, the first complex may include a second moiety which couples to the first moiety and a polynucleotide coupled to the second moiety. In some examples, the method may further include using a nuclease to polynucleotides in the sequencing flowcell. The method may include, after using the reagent and after using the nuclease, coupling a second complex to the first moiety. The second complex may include a third moiety which couples with the first moiety and an oligonucleotide coupled to the third moiety.
    Type: Application
    Filed: March 5, 2024
    Publication date: September 19, 2024
    Applicant: Illumina, Inc.
    Inventors: Jonathan Boutell, Katharina Mueller-Ott, Jason Betley, Xiaolin Wu, Wayne George, Pietro Gatti Lafranconi, Andrew Brown
  • Patent number: 12091713
    Abstract: An imaging system includes: a sample container including a flowcell that includes a plurality of attachment elements at a plurality of sample locations, wherein a single DNA template molecule is attached to each of the attachment elements, and further wherein an average distance between adjacent attachment elements is less than Abbe's limit; and an imager positioned to image photo-switching occurring at the plurality of attachment elements by capturing on and off events in a plurality of color channels at the same time as the on and off events are occurring for the attached molecules when a stochastic photo-switching chemistry is applied to all of the attached molecules at the same time causing the attached molecules to fluoresce in the on and off events in up to four different colors.
    Type: Grant
    Filed: August 5, 2021
    Date of Patent: September 17, 2024
    Assignees: ILLUMINA CAMBRIDGE LIMITED, ILLUMINA, INC.
    Inventors: Gary Mark Skinner, Geraint Wyn Evans, Stanley S. Hong
  • Patent number: 12091712
    Abstract: The present disclosure provides systems and methods for sequencing nucleic acid molecules using tunneling labels. A sequence of a nucleic acid molecule may be identified with high accuracy using a chip comprising sensors, wherein each individual sensor may comprise at least two electrodes separated by a gap. The electrodes may be configured to generate at least one electrical signal upon binding of a tunneling label associated with a nucleotide. Epigenetic information can also be determined at the same time as a nucleic acid sequence.
    Type: Grant
    Filed: October 24, 2018
    Date of Patent: September 17, 2024
    Assignee: Illumina Cambridge, Ltd.
    Inventors: Mark F. Oldham, Eric S. Nordman, Timothy M. Woudenberg, Gaurav Goyal, Masoud Vakili, Toshihiko Honkura, Sam Woo, Hisao Kawasaki, Kazusuke Mihara
  • Publication number: 20240301401
    Abstract: 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: Application
    Filed: March 27, 2024
    Publication date: September 12, 2024
    Applicant: Illumina Cambridge Limited
    Inventors: Niall Anthony Gormley, Geoffrey Paul Smith
  • Patent number: 12083514
    Abstract: An interposer for a flow cell comprises a base layer having a first surface and a second surface opposite the first surface. The base layer comprises black polyethylene terephthalate (PET). A first adhesive layer is disposed on the first surface of the base layer. The first adhesive layer comprises methyl acrylic adhesive. A second adhesive layer is disposed on the second surface of the base layer. The second adhesive layer comprises methyl acrylic adhesive. A plurality of microfluidic channels extends through each of the base layer, the first adhesive layer, and the second adhesive layer.
    Type: Grant
    Filed: April 22, 2022
    Date of Patent: September 10, 2024
    Assignee: ILLUMINA, Inc.
    Inventors: Maxwell Zimmerley, LiangLiang Qiang, M. Shane Bowen, Steven H. Modiano, Dajun Yuan, Randall Smith, Arthur J. Pitera, Hai Quang Tran, Gerald Kreindl
  • Patent number: 12084474
    Abstract: Embodiments of the present disclosure relate to methods of preparation of templates for polynucleotide sequencing. In particular, the disclosure relates to linearization of clustered polynucleotides in preparation for sequencing by cleavage of one or more first strands of double-stranded polynucleotides immobilized on a solid support by a transition metal complex, for example, a palladium complex or a nickel complex. Further disclosure relate to linearization of clustered polynucleotides by cleaving one or more second strands of double double-stranded polynucleotides immobilized on a solid support comprising azobenzene linker by Na2S2O4. Nucleotides and oligonucleotides comprising a 3? phosphate moiety blocking group, and methods of removing the same using a fluoride reagent are also disclosed.
    Type: Grant
    Filed: May 14, 2019
    Date of Patent: September 10, 2024
    Assignee: Illumina, Inc.
    Inventors: Xiaolin Wu, Randall Smith, Peyton Shieh, John M. Beierle, Wayne N. George, Elliot John Lawrence, Jie Mao, Xiaohai Liu
  • Patent number: 12087797
    Abstract: An example image sensor structure includes an image layer. The image layer includes an array of light detectors disposed therein. A device stack is disposed over the image layer. An array of light guides is disposed in the device stack. Each light guide is associated with at least one light detector of the array of light detectors. A passivation stack is disposed over the device stack. The passivation stack includes a bottom surface in direct contact with a top surface of the light guides. An array of nanowells is disposed in a top layer of the passivation stack. Each nanowell is associated with a light guide of the array of light guides. A crosstalk blocking metal structure is disposed in the passivation stack. The crosstalk blocking metal structure reduces crosstalk within the passivation stack.
    Type: Grant
    Filed: February 28, 2023
    Date of Patent: September 10, 2024
    Assignee: ILLUMINA, INC.
    Inventors: Xiuyu Cai, Ali Agah, Tracy H. Fung, Dietrich Dehlinger
  • Patent number: 12087401
    Abstract: Methods and systems are provided for determining a variant of interest by analyzing sizes and sequences of cfDNA fragments obtained from a test sample. The methods and systems provided herein implement processes that synergistically combine size and sequence information, thereby improving specificity and sensitivity of assays over conventional methods.
    Type: Grant
    Filed: April 20, 2022
    Date of Patent: September 10, 2024
    Assignee: Illumina, Inc.
    Inventors: Tingting Jiang, Chen Zhao, Han-Yu Chuang
  • Patent number: 12085499
    Abstract: One example of a flow cell includes a base support and a multi-layer stack positioned over the base support. The multi-layer stack includes a resin layer positioned over the base support; and a hydrophobic layer positioned over the resin layer. A depression is defined in the multi-layer stack through the hydrophobic material and through a portion of the resin.
    Type: Grant
    Filed: December 18, 2020
    Date of Patent: September 10, 2024
    Assignee: Illumina, Inc.
    Inventors: Sahngki Hong, M. Shane Bowen, Lewis J. Kraft, Sharis Minassian
  • Patent number: 12077789
    Abstract: Presented herein are altered polymerase enzymes for improved incorporation of nucleotides and nucleotide analogues, in particular altered polymerases that maintain low pre-phasing rates when using ambiently stored polymerases, as well as methods and kits using the same.
    Type: Grant
    Filed: June 1, 2022
    Date of Patent: September 3, 2024
    Assignee: ILLUMINA, INC.
    Inventors: Misha Golynskiy, Mariko Matsuura, Saurabh Nirantar, Hamed Tabatabaei Ghomi, Seth McDonald, Ryan Craig, Sergio Peisajovich, Kyrie Johnson, Kay Klausing, Eric Murtfeldt, Alexandra Exner
  • Patent number: 12080385
    Abstract: Methods, systems, and computer programs for compressing nucleic acid sequence data. A method can include obtaining nucleic acid sequence data representing: (i) a read sequence, and (ii) a plurality of quality scores, determining whether the read sequence includes at least one ā€œNā€ base, based on a determination that the read sequence includes at least one ā€œNā€ base, generating, by one or more computers, a first encoding data set by using a first encoding process to encode each set of four quality scores of the read sequence into a single byte of memory, and using a second encoding process to encode the first encoded data set, thereby compressing the data to be compressed.
    Type: Grant
    Filed: August 23, 2023
    Date of Patent: September 3, 2024
    Assignee: Illumina, Inc.
    Inventor: Guillaume Alexandre Pascal Rizk
  • Patent number: 12076725
    Abstract: Fluidic device includes a manifold body having first and second body sides. The first body side has receiving ports forming a port array that defines a reaction region. The second body side has open-sided recesses forming reaction chambers when the fluidic device is mounted onto a sample substrate. The reaction chambers form a chamber array that defines a fluid-delivery region. The reaction region is greater than the fluid-delivery region. The manifold body also includes vent openings that open to an exterior. The fluidic device also includes upstream channels extending through the manifold body. Each of the upstream channels fluidly couples a corresponding receiving port of the port array to a corresponding reaction chamber of the chamber array. The fluidic device also includes venting channels extending through the manifold body. Each of the venting channels fluidly couples a corresponding reaction chamber of the chamber array to a corresponding vent opening.
    Type: Grant
    Filed: April 29, 2021
    Date of Patent: September 3, 2024
    Assignee: Illumina, Inc.
    Inventor: Darryl Donovan
  • Publication number: 20240287504
    Abstract: Genomic library preparation using Cas-gRNA RNPs, and targeted epigenetic assays, are provided herein. Some compositions include, from a first species, substantially only single-stranded polynucleotides; from a second species, substantially only double-stranded polynucleotides; and amplification primers ligated to ends of the second double-stranded polynucleotides and substantially not ligated to any ends of the first double-stranded polynucleotides. Some compositions include first and second molecules of a target polynucleotide having a sequence, the first molecule having a first end at a first subsequence, the second molecule having a first end at a second subsequence, wherein the first subsequence only partially overlaps with the second subsequence. Some examples provide a composition that includes a target polynucleotide and a first fusion protein including a Cas-gRNA RNP coupled to a transposase having an amplification adapter coupled thereto.
    Type: Application
    Filed: March 8, 2022
    Publication date: August 29, 2024
    Applicants: Illumina, Inc., Illumina Cambridge Limited
    Inventors: Andrew Kennedy, Sarah Shultzaberger, Emma Bell, Oliver Miller, Kim Schneider, Esther Musgrave-Brown, Niall Gormley, Andrew Slatter, Feng Chen
  • Patent number: D1042875
    Type: Grant
    Filed: July 15, 2022
    Date of Patent: September 17, 2024
    Assignee: Illumina, Inc.
    Inventors: Erik Allegoren, Jack Godfrey Wood, Ridwan Liow, Max Warren Pollock, Robert Nicholas Dean
  • Patent number: D1042880
    Type: Grant
    Filed: July 15, 2022
    Date of Patent: September 17, 2024
    Assignee: Illumina, Inc.
    Inventors: Kameel Michael Abi-Samra, Emerico Alberto Brewer, Justin Davidson, Max Warren Pollock, Christopher George Sip
  • Patent number: D1044025
    Type: Grant
    Filed: March 5, 2024
    Date of Patent: September 24, 2024
    Assignee: Illumina, Inc.
    Inventors: Erik Allegoren, Emerico Alberto Brewer, Justin Davidson, Robert Nicholas Dean, Max Warren Pollock