Patents Assigned to Illumina, Inc.
  • Patent number: 12380561
    Abstract: Methods and systems for analysis of image data generated from various reference points. Particularly, the methods and systems provided are useful for real time analysis of image and sequence data generated during DNA sequencing methodologies.
    Type: Grant
    Filed: January 8, 2025
    Date of Patent: August 5, 2025
    Assignee: Illumina, Inc.
    Inventors: Francisco Jose Garcia, Klaus Maisinger, Stephen Tanner, John A. Moon, Tobias Mann, Michael Lawrence Parkinson, Anthony James Cox, Haifang H. Ge
  • Patent number: 12379541
    Abstract: A closure for an apparatus comprises: a plurality of light sources; a lightguide to distribute light from the plurality of light sources, the lightguide having a first primary surface opposite a second primary surface, wherein the first primary surface has a first surface treatment, and wherein light emitted from the lightguide indicates a status of the apparatus; and a frame supporting the plurality of light sources and the lightguide for selective movement of the closure vertically or horizontally relative to the apparatus.
    Type: Grant
    Filed: November 4, 2024
    Date of Patent: August 5, 2025
    Assignee: Illumina, Inc.
    Inventors: Michael Wright, Erik Allegoren, Erik Williamson
  • Patent number: 12367978
    Abstract: Computer implemented methods and computer systems are provided for estimating cancer cell fractions indicating proportions of cancer cells carrying one or more mutations of interest using one or more nucleic acid samples from a subject. The methods and systems provided herein implement processes that use a variational Bayesian mixture model to cluster initial cancer cell fractions and obtain the one or more final cancer cell fractions, the initial cancer cell fractions accounting for cancer purity and copy numbers. The disclosed methods and systems improve accuracy, validity, and reliability of tests for cancer clonality, and save time, materials, cost, and computer resources required for the tests, which can help design more affective cancer treatments.
    Type: Grant
    Filed: December 3, 2018
    Date of Patent: July 22, 2025
    Assignee: Illumina, Inc.
    Inventors: Vitor Ferreira Onuchic, Kristina M. Kruglyak
  • Patent number: 12365939
    Abstract: Compositions, systems, and methods for detecting events are provided. A composition can include a nanopore including a first side, a second side, and an aperture extending through the first and second sides; and a permanent tether including head and tail regions and an elongated body disposed there between. The head region can be anchored to or adjacent to the first or second side of the nanopore. The elongated body including a reporter region can be movable within the aperture responsive to a first event occurring adjacent to the first side of the nanopore. For example, the reporter region is translationally movable toward the first side responsive to the first event, then toward the second side, then toward the first side responsive to a second event. The first event can include adding a first nucleotide to a polynucleotide. The second event can include adding a second nucleotide to the polynucleotide.
    Type: Grant
    Filed: February 18, 2022
    Date of Patent: July 22, 2025
    Assignee: Illumina, Inc.
    Inventors: Jeffrey G. Mandell, Kevin L. Gunderson, Jens H. Gundlach
  • Patent number: 12359053
    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: August 11, 2023
    Date of Patent: July 15, 2025
    Assignees: Illumina Inc., Illumina Cambridge Limited
    Inventors: Wayne N. George, Ludovic Vincent, Andrew A. Brown, Mathieu Lessard-Viger
  • Patent number: 12361525
    Abstract: The technology disclosed relates to equalizer-based intensity correction for base calling. In particular, the technology disclosed relates to accessing an image whose pixels depict intensity emissions from a target cluster and intensity emissions from additional adjacent clusters, selecting a lookup table that contains pixel coefficients that are configured to increase a signal-to-noise ratio, applying the pixel coefficients to intensity values of the pixels in the image to produce an output, and base calling the target cluster based on the output.
    Type: Grant
    Filed: May 8, 2023
    Date of Patent: July 15, 2025
    Assignee: Illumina, Inc.
    Inventors: Eric Jon Ojard, Rami Mehio, Gavin Derek Parnaby, Nitin Udpa, John S. Vieceli
  • Patent number: 12359194
    Abstract: A structured substrate includes a substrate body having an active side. The substrate body includes reaction cavities that open along the active side and interstitial regions that separate the reaction cavities. The structured substrate includes an ensemble amplifier positioned within each of the reaction cavities. The ensemble amplifier includes a plurality of nanostructures configured to at least one of amplify electromagnetic energy that propagates into the corresponding reaction cavity or amplify electromagnetic energy that is generated within the corresponding reaction cavity.
    Type: Grant
    Filed: September 9, 2022
    Date of Patent: July 15, 2025
    Assignee: ILLUMINA, INC.
    Inventors: M. Shane Bowen, Dajun Yuan
  • Patent number: 12359256
    Abstract: 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: Grant
    Filed: December 29, 2022
    Date of Patent: July 15, 2025
    Assignee: ILLUMINA, INC.
    Inventors: Sarah E. Shultzaberger, Fiona Kaper, Sarah Kinnings, Suzanne Rohrback, Carlo Randise-Hinchliff
  • Patent number: 12352745
    Abstract: 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: Grant
    Filed: May 24, 2019
    Date of Patent: July 8, 2025
    Assignee: ILLUMINA, INC.
    Inventors: Sarah E. Shultzaberger, Fiona Kaper, Sarah Kinnings, Suzanne Rohrback, Carlo Randise-Hinchliff
  • Patent number: 12350681
    Abstract: Described herein are devices, systems, and methods for constructing and utilizing a cartridge having one or more active warming elements. A cartridge can include a housing, an active warming element, and a power source connector. The housing can define a chamber storing a volume of reagent therein. The active warming element can be embedded within the housing and positioned proximate to the chamber. The power source connector can be coupled to the housing and electrically coupled to the active warming element embedded within the housing. The active warming element is to thaw the volume of reagent within the chamber responsive to providing electrical power to the power source connector.
    Type: Grant
    Filed: November 22, 2019
    Date of Patent: July 8, 2025
    Assignee: ILLUMINA, INC.
    Inventor: Kirkpatrick W. Norton
  • Patent number: 12354008
    Abstract: The technology disclosed compresses a larger, teacher base caller into a smaller, student base caller. The student base caller has fewer processing modules and parameters than the teacher base caller. The teacher base caller is trained using hard labels (e.g., one-hot encodings). The trained teacher base caller is used to generate soft labels as output probabilities during the inference phase. The soft labels are used to train the student base caller.
    Type: Grant
    Filed: February 15, 2021
    Date of Patent: July 8, 2025
    Assignee: Illumina, Inc.
    Inventors: Anindita Dutta, Gery Vessere, Dorna Kashefhaghighi, Kishore Jaganathan, Amirali Kia
  • Patent number: 12351868
    Abstract: Presented herein are polymerase-linked nucleotides for improved distinguishing nucleotide sequences for different nucleic acid molecules. Also presented are methods and systems using the polymerase-linked nucleotides for improved distinguishing nucleotide sequences for different nucleic acid molecules.
    Type: Grant
    Filed: August 27, 2020
    Date of Patent: July 8, 2025
    Assignee: Illumina, Inc.
    Inventors: Christian Gloeckner, Matthew William Kellinger, Lea Pickering
  • Patent number: 12353136
    Abstract: In an example method, a water-soluble protective coating solution is applied over a bonding region and either i) a patterned region of a patterned structure or ii) a lane region of a non-patterned structure. The patterned region includes depressions having at least a polymeric hydrogel therein, and interstitial regions separating the depressions. The lane region includes a lane having at least the polymeric hydrogel therein. The water-soluble protective coating solution is dried to form a solid coating or a gel coating over the bonding region and over either i) the patterned region or ii) the lane region. Portions of the solid coating or the gel coating are selectively removed from the bonding region while leaving other portions of the solid coating or the gel coating over either i) the patterned region or ii) the lane region.
    Type: Grant
    Filed: December 14, 2021
    Date of Patent: July 8, 2025
    Assignee: Illumina, Inc.
    Inventors: Neil Brahma, Tyler J. Dill, Michelle Kate Fu, Brian A. Hanos, Sahngki Hong, Brinda Kodira Cariappa, Lewis J. Kraft
  • Publication number: 20250215491
    Abstract: Methods and compositions for polynucleotide sequencing. The methods include incorporating a blocked, labeled nucleotide into a copy polynucleotide strand; detecting the identity of the blocked, labeled nucleotide; and removing the blocked, labelled nucleotide. The steps may be repeated. At least one of the steps is performed in the presence of a single-stranded binding protein.
    Type: Application
    Filed: December 16, 2024
    Publication date: July 3, 2025
    Applicant: ILLUMINA, INC.
    Inventors: Christopher Winnard, Amy Charles, Philip Balding, Justin Robbins
  • Patent number: 12348874
    Abstract: A method is used to generate an analysis image of a moving sample based on one or more exposures. An illumination source illuminates a field of view of a camera for one or more pulses while the sample moves through the field of view. The distance moved by the sample during each of these one or more pulses may be less than the size of one pixel in an image captured by the camera.
    Type: Grant
    Filed: October 28, 2021
    Date of Patent: July 1, 2025
    Assignees: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITED
    Inventors: Geraint Evans, Stanley Hong, Merek Siu, Shaoping Lu, John Moon
  • Publication number: 20250207193
    Abstract: The present subject matter relates to reusable flow cells, uses of reusable flow cells, methods of manufacturing a reusable flow cell and methods of regenerating a reusable flow cell.
    Type: Application
    Filed: December 20, 2024
    Publication date: June 26, 2025
    Applicant: Illumina, Inc.
    Inventors: Jonathan Boutell, Jason Betley, Pietro Gatti Lafranconi, Xiaolin Wu, Oliver Miller
  • Publication number: 20250209042
    Abstract: A sequence data processing and retention method includes obtaining sequence data produced by a sequencer device. The sequence data includes genomic data of interest and metadata. The method processes the sequence data, and this processing includes separating the genomic data of interest from the metadata, and compressing the separated genomic data of interest based on a reference sequence to produce compressed genomic data The method additionally stores storing the compressed genomic data and the metadata. Optionally, based on a request, a process recovers the sequence data from the stored compressed genomic data and metadata, where the recovering includes decompressing the compressed genomic data to provide decompressed genomic data of interest as the separated genomic data of interest, and combining the decompressed genomic data of interest with the metadata to provide combined genomic data and metadata.
    Type: Application
    Filed: December 19, 2024
    Publication date: June 26, 2025
    Applicant: Illumina, Inc.
    Inventors: Paul SMITH, Guillaume RIZK, Michael CARNEY
  • Publication number: 20250205655
    Abstract: Nanopore devices including barriers using amphiphilic units, and methods of making the same, are provided herein. In some examples, a barrier between first and second fluids includes a first layer comprising a first plurality of amphiphilic units, a second layer comprising a second plurality of the amphiphilic units and contacting the first plurality of amphiphilic units. The amphiphilic units may be substantially the same size as one another. The amphiphilic units respectively may include hydrophobic blocks and hydrophilic blocks coupled to the hydrophobic blocks.
    Type: Application
    Filed: March 30, 2023
    Publication date: June 26, 2025
    Applicant: ILLUMINA, INC.
    Inventors: Antonio Conde-Gonzalez, Charlotte Vacogne, Oliver Uttley, Istvan Kocsis, Alexandre Richez
  • Patent number: D1085149
    Type: Grant
    Filed: February 16, 2023
    Date of Patent: July 22, 2025
    Assignee: Illumina, Inc.
    Inventor: Kevin P. Rhodes
  • Patent number: D1085458
    Type: Grant
    Filed: January 17, 2025
    Date of Patent: July 22, 2025
    Assignees: Illumina, Inc., Illumina Singapore Pte. Ltd.
    Inventors: Erik Allegoren, Emerico Alberto Brewer, Robert Nicholas Dean, Max Warren Pollock, Bashkaran Subramanian