Patents Assigned to Illumina
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Publication number: 20250197931Abstract: An image sensor structure includes an image layer having 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 a light detector. An array of nanowells is disposed over the device stack. Each nanowell is associated with a first light guide of the array of light guides. A first primer set is disposed throughout a first well region of each nanowell. A second primer set is disposed throughout a second well region of each nanowell. The second well region is adjacent the first well region. The first and second primer sets are operable to attach a forward strand cluster of forward polynucleotide strands in the first well region and a reverse strand cluster of reverse polynucleotide strands in the second well region.Type: ApplicationFiled: March 6, 2025Publication date: June 19, 2025Applicants: Illumina, Inc., Illumina Cambridge LimitedInventors: Lewis KRAFT, Craig Lee HETHERINGTON, Craig M. CIESLA, Michael BUREK, Jeffrey FISHER, Jason BETLEY
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Publication number: 20250188446Abstract: The disclosure provides methods for creating long oligonucleotide reagents that include barcodes and other element for sequencing library preparation, where the oligonucleotides are created by multiple tiers of ligation of shorter oligos. The disclosed methods work to extend short oligos that are attached to particles, thereby allowing one to create particles that carry large number of long sample preparation oligonucleotides without being required to synthesize those full-length molecules with a polymerase.Type: ApplicationFiled: January 27, 2025Publication date: June 12, 2025Applicant: Illumina, Inc.Inventors: Robert Meltzer, Kristina Fontanez, Yi Xue
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Patent number: 12325028Abstract: 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: GrantFiled: February 11, 2025Date of Patent: June 10, 2025Assignee: Illumina, Inc.Inventors: David Elliott Kaplan, Anthony John de Ruyter, Richard Alan Kelley, Ashish Kumar
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Patent number: 12320734Abstract: An analysis instrument may perform analytical operations on an analyte that is combined with multiple reagents prior to being introduced into a flow cell. The instrument may include a nozzle sipper that aspirates reagents from a recipient, along with an analyte. The reagents may be directed to a volume and may be repeatedly moved into and out of the volume by cycling of a pump. The reagents may be ejected into a destination recipient with the nozzle sipper promoting vorticity in the recipient to enhance mixing. The repeated aspiration and ejection through the nozzle sipper effectively mixes the reagents and the template in an automated or semi-automated fashion.Type: GrantFiled: May 19, 2021Date of Patent: June 3, 2025Assignee: Illumina, Inc.Inventors: Bradley Kent Drews, Michael Dai Wang, Umberto Ulmanella, James Michael Osmus, Stephen Wayne Clark, Johanna Lynn Whitacre, Steven Scott Phelps, Michelle L. Alvarez, Michael Adalbert Niziolek, Debra Sue Bryan, Joshua Augustin Darland
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Publication number: 20250171832Abstract: The invention relates to methods of preventing renaturation of single-stranded nucleic acid libraries during storage, the method comprising using blocking oligonucleotides substantially complementary to adaptor sequences in the nucleic acid library.Type: ApplicationFiled: September 30, 2022Publication date: May 29, 2025Applicant: Illumina, Inc.Inventors: Claire Bevis-Mott, Debra Sue Bryan, II
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Patent number: 12311362Abstract: A method for patterning flow cell substrates using photo-initiated chemical reactions that includes fabricating a planar waveguide flow cell by forming a layer of light coupling gratings on a glass substrate layer; depositing a core layer on the layer of light coupling gratings; depositing a cladding layer on the core layer; and forming nanowells in the cladding layer; silanizing the cladding layer; coating the silanized cladding layer and nanowells with a first group of reactants; introducing a second group of reactants into the nanowells, wherein the second group of reactants includes a target reactant and a light-sensitive photoinitiator system; coupling a light source to the light coupling gratings and directing light internally within the planar waveguide flow cell for photo-initiating a chemical reaction between the first and second groups of reactants, wherein the photo-initiated chemical reaction covalently binds the target reactant to only the bottom portion of each nanowell.Type: GrantFiled: August 10, 2020Date of Patent: May 27, 2025Assignee: ILLUMINA, INC.Inventors: Steven Modiano, Dajun Yuan, Randall Smith
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Publication number: 20250164386Abstract: Disclosed is an apparatus and method of forming, including a supporting structure, a sensor on the supporting structure, a pair of columns on the supporting structure at opposite sides of the sensor, the pair of columns having a column height relative to a top surface of the supporting structure, the column height being higher than a height of the active surface of the sensor relative to the top surface of the supporting structure, and a lidding layer on the pair of columns and over the active surface, the lidding layer being supported at opposite ends by the pair of columns. The active surface of the sensor, the lidding layer and the pair of columns form an opening above at least more than about half of the active surface of the sensor, and the supporting structure, the sensor, the lidding layer and the pair of columns together form a flow cell.Type: ApplicationFiled: January 17, 2025Publication date: May 22, 2025Applicant: Illumina, Inc.Inventors: Donglai Lu, Xiuyu Cai, Wenyi Feng, Hai Tran
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Publication number: 20250164399Abstract: An example sensor includes a flow cell, a detection device, and a controller. The flow cell includes a passivation layer having opposed surfaces and a reaction site at a first of the opposed surfaces. The flow cell also includes a lid operatively connected to the passivation layer to partially define a flow channel between the lid and the reaction site. The detection device is in contact with a second of the opposed surfaces of the passivation layer, and includes an embedded metal layer that is electrically isolated from other detection circuitry of the detection device. The controller is to ground the embedded metal layer.Type: ApplicationFiled: January 17, 2025Publication date: May 22, 2025Applicant: Illumina, Inc.Inventors: Tracy Helen Fung, Xiuyu Cai, Lisa Kwok, Hai Tran, Kevan Samiee, Liangliang Qiang, Boyan Boyanov
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Patent number: 12297565Abstract: Embodiments of systems, methods, and compositions provided herein relate to assays for selectively controlling enzymatic reactions. Some embodiments relate to methods of inhibiting, reducing, or eliminating secondary DNA (such as mitochondrial DNA) sequencing reads from open chromatic sequencing, whole genome sequencing, or targeted sequencing.Type: GrantFiled: December 13, 2019Date of Patent: May 13, 2025Assignee: Illumina, Inc.Inventors: Frank J. Steemers, Dmitry K. Pokholok, Lena Christiansen
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Patent number: 12297221Abstract: 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: August 1, 2023Date of Patent: May 13, 2025Assignee: Illumina, Inc.Inventors: Frank J. Steemers, Kevin L. Gunderson, Kerri York, Ryan Christopher Smith
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Patent number: 12298665Abstract: An example flow cell includes a multi-layer stack including a transparent base support; a patterned sacrificial layer over the transparent base support; and a transparent layer over the patterned sacrificial layer. The flow cell further includes first and second functionalized layers over different portions of the transparent layer, wherein at least one of the first and second functionalized layers aligns with a pattern of the patterned sacrificial layer; and first and second primer sets respectively attached to the first and second functionalized layer.Type: GrantFiled: September 27, 2021Date of Patent: May 13, 2025Assignee: Illumina, Inc.Inventors: Sahngki Hong, Lewis J. Kraft
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Patent number: 12297498Abstract: This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template. The method can include the steps of contacting the nucleic acid template with a conformationally labeled polymerase and at least four different nucleotide species under conditions wherein the conformationally labeled polymerase catalyzes sequential addition of the nucleotide species to form a nucleic acid complement of the nucleic acid template, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species; detecting a series of changes in the signal from the conformationally labeled polymerase under the conditions; and determining the rates or time durations for the changes in the signal, thereby determining the sequence of nucleotides for the nucleic acid template.Type: GrantFiled: March 31, 2023Date of Patent: May 13, 2025Assignee: Illumina, Inc.Inventors: Molly He, Cheng-Yao Chen, Eric Kool, Mostafa Ronaghi, Michael Previte, Rigo Pantoja
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Patent number: 12296333Abstract: Provided herein include various examples of a method for manufacturing aspects of flow cell. The method may include performing chemical processes on a surface of the patterned wafer to prepare the surface of the patterned, singulating the wafer into individual dies, orienting each die on a temporary substrate, where the orienting creates spaces between each individual die, and molding a material over the spaces to create a hybrid wafer comprised of glass and molded material. The method may also include bonding two of the hybrid wafers together, forming a bonded wafer stack.Type: GrantFiled: February 18, 2022Date of Patent: May 13, 2025Assignee: Illumina, Inc.Inventors: Jonathan Ziebarth, Jon Aday, Paul Crivelli, Gerald Kreindl, Amit Sharma
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Publication number: 20250137930Abstract: Light detection devices and related methods are provided. The devices may comprise a reaction structure for containing a reaction solution with a relatively high or low pH and a plurality of reaction sites that generate light emissions. The devices may comprise a device base comprising a plurality of light sensors, device circuitry coupled to the light sensors, and a plurality of light guides that block excitation light but permit the light emissions to pass to a light sensor. The device base may also include a shield layer extending about each light guide between each light guide and the device circuitry, and a protection layer that is chemically inert with respect to the reaction solution extending about each light guide between each light guide and the shield layer. The protection layer prevents reaction solution that passes through the reaction structure and the light guide from interacting with the device circuitry.Type: ApplicationFiled: January 6, 2025Publication date: May 1, 2025Applicant: Illumina, Inc.Inventors: Xiuyu CAI, Joseph Francis PINTO, Thomas A. BAKER, Tracy Helen FUNG
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Patent number: 12286453Abstract: Embodiments of the present disclosure relate to nucleotide with acetal 3?-OH blocking groups. Also provided herein are methods of using fully functionalized nucleotides containing the 3? acetal blocking group for sequencing applications.Type: GrantFiled: September 28, 2023Date of Patent: April 29, 2025Assignee: Illumina Cambridge LimitedInventors: Antoine Francais, Elena Cressina, Angelica Mariani, Adam Culley, Anno Koetje, Xiaohai Liu
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Patent number: 12287574Abstract: An example resin composition includes an epoxy resin matrix, a first photoacid generator, and a second photoacid generator. The first photoacid generator includes an anion having a molecular weight less than about 250 g/mol. The second photoacid generator includes an anion having a molecular weight greater than about 300 g/mol. In an example, i) a cation of the first photoacid generator has, or ii) a cation of the second photoacid generator has, or iii) the cations of the first and second photoacid generators have a mass attenuation coefficient of at least 0.1 L/(g*cm) at a wavelength of incident light to cure the resin composition.Type: GrantFiled: December 21, 2020Date of Patent: April 29, 2025Assignee: Illumina, Inc.Inventors: Yekaterina Rokhlenko, Timothy J. Merkel
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Patent number: 12287490Abstract: Apparatus and methods for controlling heating of an objective in a linescanning sequencing system to improve resolution are disclosed. In accordance with a first implementation, an apparatus includes or comprises a beam source for providing input radiation and a beam shaping group including or comprising one or more optical elements positioned to receive the input radiation from the beam source, and to perform beam shaping on the input radiation to form a shaped beam. The apparatus further including or comprising an objective positioned to receive the shaped beam and to transform the shaped beam into a probe beam and configured to provide the probe beam to a focal plane of the objective for optically probing a sample. The beam shaping group is configured to adjust one or more properties of the shaped beam over time to generally uniformly heat the objective over a region of incidence for the shaped beam.Type: GrantFiled: November 4, 2022Date of Patent: April 29, 2025Assignee: Illumina, Inc.Inventors: Danilo Condello, Dakota Watson, Andrew Carson, Vincent Hsieh, Steven Boege, Changqin Ding, Stanley Hong
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Publication number: 20250129415Abstract: Polynucleotide sequencing using ionophores is provided herein. In some examples, a sequencing method includes inhibiting current flow across a barrier; contacting a polymerase with a first polynucleotide, a second polynucleotide, and a fluid comprising a first nucleotide coupled to a first ionophore; while the polymerase adds the first nucleotide to the second polynucleotide based on a sequence of the first polynucleotide, providing a first current flow across the barrier using the first ionophore; and identifying the first nucleotide using an electrical characteristic of the first ionophore.Type: ApplicationFiled: June 30, 2022Publication date: April 24, 2025Applicant: Illumina, Inc.Inventors: Jeffrey Mandell, Boyan Boyanov
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Patent number: D1071959Type: GrantFiled: September 25, 2022Date of Patent: April 22, 2025Assignee: Illumina, Inc.Inventors: Gordana Lamb, Nahida Badran, Jacob Dessau, Jack Godfrey Wood, Raymond Lawrence Oyung, John Tate Sager
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Patent number: D1073117Type: GrantFiled: July 15, 2022Date of Patent: April 29, 2025Assignee: Illumina, Inc.Inventors: Erik Allegoren, James Michael Osmus, Max Warren Pollock, Robert Nicholas Dean