Patents Assigned to Illumina
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Patent number: 12106829Abstract: The technology disclosed relates to artificial intelligence-based base calling. The technology disclosed relates to accessing a progression of per-cycle analyte channel sets generated for sequencing cycles of a sequencing run, processing, through a neural network-based base caller (NNBC), windows of per-cycle analyte channel sets in the progression for the windows of sequencing cycles of the sequencing run such that the NNBC processes a subject window of per-cycle analyte channel sets in the progression for the subject window of sequencing cycles of the sequencing run and generates provisional base call predictions for three or more sequencing cycles in the subject window of sequencing cycles, from multiple windows in which a particular sequencing cycle appeared at different positions, using the NNBC to generate provisional base call predictions for the particular sequencing cycle, and determining a base call for the particular sequencing cycle based on the plurality of base call predictions.Type: GrantFiled: July 13, 2023Date of Patent: October 1, 2024Assignee: Illumina, Inc.Inventors: Anindita Dutta, Gery Vessere, Dorna KashefHaghighi, Kishore Jaganathan, Amirali Kia
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Patent number: 12106828Abstract: 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: GrantFiled: March 24, 2022Date of Patent: October 1, 2024Assignee: Illumina, Inc.Inventor: Emrah Kostem
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Publication number: 20240317793Abstract: In some examples, a nucleoside triphosphate analogue may include a sugar, a nucleobase coupled to the sugar, a triphosphate group coupled to the sugar, a heteroatom coupled to an alpha phosphate of the triphosphate group, and a first substituent coupled to the heteroatom. The heteroatom may be selected from the group consisting of oxygen, nitrogen, and carbon. The first substituent may include at least one of an alkyl chain or a polymer.Type: ApplicationFiled: March 18, 2024Publication date: September 26, 2024Applicant: Illumina, Inc.Inventors: Hassan Bohra, Xiangyuan Yang, Ramesh Neelakandan, Yin Nah Teo, Abdul Sadeer Abd Salam, Eric Murtfeldt
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Publication number: 20240319224Abstract: 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: ApplicationFiled: June 3, 2024Publication date: September 26, 2024Applicant: Illumina, Inc.Inventors: Wesley A. COX-MURANAMI, James OSMUS, Paul CRIVELLI, Bradley Kent DREWS
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Patent number: 12100125Abstract: 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: GrantFiled: October 5, 2023Date of Patent: September 24, 2024Assignee: Illumina, Inc.Inventors: Robert Langlois, Paul Belitz
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Patent number: 12100723Abstract: 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: GrantFiled: September 29, 2020Date of Patent: September 24, 2024Assignee: Illumina Inc.Inventors: Arvin Emadi, Ali Agah, Xiuyu Cai, Craig Lee Hetherington
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Patent number: 12097502Abstract: 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, 2023Date of Patent: September 24, 2024Assignee: Illumina, Inc.Inventors: David Elliott Kaplan, Anthony John de Ruyter, Richard Alan Kelley, Ashish Kumar
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Publication number: 20240309423Abstract: 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: ApplicationFiled: March 5, 2024Publication date: September 19, 2024Applicant: Illumina, Inc.Inventors: Jonathan Boutell, Katharina Mueller-Ott, Jason Betley, Xiaolin Wu, Wayne George, Pietro Gatti Lafranconi, Andrew Brown
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Patent number: 12091713Abstract: 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: GrantFiled: August 5, 2021Date of Patent: September 17, 2024Assignees: ILLUMINA CAMBRIDGE LIMITED, ILLUMINA, INC.Inventors: Gary Mark Skinner, Geraint Wyn Evans, Stanley S. Hong
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Patent number: 12091712Abstract: 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: GrantFiled: October 24, 2018Date of Patent: September 17, 2024Assignee: 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
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Publication number: 20240301401Abstract: 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: ApplicationFiled: March 27, 2024Publication date: September 12, 2024Applicant: Illumina Cambridge LimitedInventors: Niall Anthony Gormley, Geoffrey Paul Smith
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Patent number: 12084474Abstract: 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: GrantFiled: May 14, 2019Date of Patent: September 10, 2024Assignee: Illumina, Inc.Inventors: Xiaolin Wu, Randall Smith, Peyton Shieh, John M. Beierle, Wayne N. George, Elliot John Lawrence, Jie Mao, Xiaohai Liu
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Patent number: 12083514Abstract: 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: GrantFiled: April 22, 2022Date of Patent: September 10, 2024Assignee: 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
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Patent number: 12087797Abstract: 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: GrantFiled: February 28, 2023Date of Patent: September 10, 2024Assignee: ILLUMINA, INC.Inventors: Xiuyu Cai, Ali Agah, Tracy H. Fung, Dietrich Dehlinger
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Patent number: 12087401Abstract: 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: GrantFiled: April 20, 2022Date of Patent: September 10, 2024Assignee: Illumina, Inc.Inventors: Tingting Jiang, Chen Zhao, Han-Yu Chuang
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Patent number: 12085499Abstract: 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: GrantFiled: December 18, 2020Date of Patent: September 10, 2024Assignee: Illumina, Inc.Inventors: Sahngki Hong, M. Shane Bowen, Lewis J. Kraft, Sharis Minassian
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Patent number: 12077789Abstract: 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: GrantFiled: June 1, 2022Date of Patent: September 3, 2024Assignee: 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
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Patent number: D1042875Type: GrantFiled: July 15, 2022Date of Patent: September 17, 2024Assignee: Illumina, Inc.Inventors: Erik Allegoren, Jack Godfrey Wood, Ridwan Liow, Max Warren Pollock, Robert Nicholas Dean
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Patent number: D1042880Type: GrantFiled: July 15, 2022Date of Patent: September 17, 2024Assignee: Illumina, Inc.Inventors: Kameel Michael Abi-Samra, Emerico Alberto Brewer, Justin Davidson, Max Warren Pollock, Christopher George Sip
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Patent number: D1044025Type: GrantFiled: March 5, 2024Date of Patent: September 24, 2024Assignee: Illumina, Inc.Inventors: Erik Allegoren, Emerico Alberto Brewer, Justin Davidson, Robert Nicholas Dean, Max Warren Pollock