Patents Assigned to Illumina, Inc.
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Publication number: 20240098152Abstract: Versions of a sequencing system may be monitored to enable changing of a version of a server subsystem operating the sequencing system to service requests from client subsystems for performing analysis of sequencing data. A monitor subsystem may be utilized for receiving and authorizing requests from client subsystems. The monitor subsystem may identify a version associated with a server subsystem operating the sequencing system to be implemented for servicing the request. The monitor subsystem may allow the server subsystem to be accessed for servicing the request from the client subsystem when the version associated with the client subsystem is compatible with the version associated with the server subsystem. The monitor subsystem may prevent the server subsystem from being accessed when the version associated with the client subsystem is incompatible with the version associated with the server subsystem.Type: ApplicationFiled: September 13, 2023Publication date: March 21, 2024Applicant: Illumina, Inc.Inventors: Padmanabhan Ramchandran, Ian Patrick Hurst
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Patent number: 11932900Abstract: An example of an array includes a support, a cross-linked epoxy polyhedral oligomeric silsesquioxane (POSS) resin film on a surface of the support, and a patterned hydrophobic polymer layer on the cross-linked epoxy POSS resin film. The patterned hydrophobic polymer layer defines exposed discrete areas of the cross-linked epoxy POSS resin film, and a polymer coating is attached to the exposed discrete areas. Another example of an array includes a support, a modified epoxy POSS resin film on a surface of the support, and a patterned hydrophobic polymer layer on the modified epoxy POSS resin film. The modified epoxy POSS resin film includes a polymer growth initiation site, and the patterned hydrophobic polymer layer defines exposed discrete areas of the modified epoxy POSS resin film. A polymer brush is attached to the polymer growth initiation site in the exposed discrete areas.Type: GrantFiled: October 25, 2022Date of Patent: March 19, 2024Assignees: Illumina, Inc., Illumina Cambridge LimitedInventors: Wayne N. George, Alexandre Richez, M. Shane Bowen, Andrew A. Brown, Dajun Yuan, Audrey Rose Zak, Sean M. Ramirez, Raymond Campos
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Patent number: 11933728Abstract: Techniques are described for reducing the number of angles needed in structured illumination imaging of biological samples through the use of patterned flowcells, where nanowells of the patterned flowcells are arranged in, e.g., a square array, or an asymmetrical array. Accordingly, the number of images needed to resolve details of the biological samples is reduced. Techniques are also described for combining structured illumination imaging with line scanning using the patterned flowcells.Type: GrantFiled: January 13, 2023Date of Patent: March 19, 2024Assignees: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITEDInventors: Gary Skinner, Geraint Evans, Stanley Hong
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Patent number: 11934884Abstract: Coordinated application processing includes obtaining a plurality of images and distributing them to processing engines to perform image processing. The plurality of images cover an image area, with different sub-areas, in which a biological sample to be sequenced is present. The image processing proceeds across multiple cycles to process a respective set of images, of the plurality of images, of each sub-area of the different sub-areas, and therefore of the respective area, of the flow cell, to which that sub-area correlates. The distributing the plurality of images includes, for each sub-area of the different sub-areas, distributing, across the multiple cycles of the image processing, the images of the respective set of images of that sub-area to a respective processing engine, of a plurality of processing engines, associated with, and selected for, processing images of that sub-area.Type: GrantFiled: January 30, 2023Date of Patent: March 19, 2024Assignee: Illumina, Inc.Inventors: David Kimmel, Eunho Noh, Paul Smith
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Publication number: 20240068016Abstract: 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: ApplicationFiled: November 9, 2023Publication date: February 29, 2024Applicants: 10x Genomics Sweden AB, Illumina, Inc.Inventors: Jonas Frisen, Patrik Stahl, Joakim Lundeberg, Gordon M. Cann, Leila Bazargan, Alex Aravanis
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Patent number: 11913067Abstract: A composition for amplifying a polynucleotide is provided that includes a substrate comprising a first region and a second region. A first plurality of capture primers is coupled to the first region of the substrate. A second plurality of capture primers is coupled to the second region of the substrate. The capture primers of the second plurality of capture primers are longer than the capture primers of the first plurality of capture primers. A first plurality of orthogonal capture primers are coupled to the first region of the substrate. A second plurality of orthogonal capture primers are coupled to the second region of the substrate. The orthogonal capture primers of the second plurality of orthogonal capture primers are shorter than the orthogonal capture primers of the first plurality of orthogonal capture primers.Type: GrantFiled: August 27, 2021Date of Patent: February 27, 2024Assignees: Illumina, Inc., Illumina Cambridge LimitedInventors: Jeffrey Fisher, Jason Betley
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Patent number: 11911765Abstract: A method includes flowing an incorporation reagent through a reagent management system and a flow cell of an instrument. The flow cell having a first polynucleotide positioned therein. The incorporation reagent adding a first base onto a sequence of bases. The sequence of bases includes a second polynucleotide complementary to the first polynucleotide. An image of an identification signal emanating from the first base is captured after the first base has been added onto the second polynucleotide. A cleavage reagent is flowed through the reagent management system and flow cell to remove a first terminator from the first base in order to enable a subsequent base in the sequence of bases to be added to the second polynucleotide. A buffer reagent is flowed through the reagent management system and flow cell in a plurality of cycles of consecutive forward and reverse flow directions.Type: GrantFiled: June 16, 2020Date of Patent: February 27, 2024Assignee: ILLUMINA, INC.Inventors: Tony Yen, Eric Stava, Rajagopal Panchapakesan
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Publication number: 20240060895Abstract: There is set forth herein a light energy exciter that can include one or more light sources. A light energy exciter can emit excitation light directed toward a detector surface that can support biological or chemical samples.Type: ApplicationFiled: October 27, 2023Publication date: February 22, 2024Applicant: Illumina, Inc.Inventors: Rui JIANG, Joseph PINTO
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Patent number: 11908548Abstract: The technology disclosed relates to generating ground truth training data to train a neural network-based template generator for cluster metadata determination task. In particular, it relates to accessing sequencing images, obtaining, from a base caller, a base call classifying each subpixel in the sequencing images as one of four bases (A, C, T, and G), generating a cluster map that identifies clusters as disjointed regions of contiguous subpixels which share a substantially matching base call sequence, determining cluster metadata based on the disjointed regions in the cluster map, and using the cluster metadata to generate the ground truth training data for training the neural network-based template generator for the cluster metadata determination task.Type: GrantFiled: May 27, 2022Date of Patent: February 20, 2024Assignee: Illumina, Inc.Inventors: Anindita Dutta, Dorna Kashefhaghighi, Amirali Kia
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Patent number: 11896944Abstract: Fiducial markers are provided on patterned arrays of the type that may be used for molecular analysis, such as sequencing. The fiducials may have configurations that enhance their detection in image or detection data, that facilitate or improve processing, that provide encoding of useful information, and so forth. Examples of the fiducials may include an “always on” type that respond to multiple frequencies of radiation used during processing and detection so as to return signals during successive cycles of imaging.Type: GrantFiled: January 31, 2018Date of Patent: February 13, 2024Assignee: Illumina, Inc.Inventors: John S. Vieceli, Alex Nemiroski, Paul Belitz, Robert Langlois, M. Shane Bowen, Danny Yuan Chan, Bala Murali K. Venkatesan, Hui Han, Kevan Samiee, Stephen Tanner
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Patent number: 11898198Abstract: The disclosed embodiments concern methods, systems and computer program products for determining sequences of interest using unique molecular indexes (UMIs) that are uniquely associable with individual polynucleotide fragments, including sequences with low allele frequencies or long sequence length. In some implementations, the UMIs include variable-length nonrandom UMIs (vNRUMIs). Methods and systems for making and using sequencing adapters comprising vNRUMIs are also provided.Type: GrantFiled: August 17, 2022Date of Patent: February 13, 2024Assignee: Illumina, Inc.Inventors: Chen Zhao, Kevin Wu, Han-Yu Chuang, Jennifer Lococo, Alex So, Dwight Baker, Tatjana Singer
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Patent number: 11898983Abstract: Devices and methods of using the devices are disclosed which can provide scalability, improved sensitivity and reduced noise for sequencing polynucleotide. Examples of the devices include a biological or solid-state nanopore, a field effect transistor (FET) sensor with improved gate controllability over the channel, and a porous structure.Type: GrantFiled: June 18, 2021Date of Patent: February 13, 2024Assignee: Illumina, Inc.Inventors: Boyan Boyanov, Rico Otto, Jeffrey G. Mandell
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Patent number: 11892080Abstract: Gasket assemblies and related system and methods. An apparatus includes a system, a flow cell, and a plurality of gasket assemblies. The system includes a flow cell interface and the flow cell has one or more channels. Each channel has a first channel opening and a second channel opening. The first channel openings are positioned at a first end of the flow cell and the second channel openings are positioned at a second end of the flow cell. A gasket assembly coupled at each second channel opening. Each gasket assembly includes an adhesive stack and a gasket. The adhesive stack includes a first side bonded to the gasket and a second side bonded to the flow cell. The flow cell interface is engagable with the corresponding gaskets to establish a fluidic coupling between system and the flow cell.Type: GrantFiled: February 1, 2022Date of Patent: February 6, 2024Assignee: ILLUMINA, INC.Inventors: Ashish Kumar, James Osmus, David Kaplan, Richard Lemoine
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Patent number: 11891600Abstract: Presented herein are techniques for indexing of nucleic acid, e.g., for use in conjunction with sequencing. The techniques include generating indexed nucleic acid fragments from an individual sample, whereby the index sequence incorporated into each index site of the nucleic acid fragment is selected from a plurality of distinguishable of index sequences and such that the population of generated nucleic acid fragments represents each index sequence from the plurality. In this manner, the generated indexed nucleic acid fragments from a single sample are indexed with a diverse mix of index sequences that reduce misassignment due to index read errors associated with low sequence diversity.Type: GrantFiled: November 5, 2018Date of Patent: February 6, 2024Assignee: ILLUMINA, INC.Inventors: John S. Vieceli, Ryan Matthew Kelley
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Patent number: 11894135Abstract: The present invention provides a novel approach for storing, analyzing, and/or accessing biological data in a cloud computing environment. Sequence data generated by a particular sequencing device may be uploaded to the cloud computing environment during a sequencing run, which reduces the on-site storage needs for the sequence data. Analysis of the data may also be performed in the cloud computing environment, and the instructions for such analysis may be set at the originating sequencing device. The sequence data in the cloud computing environment may be shared according to permissions. Further, the sequence data may be modified or annotated by authorized secondary users.Type: GrantFiled: May 10, 2021Date of Patent: February 6, 2024Assignee: Illumina, Inc.Inventors: Alexander G Dickinson, Francisco Jose Garcia, Robert C. Kain, Scott D. Kahn, Andrew R. Nelson
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Patent number: 11885953Abstract: A method is used to generate a report presenting parameter values corresponding to a structured illumination microscopy (SIM) optical system. The parameter values are based at least in part on the performed modulation calculation corresponding to an image set captured with the SIM optical system. A minimum FWHM slice is identified, based at least in part on an average FWHM value across the images in the first image set. Parameter estimation is performed on the identified minimum FWHM slice. Best in-focus parameters are identified based at least in part on the performed estimation. A phase estimate is performed for each image in the set. A modulation calculation is performed based at least in part on the identified best in-focus parameters. The report is based at least in part on the performed modulation calculation.Type: GrantFiled: December 22, 2021Date of Patent: January 30, 2024Assignee: ILLUMINA, INC.Inventors: Austin Corbett, Bo Lu, Robert Langlois, Joseph Pinto, Yu Chen, Peter Newman, Hongji Ren
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Patent number: 11884976Abstract: An example of a resin composition includes a free radical curable resin matrix including an acrylate and a siloxane, and a free radical photoinitiator. When cured, the resin composition has low or no autofluorescence when exposed to blue excitation wavelengths ranging from about 380 nm to about 480 nm or green excitation wavelengths ranging from about 510 nm to about 560 nm.Type: GrantFiled: July 18, 2019Date of Patent: January 30, 2024Assignees: Illumina, Inc., Illumina Cambridge LimitedInventors: Timothy J. Merkel, Wayne N. George, Andrew A. Brown, Audrey Zak, Gianluca Andrea Artioli, Julia Morrison, Nikolai Romanov, Lorenzo Berti, Graham Boud
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Patent number: 11885323Abstract: Linear peristaltic pumps for use with fluidic cartridges. An apparatus includes a reagent cartridge configured to be received within a cartridge receptacle of a system. The reagent cartridge includes a reagent reservoir and a body including a surface that forms depressions. Each depression has a fluid inlet and a fluid outlet and is fluidly coupled to at least one other depression. The reagent cartridge also includes a deformable material coupled to the surface of the body and includes portions. Each portion covers one of the depressions to define chambers. The portions of the deformable material are movable relative to the depressions between a first position outside of a dimensional envelope of the body and a second position within the dimensional envelope of the body.Type: GrantFiled: May 15, 2020Date of Patent: January 30, 2024Assignee: ILLUMINA, INC.Inventors: Cameron Mar, Wesley A. Cox-Muranami, Steven Hendrix, Cyril Delattre
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Patent number: 11886110Abstract: An imprinting apparatus includes a silicon master and an anti-stick layer coating the silicon master. The silicon master includes a plurality of features positioned at an average pitch of less than about 425 nm, each of the plurality of features comprises a depression having an opening with its largest opening dimension being less than about 300 nm. The anti-stick layer includes a crosslinked silane polymer network.Type: GrantFiled: March 23, 2021Date of Patent: January 30, 2024Assignee: Illumina, Inc.Inventors: Timothy J. Merkel, Ruibo Wang, Daniel Wright, Danny Yuan Chan, Avishek Aiyar, Tanmay Ghonge, Neil Brahma, Arthur Pitera
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Publication number: 20240026431Abstract: Described herein are standards and methods of normalizing amplicon size bias. These standards may comprise unique molecular identifiers. In some embodiments, the standards and methods are for use with next generation sequencing (NGS) assays. Also described herein are methods for quantifying DNA damage in a sample comprising DNA using fluorescence or for determining the presence of DNA damage in a library.Type: ApplicationFiled: September 25, 2023Publication date: January 25, 2024Applicant: Illumina, Inc.Inventors: Andrew B. Kennedy, Lena Storms, Fei Shen, Olivia Benice, Eric Murtfeldt, Kaitlin Pugliese, Michael Howard