Patents by Inventor Jeffrey S. Fisher

Jeffrey S. Fisher has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).

  • Publication number: 20230410944
    Abstract: This disclosure describes methods, non-transitory computer readable media, and systems that can introduce short calibration sequences into a sequencing device and run calibration cycles to adjust or otherwise determine a sequencing parameter corresponding to the sequencing device. For instance, the disclosed systems can detect a flow cell (or other sample-nucleotide slide) with calibration sequences incorporated into samples' library fragments or into a surface of the sample-nucleotide slide. By running one or more calibration cycles to incorporate nucleobases on oligonucleotides corresponding to calibration sequences and capture corresponding images for calibration sequences—separate from genomic sequencing cycles for sample genomic sequences—the disclosed systems can determine a sequencing parameter corresponding to the sequencing device.
    Type: Application
    Filed: February 24, 2023
    Publication date: December 21, 2023
    Inventors: John S. Vieceli, Bo Lu, Jeffrey S. Fisher
  • Publication number: 20230381733
    Abstract: An example of a flow cell includes a substrate, a plurality of chambers defined on or in the substrate, and a plurality of depressions defined in the substrate and within a perimeter of each of the plurality of chambers. The depressions are separated by interstitial regions. Primers are attached within each of the plurality of depressions, and a capture site is located within each of the plurality of chambers.
    Type: Application
    Filed: August 11, 2023
    Publication date: November 30, 2023
    Inventors: Lewis J. Kraft, Tarun Kumar Khurana, Yir-Shyuan Wu, Xi-Jun Chen, Arnaud Rival, Justin Fullerton, M. Shane Bowen, Hui Han, Jeffrey S. Fisher, Yasaman Farshchi, Mathieu Lessard-Viger
  • Publication number: 20230374493
    Abstract: Embodiments of the present invention relate to analyzing components of a cell. In some embodiments, the present invention relate to analyzing components of a single cell. In some embodiments, the methods and compositions relate to sequencing nucleic acids. In some embodiments, the methods and compositions relate to identifying and/or quantitiating nucleic acid, proteins, organelles, and/or cellular metabolites.
    Type: Application
    Filed: February 27, 2023
    Publication date: November 23, 2023
    Applicant: ILLUMINA, INC.
    Inventors: Kevin L. Gunderson, Frank J. Steemers, Jeffrey S. Fisher, Roberto Rigatti
  • Patent number: 11819843
    Abstract: An example of a flow cell includes a substrate, which includes nano-depressions defined in a surface of the substrate, and interstitial regions separating the nano-depressions. A hydrophobic material layer has a surface that is at least substantially co-planar with the interstitial regions and is positioned to define a hydrophobic barrier around respective sub-sets of the nano-depressions.
    Type: Grant
    Filed: April 26, 2022
    Date of Patent: November 21, 2023
    Assignee: Illumina, Inc.
    Inventors: Tarun Kumar Khurana, Arnaud Rival, Lewis J. Kraft, Steven Barnard, M. Shane Bowen, Xi-Jun Chen, Yir-Shyuan Wu, Jeffrey S. Fisher, Dajun Yuan
  • Publication number: 20230332224
    Abstract: An example of a flow cell includes a substrate; a first primer set attached to a first region on the substrate, the first primer set including an un-cleavable first primer and a cleavable second primer; and a second primer set attached to a second region on the substrate, the second primer set including a cleavable first primer and an un-cleavable second primer.
    Type: Application
    Filed: May 15, 2023
    Publication date: October 19, 2023
    Inventors: Jeffrey S. Fisher, Brian D. Mather, Maria Candelaria Rogert Bacigalupo, Justin Fullerton, Ludovic Vincent, Lewis J. Kraft, Sahngki Hong, Boyan Boyanov, M. Shane Bowen, Sang Park, Wayne N. George, Andrew A. Brown
  • Patent number: 11779897
    Abstract: An example of a flow cell includes a substrate, a plurality of chambers defined on or in the substrate, and a plurality of depressions defined in the substrate and within a perimeter of each of the plurality of chambers. The depressions are separated by interstitial regions. Primers are attached within each of the plurality of depressions, and a capture site is located within each of the plurality of chambers.
    Type: Grant
    Filed: October 31, 2021
    Date of Patent: October 10, 2023
    Assignee: Illumina, Inc.
    Inventors: Lewis J. Kraft, Tarun Kumar Khurana, Yir-Shyuan Wu, Xi-Jun Chen, Arnaud Rival, Justin Fullerton, M. Shane Bowen, Hui Han, Jeffrey S. Fisher, Yasaman Farshchi, Mathieu Lessard-Viger
  • Publication number: 20230287476
    Abstract: Degradable polyester bead are described comprising a plurality of transposome complexes immobilized to the surface thereof, wherein each transposome complex comprises a transposase bound to a first polynucleotide and a second polynucleotide, wherein the first polynucleotide comprises a 3? portion comprising a transposon end sequence and a tag, and the second polynucleotide comprises a 5? portion that is complementary to and hybridized to the transposon end sequence, and wherein the polyester bead has a melting point of from 50° C. to 65° C. Flow cells and methods related to these polyester beads are described. Also described herein are compositions comprising a bead and at least one nanoparticle and methods of use of such compositions comprising transposome complexes immobilized to nanoparticles.
    Type: Application
    Filed: January 6, 2023
    Publication date: September 14, 2023
    Applicant: Illumina, Inc.
    Inventors: Yir-Shyuan Wu, Tarun Kumar Khurana, Elisabet Rosàs-Canyelles, Fei Shen, Jeffrey Brodin, Lena Storms, Jeffrey S. Fisher
  • Publication number: 20230279469
    Abstract: An example of a flow cell includes a substrate having depressions separated by interstitial regions. First and second primers are immobilized within the depressions. First transposome complexes are immobilized within the depressions, and the first transposome complexes include a first amplification domain. Second transposome complexes are also immobilized within the depressions, and the second transposome complexes include a second amplification domain. Some of the first transposome complexes, or some of the second transposome complexes, or some of both of the first and second transposome complexes include a modification to reduce tagmentation efficiency.
    Type: Application
    Filed: December 23, 2022
    Publication date: September 7, 2023
    Inventors: Johan Sebastian Basuki, Jonathan Mark Boutell, Jeffrey S. Fisher, Louise Jane Fraser, Wayne N. George, Niall Anthony Gormley, David Jones, Xiaoyu Ma, Maria Ines Martins Vitoriano, Zhong Mei, Oliver Jon Miller, Andrew Price, Sebastien Georg Gabriel Ricoult, Vicki S. Thomson, Jacqueline C. Weir, Xiaoy Ma, Weihua Chang, Hui Han
  • Publication number: 20230259034
    Abstract: In a method, a resin layer of a stack (e.g., resin layer over sacrificial layer over transparent substrate) is imprinted to form a convex region including first region with first height and second region with second height <first height. Stack portions are etched around the convex region to expose a substrate portion. The stack is utilized to develop a curable layer to define a cured layer over the exposed substrate portion. The convex region and cured layer are etched. The resin layer and a sacrificial layer portion underlying the second region are removed. A second substrate portion is exposed and a third substrate portion remains covered by a remaining sacrificial layer portion. The cured layer is substantially co-planar with the remaining sacrificial layer portion. A depression is formed extending to the second substrate portion. The remaining sacrificial layer portion is utilized to define functionalized layers over different depression regions.
    Type: Application
    Filed: December 19, 2022
    Publication date: August 17, 2023
    Inventors: Jeffrey S. Fisher, Tanmay Ghonge, Sahngki Hong, Lewis J Kraft
  • Patent number: 11680292
    Abstract: An example of a flow cell includes a substrate; a first primer set attached to a first region on the substrate, the first primer set including an un-cleavable first primer and a cleavable second primer; and a second primer set attached to a second region on the substrate, the second primer set including a cleavable first primer and an un-cleavable second primer.
    Type: Grant
    Filed: June 14, 2022
    Date of Patent: June 20, 2023
    Assignees: Illumina, Inc., Illumina Cambridge Limited
    Inventors: Jeffrey S. Fisher, Brian D. Mather, Maria Candelaria Rogert Bacigalupo, Justin Fullerton, Ludovic Vincent, Lewis J. Kraft, Sahngki Hong, Boyan Boyanov, M. Shane Bowen, Sang Park, Wayne N. George, Andrew A. Brown
  • Publication number: 20230139821
    Abstract: In an example method, a first functionalized layer is deposited over a resin layer including multi-depth depressions separated by interstitial regions, each depression including a deep portion and a shallow portion adjacent to the deep portion; a photoresist is deposited over the first functionalized layer; an ultraviolet light dosage is directed, through the resin layer, whereby a first photoresist portion generates an insoluble photoresist and a second photoresist portion becomes a soluble photoresist; the soluble photoresist is removed to expose a portion of the first functionalized layer; the portion of the first functionalized layer is removed to expose a portion of the resin layer; a second functionalized layer is deposited over the insoluble photoresist, and over the exposed portion of the resin layer; the insoluble photoresist is removed to expose the first functionalized layer; and the first functionalized layer or the second functionalized layer is removed from the interstitial regions.
    Type: Application
    Filed: May 9, 2022
    Publication date: May 4, 2023
    Inventors: Jeffrey S. Fisher, Anthony Flannery, Sahngki Hong, Brinda Kodira Cariappa, Lewis J. Kraft
  • Publication number: 20230137978
    Abstract: A metal film is formed over a resin layer including a plurality of multi-depth depressions (MDP) separated by interstitial regions, each MDP including a deep portion and an adjacent shallow portion. A sacrificial layer is formed over the metal film. The sacrificial layer and metal film are sequentially dry etched to expose a resin layer surface at the shallow portion and interstitial regions. Resin layer portions are removed i) at the shallow portion to form a depression region having a surface directly adjacent to a surface at the deep portion and ii) at the interstitial regions to form new interstitial regions surrounding the deep portion and the depression region. First functionalized layer is deposited over the metal film, depression region, and new interstitial regions. The metal film is removed from the deep portion. Second functionalized layer is deposited over the surface at the deep portion. New interstitial regions are polished.
    Type: Application
    Filed: May 9, 2022
    Publication date: May 4, 2023
    Inventors: Jeffrey S. Fisher, Anthony Flannery, Sahngki Hong, Brinda Kodira Cariappa, Lewis J. Kraft, Brian D. Mather
  • Patent number: 11634707
    Abstract: Embodiments of the present invention relate to analyzing components of a cell. In some embodiments, the present invention relate to analyzing components of a single cell. In some embodiments, the methods and compositions relate to sequencing nucleic acids. In some embodiments, the methods and compositions relate to identifying and/or quantitating nucleic acid, proteins, organelles, and/or cellular metabolites.
    Type: Grant
    Filed: February 10, 2016
    Date of Patent: April 25, 2023
    Assignee: ILLUMINA, INC.
    Inventors: Kevin L Gunderson, Frank J Steemers, Jeffrey S Fisher, Roberto Rigatti
  • Patent number: 11567060
    Abstract: Example nanopore sequencers include a cis well, a trans well, and a nanopore fluidically connecting the cis and trans wells. In one example sequencer, a modified electrolyte (including an electrolyte and a cation complexing agent) is present in the cis well, or the trans well, or in the cis and the trans wells. In another example sequencer, a gel state polyelectrolyte is present in the cis well, or the trans well, or in the cis and the trans wells.
    Type: Grant
    Filed: June 19, 2018
    Date of Patent: January 31, 2023
    Assignee: Illumina, Inc.
    Inventors: Boyan Boyanov, Rohan N. Akolkar, Jeffrey S. Fisher, Jeffrey G. Mandell, Liangliang Qiang, Steven M. Barnard
  • Publication number: 20230016633
    Abstract: Embodiments of the present application relate to substrate comprising a surface-bound azido functionalized organosilane wherein the substrate is free or substantially free of a hydrogel or a hydrophilic polymer. Methods of preparing such substrate surface for sequencing applications are also disclosed.
    Type: Application
    Filed: June 13, 2022
    Publication date: January 19, 2023
    Inventors: Xiaoyu Ma, Weixian Xi, Jeffrey S. Fisher, Fei Shen, Wayne N. George, Brian D. Mather
  • Publication number: 20230002822
    Abstract: An example of a flow cell includes a substrate; a first primer set attached to a first region on the substrate, the first primer set including an un-cleavable first primer and a cleavable second primer; and a second primer set attached to a second region on the substrate, the second primer set including a cleavable first primer and an un-cleavable second primer.
    Type: Application
    Filed: June 14, 2022
    Publication date: January 5, 2023
    Inventors: Jeffrey S. Fisher, Brian D. Mather, Maria Candelaria Rogert Bacigalupo, Justin Fullerton, Ludovic Vincent, Lewis J. Kraft, Sahngki Hong, Boyan Boyanov, M. Shane Bowen, Sang Park, Wayne N. George, Andrew A. Brown
  • Publication number: 20220410146
    Abstract: An example of a flow cell includes a substrate, which includes nano-depressions defined in a surface of the substrate, and interstitial regions separating the nano-depressions. A hydrophobic material layer has a surface that is at least substantially co-planar with the interstitial regions and is positioned to define a hydrophobic barrier around respective sub-sets of the nano-depressions.
    Type: Application
    Filed: August 29, 2022
    Publication date: December 29, 2022
    Inventors: Tarun Kumar Khurana, Arnaud Rival, Lewis J. Kraft, Steven Barnard, M. Shane Bowen, Xi-Jun Chen, Yir-Shyuan Wu, Jeffrey S. Fisher, Dajun Yuan
  • Publication number: 20220411859
    Abstract: Systems, methods, and compositions provided herein relate to preparation of beads encapsulating genetic material. Some embodiments include preparation of nucleic acid libraries within the bead, wherein the bead includes pores that allow diffusion of reagents while retaining genetic material.
    Type: Application
    Filed: August 1, 2018
    Publication date: December 29, 2022
    Inventors: Yir-Shyuan Wu, Xi-Jun Chen, Filiz Gorpe-Yasar, Falko Noé, Charles Lin, Tarun Kumar Khurana, Foad Mashayekhi, Pallavi Daggumati, Frank J Steemers, Kevin Gunderson, Jeffrey S Fisher
  • Publication number: 20220390348
    Abstract: An example of a flow cell includes a substrate; a plurality of reactive regions extending along the substrate; and a non-reactive region separating one of the plurality of reactive regions from an adjacent one of the plurality of reactive regions. Each of the plurality of reactive regions includes alternating first and second areas positioned along the reactive region. Each of the first areas includes a first primer set and each of the second areas includes a second primer set that is different than the first primer set. Either adjacent first and second areas directly abut each other, or) the first areas are positioned on protrusions and the second areas are positioned in depressions adjacent to the protrusions.
    Type: Application
    Filed: May 26, 2022
    Publication date: December 8, 2022
    Inventors: Eric M. Brustad, Craig Michael Ciesla, Jeffrey S. Fisher, Sahngki Hong, Lewis J. Kraft
  • Publication number: 20220331792
    Abstract: An example of a flow cell includes a substrate, which includes nano-depressions defined in a surface of the substrate, and interstitial regions separating the nano-depressions. A hydrophobic material layer has a surface that is at least substantially co-planar with the interstitial regions and is positioned to define a hydrophobic barrier around respective sub-sets of the nano-depressions.
    Type: Application
    Filed: April 26, 2022
    Publication date: October 20, 2022
    Inventors: Tarun Kumar Khurana, Arnaud Rival, Lewis J. Kraft, Steven Barnard, M. Shane Bowen, Xi-Jun Chen, Yir-Shyuan Wu, Jeffrey S. Fisher, Dajun Yuan