Patents by Inventor Yir-Shyuan Wu

Yir-Shyuan Wu 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: 20230407388
    Abstract: Described herein is a polynucleotide for use as a sequencing template comprising multiple inserts. Also described herein are method of generating and using these polynucleotides and methods of use of such templates, including analysis of contiguity information. Further, sequencing templates comprising an insert sequence and a copy of the insert sequence can be used to correct for random errors generated during sequencing or amplification or to identify nucleobase damage or other mutation that leads to non-canonical base pairing in a double-stranded nucleic acid. Methods of performing methylation analysis are also described herein.
    Type: Application
    Filed: April 20, 2023
    Publication date: December 21, 2023
    Applicants: Illumina, Inc., Illumina Cambridge Limited
    Inventors: Tarun Khurana, Yir-Shyuan Wu, Niall Anthony Gormley, Jonathan Mark Boutell
  • Patent number: 11834704
    Abstract: A method includes forming a patterned substrate including a plurality of base pads, using a nano-imprint lithography process. A capture substance is attached to each of the plurality of base pads, optionally through a linker, the capture substance being adapted to promote capture of a target molecule.
    Type: Grant
    Filed: December 7, 2020
    Date of Patent: December 5, 2023
    Assignee: Illumina, Inc.
    Inventors: M. Shane Bowen, Kevin L. Gunderson, Shengrong Lin, Maria Candelaria Rogert Bacigalupo, Kandaswamy Vijayan, Yir-Shyuan Wu, Bala Murali Venkatesan, James Tsay, John M. Beierle, Lorenzo Berti, Sang Ryul Park
  • 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
  • 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: 20230348974
    Abstract: Described herein are systems and methods for analyzing biological samples. Including a method for processing an analyte, comprising providing a fluidic device comprising the analyte and one or more polymer precursors; selecting a discrete area within said fluidic device; providing an energy source in optical communication with fluidic device; and selectively supplying a unit of energy generated from the energy source to the fluidic device to generate a polymer matrix within the fluidic device, wherein the polymer matrix is within the discrete area or adjacent to the discrete area.
    Type: Application
    Filed: July 7, 2023
    Publication date: November 2, 2023
    Inventors: Tarun Kumar KHURANA, Ali AGAH, Yir-Shyuan WU, Filiz Gorpe YASAR
  • 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: 20230242967
    Abstract: The disclosure provides methods to calibrate polynucleotide seeding efficiency in flow cells.
    Type: Application
    Filed: July 2, 2021
    Publication date: August 3, 2023
    Inventors: Yir-Shyuan Wu, Filiz Gorpe-Yasar, Jeff Fisher, Jeff Brodin
  • Patent number: 11702695
    Abstract: Embodiments provided herewith are directed to self-assembled methods of preparing a patterned surface for sequencing applications including, for example, a patterned flow cell or a patterned surface for digital fluidic devices. The methods utilize photolithography to create a patterned surface with a plurality of microscale or nanoscale contours, separated by hydrophobic interstitial regions, without the need of oxygen plasma treatment during the photolithography process. In addition, the methods avoid the use of any chemical or mechanical polishing steps after the deposition of a gel material to the contours.
    Type: Grant
    Filed: May 5, 2022
    Date of Patent: July 18, 2023
    Assignee: Illumina, Inc.
    Inventors: Yir-Shyuan Wu, Yan-You Lin, M. Shane Bowen, Cyril Delattre, Fabien Abeille, Tarun Khurana, Arnaud Rival, Poorya Sabounchi, Dajun Yuan, Maria Candelaria Rogert Bacigalupo
  • Publication number: 20230220462
    Abstract: Implementations of a method for seeding sequence libraries on a surface of a sequencing flow cell that allow for spatial segregation of the libraries on the surface are provided. The spatial segregation can be used to index sequence reads from individual sequencing libraries to increase efficiency of subsequent data analysis. In some examples, hydrogel beads containing encapsulated sequencing libraries are captured on a sequencing flow cell and degraded in the presence of a liquid diffusion barrier to allow for the spatial segregation and seeding of the sequencing libraries on the surface of the flow cell. Additionally, examples of systems, methods and compositions are provided relating to flow cell devices configured for nucleic acid library preparation and single cell sequencing. Some examples include flow cell devices having a hydrogel with genetic material disposed therein, and which is retained within the hydrogel during nucleic acid processing.
    Type: Application
    Filed: March 8, 2023
    Publication date: July 13, 2023
    Inventors: Tarun Kumar Khurana, Yir-Shyuan Wu, Xi-Jun Chen, Filiz Gorpe-Yasar, Yan-You Lin, Victoria Popic, Erich B. Jaeger, Mostafa Ronaghi
  • Patent number: 11697847
    Abstract: A detection apparatus that includes (a) an array of responsive pads on a substrate surface; (b) an array of pixels, wherein each pixel in the array has a detection zone on the surface that includes a subset of at least two of the pads; and (c) an activation circuit to apply a force at a first and second pad in the subset, wherein the activation circuit is configured to apply a different force at the first pad compared to the second pad, and wherein the activation circuit has a switch to selectively alter the force at the first pad and the second pad.
    Type: Grant
    Filed: April 1, 2020
    Date of Patent: July 11, 2023
    Assignee: ILLUMINA, INC.
    Inventors: Robert C. Kain, Tarun Khurana, Kevin L. Gunderson, Yir-Shyuan Wu
  • Publication number: 20230183682
    Abstract: This application describes methods of preparing an immobilized library of tagged RNA fragments. Also described herein are a number of methods of preparing DNA and RNA sequencing libraries from a single sample. These methods can include library preparation from single cells.
    Type: Application
    Filed: February 2, 2023
    Publication date: June 15, 2023
    Applicants: Illumina, Inc., Illumina Cambridge Limited
    Inventors: Niall Anthony Gormley, Andrew B. Kennedy, Robert Scott Kuersten, Gary Schroth, Carlo Randise-Hinchliff, Sarah E. Shultzaberger, Fiona Kaper, Yir-Shyuan Wu, Tarun Khurana, Foad Mashayekhi
  • Patent number: 11649498
    Abstract: Implementations of a method for seeding sequence libraries on a surface of a sequencing flow cell that allow for spatial segregation of the libraries on the surface are provided. The spatial segregation can be used to index sequence reads from individual sequencing libraries to increase efficiency of subsequent data analysis. In some examples, hydrogel beads containing encapsulated sequencing libraries are captured on a sequencing flow cell and degraded in the presence of a liquid diffusion barrier to allow for the spatial segregation and seeding of the sequencing libraries on the surface of the flow cell. Additionally, examples of systems, methods and compositions are provided relating to flow cell devices configured for nucleic acid library preparation and single cell sequencing. Some examples include flow cell devices having a hydrogel with genetic material disposed therein, and which is retained within the hydrogel during nucleic acid processing.
    Type: Grant
    Filed: April 13, 2022
    Date of Patent: May 16, 2023
    Assignee: ILLUMINA, INC.
    Inventors: Tarun Kumar Khurana, Yir-Shyuan Wu, Xi-Jun Chen, Filiz Gorpe-Yasar, Yan-You Lin, Victoria Popic, Erich B. Jaeger, Mostafa Ronaghi
  • Publication number: 20230063675
    Abstract: An example of a sequencing kit includes a flow cell and an encapsulation matrix precursor composition. The flow cell includes a plurality of chambers and primers attached within each of the plurality of chambers. The encapsulation matrix precursor composition consists of a fluid and a polymer selected from the group consisting of agar, agarose, alginate, heparin, alginate sulfate, dextran sulfate, hyaluronan, pectin, carrageenan, gelatin, chitosan, cellulose, a collagen polymer, and combinations thereof.
    Type: Application
    Filed: October 31, 2022
    Publication date: March 2, 2023
    Inventors: Xi-Jun Chen, Yir-Shyuan Wu, Tarun Kumar Khurana, Liangliang Qiang, Andrew J. Price, Elisabet Rosas
  • Patent number: 11554370
    Abstract: Described herein are systems and methods for analyzing biological samples. Including a method for processing an analyte, comprising providing a fluidic device comprising the analyte and one or more polymer precursors; selecting a discrete area within said fluidic device; providing an energy source in optical communication with fluidic device; and selectively supplying a unit of energy generated from the energy source to the fluidic device to generate a polymer matrix within the fluidic device, wherein the polymer matrix is within the discrete area or adjacent to the discrete area.
    Type: Grant
    Filed: April 7, 2022
    Date of Patent: January 17, 2023
    Assignee: Cellanome, Inc.
    Inventors: Tarun Kumar Khurana, Ali Agah, Yir-Shyuan Wu, Filiz Gorpe Yasar
  • Publication number: 20230001413
    Abstract: Described herein are systems and methods for analyzing biological samples. Including a method for processing an analyte, comprising providing a fluidic device comprising the analyte and one or more polymer precursors; selecting a discrete area within said fluidic device; providing an energy source in optical communication with fluidic device; and selectively supplying a unit of energy generated from the energy source to the fluidic device to generate a polymer matrix within the fluidic device, wherein the polymer matrix is within the discrete area or adjacent to the discrete area.
    Type: Application
    Filed: August 26, 2022
    Publication date: January 5, 2023
    Inventors: Tarun Kumar KHURANA, Ali AGAH, Yir-Shyuan WU, Filiz Gorpe YASAR
  • 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: 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
  • Patent number: 11535890
    Abstract: An example of a sequencing kit includes a flow cell, an encapsulation matrix precursor composition, and a radical initiator. The flow cell includes a plurality of chambers and primers attached within each of the plurality of chambers. The encapsulation matrix precursor composition consists of a fluid, a monomer or polymer including a radical generating and chain elongating functional group, a radical source, and a crosslinker. The radical initiator is part of the encapsulation matrix precursor composition or is a separate component.
    Type: Grant
    Filed: January 23, 2020
    Date of Patent: December 27, 2022
    Assignee: Illumina, Inc.
    Inventors: Xi-Jun Chen, Yir-Shyuan Wu, Tarun Kumar Khurana, Liangliang Qiang, Andrew J. Price, Elisabet Rosas
  • Patent number: 11499192
    Abstract: An example of a sequencing kit includes a flow cell, an encapsulation matrix precursor composition, and a radical initiator. The flow cell includes a plurality of chambers and primers attached within each of the plurality of chambers. The encapsulation matrix precursor composition consists of a fluid, a monomer or polymer including a radical generating and chain elongating functional group, a radical source, and a crosslinker. The radical initiator is part of the encapsulation matrix precursor composition or is a separate component.
    Type: Grant
    Filed: January 23, 2020
    Date of Patent: November 15, 2022
    Assignee: Illumina, Inc.
    Inventors: Xi-Jun Chen, Yir-Shyuan Wu, Tarun Kumar Khurana, Liangliang Qiang, Andrew J. Price, Elisabet Rosas