Patents by Inventor Kandaswamy Vijayan

Kandaswamy Vijayan 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).

  • Patent number: 11499185
    Abstract: The present disclosure provides compositions, methods and systems for sequencing a template nucleic acid using a polymerase based, nucleic acid binding reaction involving examination of the interaction between a polymerase and template nucleic acid in the presence of one or more unlabeled nucleotides. The methods rely, in part, on identifying a base of a template nucleic acid during nucleic acid synthesis by controlling the sequencing reaction conditions. Template nucleic acid bases may be identified during an examination step followed by an optional incorporation step.
    Type: Grant
    Filed: July 26, 2018
    Date of Patent: November 15, 2022
    Assignee: PACIFIC BIOSCIENCES OF CALIFORNIA, INC.
    Inventors: Kandaswamy Vijayan, Eugene Tu, Mark A. Bernard
  • Publication number: 20220298553
    Abstract: Method of identifying a cognate nucleotide (i.e., the “next correct nucleotide”) for a primed template nucleic acid molecule. In some embodiments, an ordered or random array of primed target nucleic acids characterized by different cognate nucleotides can be evaluated using a single imaging step to identify different cognate nucleotides for a collection of different primed template nucleic acid molecules. An optional incorporation step can follow the identifying step. A polymerase different from the ones used in the binding and examination steps can be used to incorporate a nucleotide, such as a reversible terminator nucleotide, preliminary to identification of the next cognate nucleotide.
    Type: Application
    Filed: December 29, 2021
    Publication date: September 22, 2022
    Applicant: Omniome, Inc.
    Inventors: Corey M. DAMBACHER, Devon CAYER, Richard LECOULTRE, Joseph ROKICKI, Kerry WILSON, Eugene TU, Kandaswamy VIJAYAN
  • Patent number: 11447823
    Abstract: A method of determining a nucleic acid sequence that includes steps of: (a) contacting a primed template nucleic acid with a series of mixtures for forming ternary complexes, wherein each of the mixtures includes a polymerase and nucleotide cognates for at least two different base types suspected of being present at the next template position of the template nucleic acid; (b) monitoring the next template position for ternary complexes formed by the series of mixtures, wherein a signal state indicates presence or absence of ternary complex formed at the next template position by each individual mixture, thereby determining a series of signal states that encodes a base call for the next template position; and (c) decoding the series of signal states to distinguish a correct base call for the next template position from an error in the base call.
    Type: Grant
    Filed: April 9, 2020
    Date of Patent: September 20, 2022
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Sean Stromberg, John Vieceli, Kandaswamy Vijayan, Arnold Oliphant
  • Publication number: 20220243261
    Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.
    Type: Application
    Filed: January 13, 2022
    Publication date: August 4, 2022
    Applicant: Illumina, Inc.
    Inventors: Min-Jui Richard Shen, Jonathan Mark Boutell, Kathryn M. Stephens, Mostafa Ronaghi, Kevin L. Gunderson, Bala Murali Venkatesan, M. Shane Bowen, Kandaswamy Vijayan
  • Publication number: 20220203357
    Abstract: Disclosed is an assay device comprising a high density of wells aligned thereon.
    Type: Application
    Filed: March 18, 2022
    Publication date: June 30, 2022
    Inventors: Yi Zhang, Jesse Lu, Alex Price, Pengyu Yang, Kandaswamy Vijayan
  • Publication number: 20220162690
    Abstract: Provided are compositions, methods and systems for determining the sequence of a template nucleic acid using a polymerase-based, sequencing-by-binding procedure. An examination step involves monitoring the interaction between a polymerase and template nucleic acid in the presence of one or more nucleotides. Identity of the next correct nucleotide in the sequence is determined without incorporation of any nucleotide into the structure of the primer by formation of a phosphodiester bond. An optional incorporation step can be used after the examination step to extend the primer by one or more nucleotides, thereby incrementing the template nucleotides that can be examined in a subsequent examination step. The sequencing-by-binding procedure does not require the use of labeled nucleotides or polymerases, but optionally can employ these reagents.
    Type: Application
    Filed: October 6, 2021
    Publication date: May 26, 2022
    Inventors: Kandaswamy VIJAYAN, Corey M. DAMBACHER, Eugene TU, Mark A. BERNARD, Joseph ROKICKI, Kerry WILSON
  • Patent number: 11326206
    Abstract: The present disclosure provides compositions, methods and systems for quantifying target sequences and identifying target sequence variants.
    Type: Grant
    Filed: April 6, 2017
    Date of Patent: May 10, 2022
    Assignee: PACIFIC BIOSCIENCES OF CALIFORNIA, INC.
    Inventors: Yi Zhang, Steven Brentano, Eugene Tu, Kandaswamy Vijayan
  • Patent number: 11305288
    Abstract: Disclosed is an assay device comprising a high density of wells aligned thereon.
    Type: Grant
    Filed: January 28, 2020
    Date of Patent: April 19, 2022
    Assignee: Plexium, Inc.
    Inventors: Yi Zhang, Jesse Lu, Alex Price, Pengyu Yang, Kandaswamy Vijayan
  • Patent number: 11254976
    Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.
    Type: Grant
    Filed: August 19, 2019
    Date of Patent: February 22, 2022
    Assignee: Illumina, Inc.
    Inventors: Min-Jui Richard Shen, Jonathan Mark Boutell, Kathryn M. Stephens, Mostafa Ronaghi, Kevin L. Gunderson, Bala Murali Venkatesan, M. Shane Bowen, Kandaswamy Vijayan
  • Patent number: 11248254
    Abstract: Method of identifying a cognate nucleotide (i.e., the “next correct nucleotide”) for a primed template nucleic acid molecule. In some embodiments, an ordered or random array of primed target nucleic acids characterized by different cognate nucleotides can be evaluated using a single imaging step to identify different cognate nucleotides for a collection of different primed template nucleic acid molecules. An optional incorporation step can follow the identifying step. A polymerase different from the ones used in the binding and examination steps can be used to incorporate a nucleotide, such as a reversible terminator nucleotide, preliminary to identification of the next cognate nucleotide.
    Type: Grant
    Filed: December 21, 2017
    Date of Patent: February 15, 2022
    Assignee: OMNIOME, INC.
    Inventors: Corey M. Dambacher, Devon Cayer, Richard LeCoultre, Joseph Rokicki, Kerry Wilson, Eugene Tu, Kandaswamy Vijayan
  • Publication number: 20220025358
    Abstract: This application provides a bead with a covalently attached chemical compound and a covalently attached DNA barcode and methods for using such beads. The bead has many substantially identical copies of the chemical compound and many substantially identical copies of the DNA barcode. The compound consists of one or more chemical monomers, where the DNA barcode takes the form of barcode modules, where each module corresponds to and allows identification of a corresponding chemical monomer. The nucleic acid barcode can have a concatenated structure or an orthogonal structure. Provided are method for sequencing the bead-bound nucleic acid barcode, for cleaving the compound from the bead, and for assessing biological activity of the released compound.
    Type: Application
    Filed: March 12, 2021
    Publication date: January 27, 2022
    Inventors: Kandaswamy VIJAYAN, Andrew Boyd MACCONNELL, Joseph Franklin ROKICKI, Michael VAN NGUYEN
  • Publication number: 20210394178
    Abstract: This application provides a bead with a covalently attached chemical compound and a covalently attached DNA barcode and methods for using such beads. The bead has many substantially identical copies of the chemical compound and many substantially identical copies of the DNA barcode. The compound consists of one or more chemical monomers, where the DNA barcode takes the form of barcode modules, where each module corresponds to and allows identification of a corresponding chemical monomer. The nucleic acid barcode can have a concatenated structure or an orthogonal structure. Provided are method for sequencing the bead-bound nucleic acid barcode, for cleaving the compound from the bead, and for assessing biological activity of the released compound.
    Type: Application
    Filed: April 21, 2021
    Publication date: December 23, 2021
    Inventors: Kandaswamy Vijayan, Andrew Boyd MacConnell, Joseph Franklin Rokicki
  • Patent number: 11203779
    Abstract: Provided are methods and systems for reducing the time needed for sequencing nucleic acids. The approach relies on detecting formation of nucleotide-specific ternary complexes comprising a polymerase (e.g., a DNA polymerizing enzyme), a primed template nucleic acid molecule, and a nucleotide complementary to the templated base of the primed template nucleic acid. The methods and systems facilitate determination of the next correct nucleotide, as well as the subsequent next correct nucleotide from a cycle of examining four different nucleotides without requiring chemical incorporation of any nucleotide into the primer.
    Type: Grant
    Filed: August 14, 2019
    Date of Patent: December 21, 2021
    Assignee: OMNIONIE, INC.
    Inventors: Pinar Iyidogan, Kandaswamy Vijayan
  • Patent number: 11203778
    Abstract: Provided are methods and systems for detecting formation of nucleotide-specific ternary complexes comprising a DNA polymerase, a nucleic acid, and a nucleotide complementary to the templated base of the primed template nucleic acid. The methods and systems facilitate determination of the next correct nucleotide without requiring chemical incorporation of the nucleotide into the primer. These results can even be achieved in procedures employing unlabeled, native nucleotides.
    Type: Grant
    Filed: March 19, 2020
    Date of Patent: December 21, 2021
    Assignee: OMNIOME, INC.
    Inventors: Pinar Iyidogan, Kandaswamy Vijayan
  • Patent number: 11168364
    Abstract: Provided are compositions, methods and systems for determining the sequence of a template nucleic acid using a polymerase-based, sequencing-by-binding procedure. An examination step involves monitoring the interaction between a polymerase and template nucleic acid in the presence of one or more nucleotides. Identity of the next correct nucleotide in the sequence is determined without incorporation of any nucleotide into the structure of the primer by formation of a phosphodiester bond. An optional incorporation step can be used after the examination step to extend the primer by one or more nucleotides, thereby incrementing the template nucleotides that can be examined in a subsequent examination step. The sequencing-by-binding procedure does not require the use of labeled nucleotides or polymerases, but optionally can employ these reagents.
    Type: Grant
    Filed: September 13, 2019
    Date of Patent: November 9, 2021
    Assignee: OMNIOME, INC.
    Inventors: Kandaswamy Vijayan, Corey M. Dambacher, Eugene Tu, Mark A. Bernard, Joseph Rokicki, Kerry Wilson
  • Publication number: 20210340612
    Abstract: Method and composition for identifying cognate nucleotides in a Sequencing By Binding™ procedure, wherein one or more labeled nucleotides are detected in ternary complexes but never incorporated. Labeled nucleotides can be incorporable nucleotides that contact preformed blocked primed template nucleic acids. Alternatively, labeled nucleotides are labeled non-incorporable nucleotides. Labeled nucleotides, including labeled non-incorporable nucleotides, can be detected in ternary complexes in the same reaction mixture that incorporates a reversible terminator nucleotide to create a blocked primed template nucleic acid. Detection of ternary complexes can take place in the presence of a catalytic metal ion.
    Type: Application
    Filed: March 3, 2021
    Publication date: November 4, 2021
    Applicant: Omniome, Inc.
    Inventors: Corey M. DAMBACHER, Joseph ROKICKI, Keunho AHN, Brittany Ann ROHRMAN, Michael NGUYEN, Kandaswamy VIJAYAN
  • Patent number: 11084037
    Abstract: This application provides a bead with a covalently attached chemical compound and a covalently attached DNA barcode and methods for using such beads. The bead has many substantially identical copies of the chemical compound and many substantially identical copies of the DNA barcode. The compound consists of one or more chemical monomers, where the DNA barcode takes the form of barcode modules, where each module corresponds to and allows identification of a corresponding chemical monomer. The nucleic acid barcode can have a concatenated structure or an orthogonal structure. Provided are method for sequencing the bead-bound nucleic acid barcode, for cleaving the compound from the bead, and for assessing biological activity of the released compound.
    Type: Grant
    Filed: September 24, 2018
    Date of Patent: August 10, 2021
    Assignee: Plexium, Inc.
    Inventors: Kandaswamy Vijayan, Andrew Boyd MacConnell, Joseph Franklin Rokicki
  • Publication number: 20210229087
    Abstract: Disclosed is an assay device comprising a high density of wells aligned thereon.
    Type: Application
    Filed: January 28, 2020
    Publication date: July 29, 2021
    Inventors: Yi ZHANG, Jesse LU, Alex PRICE, Pengyu YANG, Kandaswamy VIJAYAN
  • Patent number: 11060135
    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: August 30, 2018
    Date of Patent: July 13, 2021
    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
  • Patent number: 11027272
    Abstract: Disclosed are transfer dispensers for assay devices. These dispensers provide for transfer of a single assay component into a single well in the assay device. This ensures that the assay conducted in each well contains only a single component.
    Type: Grant
    Filed: January 28, 2020
    Date of Patent: June 8, 2021
    Assignee: Plexium, Inc.
    Inventors: Kandaswamy Vijayan, Kapil Mahakalkar, Yi Zhang