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: 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
  • Patent number: 10981170
    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: May 8, 2020
    Date of Patent: April 20, 2021
    Assignee: Plexium, Inc.
    Inventors: Kandaswamy Vijayan, Andrew Boyd MacConnell, Joseph Franklin Rokicki, Michael Van Nguyen
  • Publication number: 20210108258
    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: Application
    Filed: December 7, 2020
    Publication date: April 15, 2021
    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: 10975427
    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: Grant
    Filed: January 17, 2018
    Date of Patent: April 13, 2021
    Assignee: OMNIOME, INC.
    Inventors: Corey M. Dambacher, Joseph Rokicki, Keunho Ahn, Brittany Ann Rohrman, Michael Nguyen, Kandaswamy Vijayan
  • Patent number: 10946383
    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: August 7, 2019
    Date of Patent: March 16, 2021
    Assignee: Plexium, Inc.
    Inventors: Kandaswamy Vijayan, Andrew Boyd MacConnell, Joseph Franklin Rokicki
  • Patent number: 10828643
    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: August 7, 2019
    Date of Patent: November 10, 2020
    Assignee: Plexium, Inc.
    Inventors: Kandaswamy Vijayan, Andrew Boyd MacConnell, Joseph Franklin Rokicki
  • Publication number: 20200347451
    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: Application
    Filed: April 9, 2020
    Publication date: November 5, 2020
    Inventors: Sean STROMBERG, John VIECELI, Kandaswamy VIJAYAN, Arnold OLIPHANT
  • Publication number: 20200324287
    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: May 8, 2020
    Publication date: October 15, 2020
    Applicant: Plexium, Inc.
    Inventors: Kandaswamy VIJAYAN, Andrew Boyd MACCONNELL, Joseph Franklin ROKICKI, Michael VAN NGUYEN
  • Publication number: 20200224251
    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: Application
    Filed: March 19, 2020
    Publication date: July 16, 2020
    Applicant: Omniome, Inc.
    Inventors: Pinar IYIDOGAN, Kandaswamy VIJAYAN
  • Publication number: 20200199668
    Abstract: Provided are sequencing-by-binding methods of detecting cognate nucleotides using a crippled DNA polymerizing enzyme that possesses the ability to bind the next correct nucleotide downstream of a primer in a template-dependent fashion, but does not possess the activity needed to promote phosphodiester bond formation. Use of the crippled DNA polymerase permits interrogation of one nucleotide at a time, without incorporation of any nucleotide. Labeled nucleotides, such as fluorescently labeled nucleotides, can be used in conjunction with the crippled DNA polymerase to establish cognate nucleotide identity in a rapid manner.
    Type: Application
    Filed: January 7, 2020
    Publication date: June 25, 2020
    Applicant: Omniome, Inc.
    Inventors: Kandaswamy VIJAYAN, Pinar IYIDOGAN
  • Patent number: 10655176
    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: October 8, 2018
    Date of Patent: May 19, 2020
    Assignee: OMNIOME, INC.
    Inventors: Sean Stromberg, John Vieceli, Kandaswamy Vijayan, Arnold Oliphant
  • Publication number: 20200131486
    Abstract: Provided are engineered DNA polymerases exhibiting modified functionality, and polynucleotides encoding same. Modified features include: (1) reduced catalytic activity in the presence of magnesium ions and/or (2) reduced affinity for primed template nucleic acid molecules in the absence of cognate nucleotide, and an ability to discriminate between cognate and non-cognate nucleotides under low salt conditions. Sequencing By Binding™ procedures employing the engineered polymerases have certain advantages. The engineered polymerases can have other uses as well.
    Type: Application
    Filed: January 9, 2020
    Publication date: April 30, 2020
    Applicant: Omniome, inc.
    Inventors: Pinar IYIDOGAN, Mark C. WALLEN, Ying L. LIU, Kandaswamy VIJAYAN
  • Patent number: 10633692
    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: April 2, 2019
    Date of Patent: April 28, 2020
    Assignee: OMNIOME, INC.
    Inventors: Pinar Iyidogan, Kandaswamy Vijayan
  • Patent number: 10597643
    Abstract: Provided are engineered DNA polymerases exhibiting modified functionality, and polynucleotides encoding same. Modified features include: (1) reduced catalytic activity in the presence of magnesium ions and/or (2) reduced affinity for primed template nucleic acid molecules in the absence of cognate nucleotide, and an ability to discriminate between cognate and non-cognate nucleotides under low salt conditions. Sequencing By Binding™ procedures employing the engineered polymerases have certain advantages. The engineered polymerases can have other uses as well.
    Type: Grant
    Filed: January 9, 2018
    Date of Patent: March 24, 2020
    Assignee: OMNIOME, INC.
    Inventors: Pinar Iyidogan, Mark C. Wallen, Ying L. Liu, Kandaswamy Vijayan
  • Patent number: 10584379
    Abstract: Provided are sequencing-by-binding methods of detecting cognate nucleotides using a crippled DNA polymerizing enzyme that possesses the ability to bind the next correct nucleotide downstream of a primer in a template-dependent fashion, but does not possess the activity needed to promote phosphodiester bond formation. Use of the crippled DNA polymerase permits interrogation of one nucleotide at a time, without incorporation of any nucleotide. Labeled nucleotides, such as fluorescently labeled nucleotides, can be used in conjunction with the crippled DNA polymerase to establish cognate nucleotide identity in a rapid manner.
    Type: Grant
    Filed: April 28, 2017
    Date of Patent: March 10, 2020
    Assignee: OMNIOME, INC.
    Inventors: Kandaswamy Vijayan, Pinar Iyidogan