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).
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Patent number: 11168364Abstract: 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: GrantFiled: September 13, 2019Date of Patent: November 9, 2021Assignee: OMNIOME, INC.Inventors: Kandaswamy Vijayan, Corey M. Dambacher, Eugene Tu, Mark A. Bernard, Joseph Rokicki, Kerry Wilson
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Publication number: 20210340612Abstract: 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: ApplicationFiled: March 3, 2021Publication date: November 4, 2021Applicant: Omniome, Inc.Inventors: Corey M. DAMBACHER, Joseph ROKICKI, Keunho AHN, Brittany Ann ROHRMAN, Michael NGUYEN, Kandaswamy VIJAYAN
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Patent number: 11084037Abstract: 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: GrantFiled: September 24, 2018Date of Patent: August 10, 2021Assignee: Plexium, Inc.Inventors: Kandaswamy Vijayan, Andrew Boyd MacConnell, Joseph Franklin Rokicki
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Publication number: 20210229087Abstract: Disclosed is an assay device comprising a high density of wells aligned thereon.Type: ApplicationFiled: January 28, 2020Publication date: July 29, 2021Inventors: Yi ZHANG, Jesse LU, Alex PRICE, Pengyu YANG, Kandaswamy VIJAYAN
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Patent number: 11060135Abstract: 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: GrantFiled: August 30, 2018Date of Patent: July 13, 2021Assignee: 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
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Patent number: 11027272Abstract: 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: GrantFiled: January 28, 2020Date of Patent: June 8, 2021Assignee: Plexium, Inc.Inventors: Kandaswamy Vijayan, Kapil Mahakalkar, Yi Zhang
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Patent number: 10981170Abstract: 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: GrantFiled: May 8, 2020Date of Patent: April 20, 2021Assignee: Plexium, Inc.Inventors: Kandaswamy Vijayan, Andrew Boyd MacConnell, Joseph Franklin Rokicki, Michael Van Nguyen
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Publication number: 20210108258Abstract: 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: ApplicationFiled: December 7, 2020Publication date: April 15, 2021Inventors: 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
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Patent number: 10975427Abstract: 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: GrantFiled: January 17, 2018Date of Patent: April 13, 2021Assignee: OMNIOME, INC.Inventors: Corey M. Dambacher, Joseph Rokicki, Keunho Ahn, Brittany Ann Rohrman, Michael Nguyen, Kandaswamy Vijayan
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Patent number: 10946383Abstract: 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: GrantFiled: August 7, 2019Date of Patent: March 16, 2021Assignee: Plexium, Inc.Inventors: Kandaswamy Vijayan, Andrew Boyd MacConnell, Joseph Franklin Rokicki
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Patent number: 10828643Abstract: 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: GrantFiled: August 7, 2019Date of Patent: November 10, 2020Assignee: Plexium, Inc.Inventors: Kandaswamy Vijayan, Andrew Boyd MacConnell, Joseph Franklin Rokicki
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Publication number: 20200347451Abstract: 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: ApplicationFiled: April 9, 2020Publication date: November 5, 2020Inventors: Sean STROMBERG, John VIECELI, Kandaswamy VIJAYAN, Arnold OLIPHANT
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Publication number: 20200324287Abstract: 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: ApplicationFiled: May 8, 2020Publication date: October 15, 2020Applicant: Plexium, Inc.Inventors: Kandaswamy VIJAYAN, Andrew Boyd MACCONNELL, Joseph Franklin ROKICKI, Michael VAN NGUYEN
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Publication number: 20200224251Abstract: 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: ApplicationFiled: March 19, 2020Publication date: July 16, 2020Applicant: Omniome, Inc.Inventors: Pinar IYIDOGAN, Kandaswamy VIJAYAN
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Publication number: 20200199668Abstract: 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: ApplicationFiled: January 7, 2020Publication date: June 25, 2020Applicant: Omniome, Inc.Inventors: Kandaswamy VIJAYAN, Pinar IYIDOGAN
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Patent number: 10655176Abstract: 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: GrantFiled: October 8, 2018Date of Patent: May 19, 2020Assignee: OMNIOME, INC.Inventors: Sean Stromberg, John Vieceli, Kandaswamy Vijayan, Arnold Oliphant
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Publication number: 20200131486Abstract: 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: ApplicationFiled: January 9, 2020Publication date: April 30, 2020Applicant: Omniome, inc.Inventors: Pinar IYIDOGAN, Mark C. WALLEN, Ying L. LIU, Kandaswamy VIJAYAN
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Patent number: 10633692Abstract: 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: GrantFiled: April 2, 2019Date of Patent: April 28, 2020Assignee: OMNIOME, INC.Inventors: Pinar Iyidogan, Kandaswamy Vijayan
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Patent number: 10597643Abstract: 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: GrantFiled: January 9, 2018Date of Patent: March 24, 2020Assignee: OMNIOME, INC.Inventors: Pinar Iyidogan, Mark C. Wallen, Ying L. Liu, Kandaswamy Vijayan
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Patent number: 10584379Abstract: 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: GrantFiled: April 28, 2017Date of Patent: March 10, 2020Assignee: OMNIOME, INC.Inventors: Kandaswamy Vijayan, Pinar Iyidogan