Patents by Inventor Mark S. Chee

Mark S. Chee 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: 11286515
    Abstract: The present disclosure provides methods and assay systems for use in spatially encoded biological assays, including assays to determine a spatial pattern of abundance, expression, and/or activity of one or more biological targets across multiple sites in a sample. In particular, the biological targets comprise proteins, and the methods and assay systems do not depend on imaging techniques for the spatial information of the targets. The present disclosure provides methods and assay systems capable of high levels of multiplexing where reagents are provided to a biological sample in order to address tag the sites to which reagents are delivered; instrumentation capable of controlled delivery of reagents; and a decoding scheme providing a readout that is digital in nature.
    Type: Grant
    Filed: June 25, 2021
    Date of Patent: March 29, 2022
    Assignee: Prognosys Biosciences, Inc.
    Inventors: Mark S. Chee, David A. Routenberg
  • Publication number: 20220049246
    Abstract: Provided herein are methods for preparing and treating an analyte (e.g., a macromolecule or a plurality of macromolecules, peptides, polypeptides, and proteins) for analysis. In some embodiments, the analyte is prepared and treated in a method that includes the use of bait and capture nucleic acids, solid supports, and reaction mixtures including the bait and capture nucleic acids. In some embodiments, the analyte is coupled to a solid support. Also provided are kits containing components for performing the provided methods for preparing the analytes. In some embodiments, the methods are for preparing an analyte for sequencing. Provided herein are methods for preparing and treating an analyte (e.g., a macromolecule or a plurality of macromolecules, peptides, polypeptides, and proteins) for analysis. In some embodiments, the analyte is prepared and treated in a method that includes the use of bait and capture nucleic acids, solid supports, and reaction mixtures including the bait and capture nucleic acids.
    Type: Application
    Filed: August 26, 2021
    Publication date: February 17, 2022
    Applicant: Encodia, Inc.
    Inventors: Mark S Chee, Kevin L. Gunderson, Norihito Muranaka, Brian T. Weinert
  • Patent number: 11231419
    Abstract: Provided herein are compositions and methods for detecting the binding of a peptide to an MHC molecule, and the binding of a peptide:MHC complex to a TCR. In preferred embodiments, the compositions and methods are in a highly-multiplexed way. The compositions and methods disclosed herein can be used to provide direct information on which peptides are bound to an MHC molecule. Also provided is a method for simultaneously detecting a large number of peptides for binding to an MHC molecule and/or a T cell. A method for detecting competitive binding of a large number of peptides to an MHC molecule and/or a T cell is also disclosed. Also provided herein is a method for simultaneously detecting a large number of specific TCRs. The compositions and methods of the present invention are useful for vaccine design, research and monitoring of autoimmune and infectious disease, immunogenicity testing of therapeutics, and tissue typing.
    Type: Grant
    Filed: March 14, 2014
    Date of Patent: January 25, 2022
    Assignee: Prognosys Biosciences, Inc.
    Inventors: John Andrew Altin, Mark S. Chee
  • Publication number: 20220003755
    Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.
    Type: Application
    Filed: September 21, 2021
    Publication date: January 6, 2022
    Applicant: Prognosys Biosciences, Inc.
    Inventor: Mark S. Chee
  • Publication number: 20210405058
    Abstract: A method for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding is disclosed.
    Type: Application
    Filed: August 27, 2021
    Publication date: December 30, 2021
    Applicant: Encodia, Inc.
    Inventors: Mark S. CHEE, Kevin L. GUNDERSON, Michael Phillip Weiner
  • Patent number: 11208684
    Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.
    Type: Grant
    Filed: April 6, 2021
    Date of Patent: December 28, 2021
    Assignee: Prognosys Biosciences, Inc.
    Inventor: Mark S. Chee
  • Publication number: 20210396762
    Abstract: The present disclosure relates to methods and kits for analysis of peptides, polypeptides and proteins, employing a multi-component detection agent(s). In some embodiments, the method is useful for identifying the terminal amino acid of the peptide. In some embodiments, the multi-component detection agent includes a first detection agent and second detection agent which, when in proximity, is capable of generating a detectable signal.
    Type: Application
    Filed: June 15, 2021
    Publication date: December 23, 2021
    Applicant: Encodia, Inc.
    Inventors: Mark S. CHEE, Michael Phillip WEINER
  • Publication number: 20210355483
    Abstract: Methods and Kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and/or nucleic acid recording of a molecular interaction and/or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Assays that do not require the cyclic transfer of information between a coding tag and a recording tag are also disclosed, including single cycle assays.
    Type: Application
    Filed: October 31, 2018
    Publication date: November 18, 2021
    Applicant: Encodia, Inc.
    Inventors: Mark S. CHEE, Kevin GUNDERSON, Michael Phillip WEINER, Lei SHI, Norihito MURANAKA
  • Patent number: 11156603
    Abstract: Provided herein are methods of identifying a target protein in a tissue sample that include delivering a plurality of probes to a tissue sample, where a probe of the plurality of probes comprises an antibody conjugated to an oligonucleotide having a sequence, where the antibody specifically binds to the target protein in the tissue sample; amplifying the oligonucleotide to generate an amplicon comprising copies of the oligonucleotide; detecting all or a portion of a copy of the oligonucleotide in the amplicon; and using the detected sequence to identify the target protein in the tissue sample.
    Type: Grant
    Filed: May 14, 2021
    Date of Patent: October 26, 2021
    Assignee: Prognosys Biosciences, Inc.
    Inventor: Mark S. Chee
  • Publication number: 20210317510
    Abstract: The present disclosure provides methods and assay systems for use in spatially encoded biological assays, including assays to determine a spatial pattern of abundance, expression, and/or activity of one or more biological targets across multiple sites in a sample. In particular, the biological targets comprise proteins, and the methods and assay systems do not depend on imaging techniques for the spatial information of the targets. The present disclosure provides methods and assay systems capable of high levels of multiplexing where reagents are provided to a biological sample in order to address tag the sites to which reagents are delivered; instrumentation capable of controlled delivery of reagents; and a decoding scheme providing a readout that is digital in nature.
    Type: Application
    Filed: June 25, 2021
    Publication date: October 14, 2021
    Applicant: Prognosys Biosciences, Inc.
    Inventors: Mark S. CHEE, David A. ROUTENBERG
  • Publication number: 20210302431
    Abstract: A method for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding is disclosed.
    Type: Application
    Filed: March 10, 2021
    Publication date: September 30, 2021
    Applicant: Encodia, Inc.
    Inventors: Mark S. CHEE, Kevin L. GUNDERSON, Michael Phillip Weiner
  • Publication number: 20210269864
    Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.
    Type: Application
    Filed: May 17, 2021
    Publication date: September 2, 2021
    Applicant: Prognosys Biosciences, Inc.
    Inventor: Mark S. CHEE
  • Publication number: 20210270822
    Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.
    Type: Application
    Filed: May 14, 2021
    Publication date: September 2, 2021
    Applicant: Prognosys Biosciences, Inc.
    Inventor: Mark S. Chee
  • Publication number: 20210255175
    Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.
    Type: Application
    Filed: May 3, 2021
    Publication date: August 19, 2021
    Applicant: Prognosys Biosciences, Inc.
    Inventor: Mark S. CHEE
  • Publication number: 20210254047
    Abstract: The present disclosure relates to methods for assessing identity and spatial relationship between a polypeptide and a moiety in a sample. In some embodiments, both the polypeptide and the moiety are parts of a larger polypeptide, and the present methods can be used assess identity and spatial relationship between the polypeptide and the moiety in the same polypeptide or protein. In other embodiments, the polypeptide and the moiety belong to different molecules, and the present methods can be used assess identity and spatial relationship between the polypeptide and the moiety different molecules, e.g., in a protein-protein complex, a protein-DNA complex or a protein-KNA complex.
    Type: Application
    Filed: September 4, 2019
    Publication date: August 19, 2021
    Applicant: Encodia, Inc.
    Inventors: Mark S. CHEE, Kevin L. GUNDERSON
  • Patent number: 11092601
    Abstract: Provided herein are compositions and methods for detecting the binding of a peptide to an MHC molecule, and the binding of a peptide:MHC complex to a TCR. In preferred embodiments, the compositions and methods are in a highly-multiplexed way. The compositions and methods disclosed herein can be used to provide direct information on which peptides are bound to an MHC molecule. Also provided is a method for simultaneously detecting a large number of peptides for binding to an MHC molecule and/or a T cell. A method for detecting competitive binding of a large number of peptides to an MHC molecule and/or a T cell is also disclosed. Also provided herein is a method for simultaneously detecting a large number of specific TCRs. The compositions and methods of the present invention are useful for vaccine design, research and monitoring of autoimmune and infectious disease, immunogenicity testing of therapeutics, and tissue typing.
    Type: Grant
    Filed: May 21, 2019
    Date of Patent: August 17, 2021
    Assignee: Prognosys Biosciences, Inc.
    Inventors: John Andrew Altin, Mark S. Chee
  • Publication number: 20210238671
    Abstract: The present invention provides oligonucleotide constructs, sets of such oligonucleotide constructs, and methods of using such oligonucleotide constructs to provide validated sequences or sets of validated sequences corresponding to desired ROIs. Such validated ROIs and constructs containing these have a wide variety of uses, including in synthetic biology, quantitative nucleic acid analysis, polymorphism and/or mutation screening, and the like.
    Type: Application
    Filed: April 22, 2021
    Publication date: August 5, 2021
    Applicant: Prognosys Biosciences, Inc.
    Inventor: Mark S. CHEE
  • Publication number: 20210238670
    Abstract: The present invention provides oligonucleotide constructs, sets of such oligonucleotide constructs, and methods of using such oligonucleotide constructs to provide validated sequences or sets of validated sequences corresponding to desired ROIs. Such validated ROIs and constructs containing these have a wide variety of uses, including in synthetic biology, quantitative nucleic acid analysis, polymorphism and/or mutation screening, and the like.
    Type: Application
    Filed: April 22, 2021
    Publication date: August 5, 2021
    Applicant: Prognosys Biosciences, Inc.
    Inventor: Mark S. CHEE
  • Publication number: 20210222235
    Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.
    Type: Application
    Filed: April 6, 2021
    Publication date: July 22, 2021
    Inventor: Mark S. CHEE
  • Patent number: 11067567
    Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.
    Type: Grant
    Filed: January 8, 2021
    Date of Patent: July 20, 2021
    Assignee: Prognosys Biosciences, Inc.
    Inventor: Mark S. Chee