Patents Assigned to Prognosys Biosciences, Inc.
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Publication number: 20220146513Abstract: 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: ApplicationFiled: November 22, 2021Publication date: May 12, 2022Applicant: Prognosys Biosciences, Inc.Inventors: John Andrew ALTIN, Mark S. CHEE
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Patent number: 11313856Abstract: Provided herein are methods for determining presence of a target enzyme in a tissue section that include delivering a plurality of probes to a tissue section, where a probe of the plurality of probes comprises a capture agent that comprises a substrate for the target enzyme in the tissue section, and where the capture agent is conjugated to an oligonucleotide.Type: GrantFiled: May 3, 2021Date of Patent: April 26, 2022Assignee: Prognosys Biosciences, Inc.Inventor: Mark S. Chee
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Publication number: 20220112545Abstract: 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: ApplicationFiled: December 20, 2021Publication date: April 14, 2022Applicant: Prognosys Biosciences, Inc.Inventor: Mark S. Chee
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Patent number: 11293917Abstract: 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: GrantFiled: June 5, 2020Date of Patent: April 5, 2022Assignee: Prognosys Biosciences, Inc.Inventor: Mark S. Chee
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Patent number: 11286515Abstract: 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: GrantFiled: June 25, 2021Date of Patent: March 29, 2022Assignee: Prognosys Biosciences, Inc.Inventors: Mark S. Chee, David A. Routenberg
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Patent number: 11231419Abstract: 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: GrantFiled: March 14, 2014Date of Patent: January 25, 2022Assignee: Prognosys Biosciences, Inc.Inventors: John Andrew Altin, Mark S. Chee
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Publication number: 20220003755Abstract: 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: ApplicationFiled: September 21, 2021Publication date: January 6, 2022Applicant: Prognosys Biosciences, Inc.Inventor: Mark S. Chee
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Patent number: 11208684Abstract: 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: GrantFiled: April 6, 2021Date of Patent: December 28, 2021Assignee: Prognosys Biosciences, Inc.Inventor: Mark S. Chee
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Patent number: 11156603Abstract: 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: GrantFiled: May 14, 2021Date of Patent: October 26, 2021Assignee: Prognosys Biosciences, Inc.Inventor: Mark S. Chee
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Publication number: 20210317510Abstract: 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: ApplicationFiled: June 25, 2021Publication date: October 14, 2021Applicant: Prognosys Biosciences, Inc.Inventors: Mark S. CHEE, David A. ROUTENBERG
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Publication number: 20210270822Abstract: 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: ApplicationFiled: May 14, 2021Publication date: September 2, 2021Applicant: Prognosys Biosciences, Inc.Inventor: Mark S. Chee
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Publication number: 20210269864Abstract: 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: ApplicationFiled: May 17, 2021Publication date: September 2, 2021Applicant: Prognosys Biosciences, Inc.Inventor: Mark S. CHEE
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Publication number: 20210255175Abstract: 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: ApplicationFiled: May 3, 2021Publication date: August 19, 2021Applicant: Prognosys Biosciences, Inc.Inventor: Mark S. CHEE
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Patent number: 11092601Abstract: 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: GrantFiled: May 21, 2019Date of Patent: August 17, 2021Assignee: Prognosys Biosciences, Inc.Inventors: John Andrew Altin, Mark S. Chee
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Publication number: 20210238670Abstract: 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: ApplicationFiled: April 22, 2021Publication date: August 5, 2021Applicant: Prognosys Biosciences, Inc.Inventor: Mark S. CHEE
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Publication number: 20210238671Abstract: 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: ApplicationFiled: April 22, 2021Publication date: August 5, 2021Applicant: Prognosys Biosciences, Inc.Inventor: Mark S. CHEE
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Patent number: 11067567Abstract: 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: GrantFiled: January 8, 2021Date of Patent: July 20, 2021Assignee: Prognosys Biosciences, Inc.Inventor: Mark S. Chee
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Publication number: 20210207202Abstract: 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: ApplicationFiled: March 24, 2021Publication date: July 8, 2021Applicant: Prognosys Biosciences, Inc.Inventor: Mark S. CHEE
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Patent number: 11046996Abstract: 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: GrantFiled: February 19, 2021Date of Patent: June 29, 2021Assignee: Prognosys Biosciences, Inc.Inventors: Mark S. Chee, David A. Routenberg
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Publication number: 20210172007Abstract: 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: ApplicationFiled: February 19, 2021Publication date: June 10, 2021Applicant: Prognosys Biosciences, Inc.Inventors: Mark S. CHEE, David A. ROUTENBERG