Patents by Inventor Stephen R. Quake

Stephen R. Quake 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: 10450620
    Abstract: Methods, devices, compositions and kits are provided for analysis of the microbiome or individual components thereof in an individual. The methods find use in a determination of infection, in analysis of the microbiome structure, in determining the immunocompetence of an individual, and the like. In some embodiments of the invention, the individual is treated with a therapeutic regimen, e.g. drugs, diet, radiation therapy, and the like.
    Type: Grant
    Filed: November 7, 2014
    Date of Patent: October 22, 2019
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Iwijn de Vlaminick, Michael Kertesz, Kiran Kaur Khush, Mark Alec Kowarsky, Lance Martin, Stephen R. Quake, Hannah Valantine
  • Publication number: 20190226029
    Abstract: The invention generally relates to methods for assessing the health of a tissue by characterizing circulating nucleic acids in a biological sample. According to certain embodiments, methods for assessing the health of a tissue include the steps of detecting a sample level of RNA in a biological sample, comparing the sample level of RNA to a reference level of RNA specific to the tissue, determining whether a difference exists between the sample level and the reference level, and characterizing the tissue as abnormal if a difference is detected.
    Type: Application
    Filed: April 3, 2019
    Publication date: July 25, 2019
    Inventors: Lian Chye Winston Koh, Stephen R. Quake, Hei-Mun Christina Fan, Wenying Pan
  • Publication number: 20190224284
    Abstract: Herpes simplex virus (HSV) including herpes simplex virus 1 and 2 (HSV-1 and HSV-2) are a persistent cause of human disease with no known cure. Guided nuclease systems target specific regions of the HSV-1 and HSV-2 genomes, disrupting the virus' nucleic acid and rendering even latent viruses incapacitated.
    Type: Application
    Filed: September 5, 2018
    Publication date: July 25, 2019
    Inventors: Stephen R. Quake, Jianbin Wang
  • Publication number: 20190211376
    Abstract: The invention provides methods, devices, compositions and kits for diagnosing or predicting transplant status or outcome in a subject who has received a transplant.
    Type: Application
    Filed: March 22, 2019
    Publication date: July 11, 2019
    Inventors: Stephen R. Quake, Thomas M. Snyder, Hannah Valantine
  • Publication number: 20190211375
    Abstract: The invention provides methods, devices, compositions and kits for diagnosing or predicting transplant status or outcome in a subject who has received a transplant.
    Type: Application
    Filed: March 22, 2019
    Publication date: July 11, 2019
    Inventors: Stephen R. Quake, Thomas M. Snyder, Hannah Valantine
  • Publication number: 20190203264
    Abstract: The invention provides methods, devices, compositions and kits for diagnosing or predicting transplant status or outcome in a subject who has received a transplant.
    Type: Application
    Filed: March 13, 2019
    Publication date: July 4, 2019
    Inventors: Stephen R. Quake, Thomas M. Snyder, Hannah Valantine
  • Publication number: 20190201501
    Abstract: The invention provides compositions and methods for treating human papillomavirus (HPV) infections using a targetable nuclease, which compositions and methods can be used to selectively target the HPV genome or selectively express the targetable nuclease within cells that infected by HPV. By selectively targeting cells infected by HPV, the HPV genome within infected cells, or both, the nuclease is able to cleave the HPV genome thereby inactivating it and rendering it inoperable, interfering with the virus's ability to propagate even where the virus is in a latent stage of infection. Since latent HPV can be cleaved and eradicated from the host cells, compositions and methods of the invention may be used to treat HPV infections and potentially prevent many of the adverse health consequences associated with the papillomavirus.
    Type: Application
    Filed: December 18, 2018
    Publication date: July 4, 2019
    Inventors: Stephen R. Quake, Jianbin Wang
  • Patent number: 10329607
    Abstract: The invention provides methods, devices, compositions and kits for diagnosing or predicting transplant status or outcome in a subject who has received a transplant.
    Type: Grant
    Filed: August 23, 2018
    Date of Patent: June 25, 2019
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Stephen R. Quake, Thomas M. Snyder, Hannah Valantine
  • Patent number: 10328428
    Abstract: Nucleic acid from cells and viruses sampled from a variety of environments may purified and expressed utilizing microfluidic techniques. In accordance with one embodiment of the present invention, individual or small groups of cells or viruses may be isolated in microfluidic chambers by dilution, sorting, and/or segmentation. The isolated cells or viruses may be lysed directly in the microfluidic chamber, and the resulting nucleic acid purified by exposure to affinity beads. Subsequent elution of the purified nucleic acid may be followed by ligation and cell transformation, all within the same microfluidic chip. In one specific application, cell isolation, lysis, and nucleic acid purification may be performed utilizing a highly parallelized microfluidic architecture to construct gDNA and cDNA libraries.
    Type: Grant
    Filed: January 13, 2017
    Date of Patent: June 25, 2019
    Assignee: California Institute of Technology
    Inventors: Jong Wook Hong, Vincent Studer, W. French Anderson, Stephen R. Quake, Jared Leadbetter
  • Publication number: 20190185882
    Abstract: The invention provides delivery methods and compositions for antiviral therapeutics. Methods and compositions are provided for targeted delivery of antiviral therapeutics into cells of interest using, for example, viral vectors such as adenovirus, AAV, and replication incompetent HSV. These and other delivery systems can be used as vehicles to deliver DNA vectors encoding a nuclease or a cell-killing gene. These delivery methods can also be used to deliver naked DNA or RNA, protein products, plasmids containing a promoter that is active only in a latent viral state which drives a cell-killing gene, or other therapeutic agents.
    Type: Application
    Filed: July 26, 2018
    Publication date: June 20, 2019
    Applicant: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Stephen R. Quake, Jianbin Wang
  • Patent number: 10287632
    Abstract: The invention generally relates to methods for assessing the health of a tissue by characterizing circulating nucleic acids in a biological sample. According to certain embodiments, methods for assessing the health of a tissue include the steps of detecting a sample level of RNA in a biological sample, comparing the sample level of RNA to a reference level of RNA specific to the tissue, determining whether a difference exists between the sample level and the reference level, and characterizing the tissue as abnormal if a difference is detected.
    Type: Grant
    Filed: December 13, 2016
    Date of Patent: May 14, 2019
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Lian Chye Winston Koh, Stephen R. Quake, Hei-Mun Christina Fan, Wenying Pan
  • Patent number: 10240200
    Abstract: The invention generally relates to methods for assessing the health of a tissue by characterizing circulating nucleic acids in a biological sample. According to certain embodiments, methods for assessing the health of a tissue include the steps of detecting a sample level of RNA in a biological sample, comparing the sample level of RNA to a reference level of RNA specific to the tissue, determining whether a difference exists between the sample level and the reference level, and characterizing the tissue as abnormal if a difference is detected.
    Type: Grant
    Filed: September 22, 2015
    Date of Patent: March 26, 2019
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Lian Chye Winston Koh, Stephen R. Quake, Hei-Mun Christina Fan, Wenying Pan
  • Patent number: 10240204
    Abstract: The invention generally relates to methods for assessing the health of a tissue by characterizing circulating nucleic acids in a biological sample. According to certain embodiments, methods for assessing the health of a tissue include the steps of detecting a sample level of RNA in a biological sample, comparing the sample level of RNA to a reference level of RNA specific to the tissue, determining whether a difference exists between the sample level and the reference level, and characterizing the tissue as abnormal if a difference is detected.
    Type: Grant
    Filed: December 13, 2016
    Date of Patent: March 26, 2019
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Lian Chye Winston Koh, Stephen R. Quake, Hei-Mun Christina Fan, Wenying Pan
  • Patent number: 10219696
    Abstract: Continuous pressure sensing is important for patients with several different conditions. We provide an implantable sensor, based on microfluidic principles, which in one example has 1 mmHg limit of detection, high sensitivity and excellent reproducibility. This sensor has an optical interface, which enables pressure to be read with, for example, a cell phone camera. The design and fabrication, along with the option of self-monitoring are promising steps toward better patient care and treatment.
    Type: Grant
    Filed: September 21, 2015
    Date of Patent: March 5, 2019
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Ismail E Araci, Stephen R Quake, Melanie Hayden Gephart
  • Patent number: 10196689
    Abstract: A precise measurement of the immunological receptor diversity present in a sample is obtained by sequence analysis. Samples of interest are generally complex, comprising more than 102, 103, 104, 105, 106, 107, 108, 109, 1010, 1011, 1012 or more different sequences for a receptor of interest. Immunological receptors of interest include immunoglobulins, T cell antigen receptors, and major histocompatibility receptors. The specific composition of immunological receptor sequence variations in the sample can be recorded and output. The composition is useful for predictive, diagnostic and therapeutic methods relating to the immune capabilities and history of an individual. Such predictions and diagnoses are used to guide clinical decisions.
    Type: Grant
    Filed: February 10, 2016
    Date of Patent: February 5, 2019
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Stephen R. Quake, Joshua Weinstein, Ning Jiang, Daniel S. Fisher
  • Publication number: 20190032090
    Abstract: Viral infection is a persistent cause of human disease. Guided nuclease systems target the genomes of viral infections, rendering the viruses incapacitated.
    Type: Application
    Filed: March 20, 2018
    Publication date: January 31, 2019
    Applicant: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Stephen R. Quake, Jianbin Wang
  • Publication number: 20190024171
    Abstract: A precise measurement of the immunological receptor diversity present in a sample is obtained by sequence analysis. Samples of interest are generally complex, comprising more than 102, 103, 104, 105, 106, 107, 108, 109, 1010, 1011, 1012 or more different sequences for a receptor of interest. Immunological receptors of interest include immunoglobulins, T cell antigen receptors, and major histocompatibility receptors. The specific composition of immunological receptor sequence variations in the sample can be recorded and output. The composition is useful for predictive, diagnostic and therapeutic methods relating to the immune capabilities and history of an individual. Such predictions and diagnoses are used to guide clinical decisions.
    Type: Application
    Filed: August 31, 2018
    Publication date: January 24, 2019
    Inventors: Stephen R. Quake, Joshua Weinstein, Ning Jiang, Daniel S. Fisher
  • Publication number: 20190017109
    Abstract: Provided herein is a method of sequencing hydroxymethyated cell-free DNA. In some embodiments, the method comprises adding an affinity tag to only hydroxymethyated DNA molecules in a sample of cfDNA, enriching for the DNA molecules that are tagged with the affinity tag; and sequencing the enriched DNA molecules.
    Type: Application
    Filed: September 28, 2018
    Publication date: January 17, 2019
    Inventors: Chunxiao Song, Stephen R. Quake
  • Publication number: 20190010518
    Abstract: Viral infection is a persistent cause of human disease. Guided nuclease systems of the invention target the genomes of viral infections, rendering the viruses incapacitated. The invention further provides delivery methods and compositions for antiviral therapeutics. Methods and compositions are provided for targeted delivery of antiviral therapeutics into cells of interest using, for example, viral vectors such as adenovirus, AAV, and replication incompetent HSV. These and other delivery systems can be used as vehicles to deliver DNA vectors encoding a nuclease or a cell-killing gene. These delivery methods can also be used to deliver naked DNA or RNA, protein products, plasmids containing a promoter that is active only in a latent viral state which drives a cell-killing gene, or other therapeutic agents.
    Type: Application
    Filed: January 23, 2018
    Publication date: January 10, 2019
    Applicant: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Stephen R. Quake, Jianbin Wang
  • Publication number: 20190009272
    Abstract: Nucleic acid from cells and viruses sampled from a variety of environments may purified and expressed utilizing microfluidic techniques. In accordance with one embodiment of the present invention, individual or small groups of cells or viruses may be isolated in microfluidic chambers by dilution, sorting, and/or segmentation. The isolated cells or viruses may be lysed directly in the microfluidic chamber, and the resulting nucleic acid purified by exposure to affinity beads. Subsequent elution of the purified nucleic acid may be followed by ligation and cell transformation, all within the same microfluidic chip. In one specific application, cell isolation, lysis, and nucleic acid purification may be performed utilizing a highly parallelized microfluidic architecture to construct gDNA and cDNA libraries.
    Type: Application
    Filed: January 13, 2017
    Publication date: January 10, 2019
    Inventors: Jong Wook Hong, Vincent Studer, W. French Anderson, Stephen R. Quake, Jared Leadbetter