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: 10988804
    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: March 22, 2019
    Date of Patent: April 27, 2021
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Stephen R. Quake, Thomas M. Snyder, Hannah Valantine
  • Publication number: 20210115506
    Abstract: Prediction of allograft rejection is provided based on the quantification of transplant-derived circulating cell-free DNA (dd-cfDNA levels) in the absence of a donor genotype. The technology provided herein alleviates some of the barriers to the implementation of Genome Transplant Dynamics (GTD), which will further widen its clinical application.
    Type: Application
    Filed: April 2, 2018
    Publication date: April 22, 2021
    Inventors: Iwijn De Vlaminck, Eilon Sharon, Jonathan Pritchard, Stephen R Quake, Hannah Valantine, Kiran Khush
  • Patent number: 10982275
    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: October 8, 2019
    Date of Patent: April 20, 2021
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Stephen R. Quake, Thomas M. Snyder, Hannah Valantine
  • Patent number: 10968479
    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: October 30, 2019
    Date of Patent: April 6, 2021
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Stephen R. Quake, Thomas M. Snyder, Hannah Valantine
  • Patent number: 10940473
    Abstract: Nucleic acid from cells and viruses sampled from a variety of environments may purified and expressed utilizing microfluidic techniques. 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. 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: April 26, 2019
    Date of Patent: March 9, 2021
    Assignee: California Institute of Technology
    Inventors: Jong Wook Hong, Vincent Studer, W. French Anderson, Stephen R. Quake, Jared Leadbetter
  • Publication number: 20210054461
    Abstract: High-throughput long read sequencing is used to perform immunogenomic characterization of expressed antibody repertoires in the context of vaccination. Informatic analysis allows global characterizations of isotype distributions, determination of the lineage structure of the repertoire and measure age and antigen related mutational activity. Global analysis of the immune system's clonal structure provides direct insight into the effects of vaccination and provides a detailed molecular portrait of age-related effects.
    Type: Application
    Filed: September 1, 2020
    Publication date: February 25, 2021
    Inventors: Stephen R. Quake, Joshua Weinstein, Ning Jiang, Daniel S. Fisher
  • Publication number: 20210002722
    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: July 16, 2020
    Publication date: January 7, 2021
    Inventors: Stephen R. Quake, Joshua Weinstein, Ning Jiang, Daniel S. Fisher
  • Publication number: 20200370121
    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: August 5, 2020
    Publication date: November 26, 2020
    Inventors: Lian Chye Winston Koh, Stephen R. Quake, Hei-Mun Christina Fan, Wenying Pan
  • Publication number: 20200362416
    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: August 5, 2020
    Publication date: November 19, 2020
    Inventors: Lian Chye Winston Koh, Stephen R. Quake, Hei-Mun Christina Fan, Wenying Pan
  • Publication number: 20200299760
    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: April 15, 2020
    Publication date: September 24, 2020
    Inventors: Chunxiao Song, Stephen R. Quake
  • Patent number: 10774383
    Abstract: High-throughput long read sequencing is used to perform immunogenomic characterization of expressed antibody repertoires in the context of vaccination. Informatic analysis allows global characterizations of isotype distributions, determination of the lineage structure of the repertoire and measure age and antigen related mutational activity. Global analysis of the immune system's clonal structure provides direct insight into the effects of vaccination and provides a detailed molecular portrait of age-related effects.
    Type: Grant
    Filed: June 21, 2018
    Date of Patent: September 15, 2020
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Stephen R. Quake, Joshua Weinstein, Ning Jiang, Daniel S. Fisher
  • Patent number: 10774382
    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: August 31, 2018
    Date of Patent: September 15, 2020
    Assignee: The Board of Trustees of the Leland Stanford University Junior University
    Inventors: Stephen R. Quake, Joshua Weinstein, Ning Jiang, Daniel S. Fisher
  • Publication number: 20200283838
    Abstract: Provided herein is a method of sequencing hydroxymethylated cell-free DNA. In some embodiments, the method comprises adding an affinity tag to only hydroxymethylated 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: April 14, 2020
    Publication date: September 10, 2020
    Inventors: Chunxiao Song, Stephen R. Quake
  • Publication number: 20200277666
    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: April 15, 2020
    Publication date: September 3, 2020
    Inventors: Chunxiao Song, Stephen R. Quake
  • Publication number: 20200277667
    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: April 15, 2020
    Publication date: September 3, 2020
    Inventors: Chunxiao Song, Stephen R. Quake
  • Publication number: 20200270700
    Abstract: Disclosed is a method to achieve digital quantification of DNA (i.e., counting differences between identical sequences) using direct shotgun sequencing followed by mapping to the chromosome of origin and enumeration of fragments per chromosome. The preferred method uses massively parallel sequencing, which can produce tens of millions of short sequence tags in a single run and enabling a sampling that can be statistically evaluated. By counting the number of sequence tags mapped to a predefined window in each chromosome, the over- or under-representation of any chromosome in maternal plasma DNA contributed by an aneuploid fetus can be detected. This method does not require the differentiation of fetal versus maternal DNA. The median count of autosomal values is used as a normalization constant to account for differences in total number of sequence tags is used for comparison between samples and between chromosomes.
    Type: Application
    Filed: April 20, 2020
    Publication date: August 27, 2020
    Applicant: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Hei-Mun Christina FAN, Stephen R. QUAKE
  • Publication number: 20200270698
    Abstract: The invention generally relates to methods for assessing a neurological disorder by characterizing circulating nucleic acids in a blood sample. According to certain embodiments, methods for assessing a neurological disorder include obtaining RNA present in a blood sample of a patient suspected of having a neurological disorder, determining a level of RNA present in the sample that is specific to brain tissue, comparing the sample level of RNA to a reference level of RNA specific to brain tissue, determining whether a difference exists between the sample level and the reference level, and indicating a neurological disorder if a difference is determined.
    Type: Application
    Filed: March 31, 2020
    Publication date: August 27, 2020
    Inventors: Lian Chye Winston Koh, Stephen R. Quake, Hei-Mun Christina Fan, Wenying Pan
  • Publication number: 20200248248
    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: April 14, 2020
    Publication date: August 6, 2020
    Inventors: Chunxiao Song, Stephen R. Quake
  • Publication number: 20200248249
    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: April 14, 2020
    Publication date: August 6, 2020
    Inventors: Chunxiao Song, Stephen R. Quake
  • Patent number: 10718010
    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: Grant
    Filed: September 28, 2018
    Date of Patent: July 21, 2020
    Assignee: THE BOARD OF TRUSTEES OF THE LELAND STANFORD JUNIOR UNIVERSITY
    Inventors: Chunxiao Song, Stephen R. Quake