Patents by Inventor John Zachary Sanborn

John Zachary Sanborn 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).

  • Distributed System Providing Dynamic Indexing And Visualization Of Genomic Data
    Publication number: 20190066262
    Abstract: Systems and methods for dynamic visualization of genomic data are provided in which a genomic visualization system adapts presentation of information content according to scale-relevant annotations within a sequence object.
    Type: Application
    Filed: October 24, 2018
    Publication date: February 28, 2019
    Inventors: Charles Joseph Vaske, John Zachary Sanborn, Stephen Charles Benz
  • High-Throughput Identification of Patient-Specific Neoepitopes As Therapeutic Targets For Cancer Immunotherapies
    Publication number: 20190034582
    Abstract: Systems and methods are presented that allow for selection of tumor neoepitopes that are filtered for various criteria. In particularly contemplated aspects, filtering includes a step in which the mutation leading to the neoepitope is ascertained as being located in a cancer driver gene.
    Type: Application
    Filed: February 10, 2017
    Publication date: January 31, 2019
    Inventors: Andrew Nguyen, John Zachary Sanborn, Steven Charles Benz, Kayvan Niazi, Shahrooz Rabizadeh, Patrick Soon-Shiong, Charles Joseph Vaske
  • Systems and methods for RNA analysis in functional confirmation of cancer mutations
    Patent number: 10192027
    Abstract: Contemplated systems and methods integrate genomic/exomic data with transcriptomic data by correlating a cancer associated mutation in the genome/exome with the transcription level of the affected gene carrying the mutation, particularly where the mutation is a 3-terminal nonsense mutation.
    Type: Grant
    Filed: March 25, 2015
    Date of Patent: January 29, 2019
    Assignee: FIVE3 GENOMICS, LLC
    Inventor: John Zachary Sanborn
  • Grouping and transferring omic sequence data for sequence analysis
    Patent number: 10193956
    Abstract: “Omic” digital data transport systems and methods are disclosed. The disclosed systems and methods employ a transport server that assembles a transport group larger numbers of omic output files on the basis of machine specific annotation from one or more sequencing devices and user input related to one or more attributes for the omic output files.
    Type: Grant
    Filed: November 13, 2014
    Date of Patent: January 29, 2019
    Assignee: FIVE3 GENOMICS, LLC
    Inventors: Stephen Charles Benz, John Zachary Sanborn, Charles Joseph Vaske
  • Integrated Analysis To Determine Prognosis After Treatment For Primary Breast Cancer
    Publication number: 20190018017
    Abstract: Various protein markers can be used as post-treatment relapse predictors in HER2 positive breast cancer. Notably, these markers appear to be independent of the size of the tumor, metastasis status, grade, and hormone receptor status. In addition, HER2 quantities were in large part not correlated with likelihood of relapse.
    Type: Application
    Filed: December 11, 2016
    Publication date: January 17, 2019
    Applicants: NantOmics, LLC, Nant Holdings IP, LLC
    Inventors: Stephen Charles Benz, Todd Hembrough, Shahrooz Rabizadeh, John Zachary Sanborn, Charles Joseph Vaske, Fabiola Cecchi, Peter Fasching, Patrick Soon-Shiong
  • Systems, methods, and compositions for viral-associated tumors
    Patent number: 10176295
    Abstract: Contemplated systems and methods employ chimeric reference sequences that include a plurality of viral genome sequences to identify/quantify integration and co-amplification events. Most typically, the viral genome sequences are organized in the chimeric reference sequences as single chromosomes and the chimeric reference sequences are in BAM format.
    Type: Grant
    Filed: September 26, 2014
    Date of Patent: January 8, 2019
    Assignees: Five3 Genomics, LLC, Nant Holdings IP, LLC
    Inventors: John Zachary Sanborn, Charles Joseph Vaske, Stephen Charles Benz, Shahrooz Rabizadeh, Nicole Hensley, Patrick Soon-Shiong
  • BAMBAM: PARALLEL COMPARATIVE ANALYSIS OF HIGH-THROUGHPUT SEQUENCING DATA
    Publication number: 20180373835
    Abstract: The present invention relates to methods for evaluating and/or predicting the outcome of a clinical condition, such as cancer, metastasis, AIDS, autism, Alzheimer's, and/or Parkinson's disorder. The methods can also be used to monitor and track changes in a patient's DNA and/or RNA during and following a clinical treatment regime. The methods may also be used to evaluate protein and/or metabolite levels that correlate with such clinical conditions. The methods are also of use to ascertain the probability outcome for a patient's particular prognosis.
    Type: Application
    Filed: August 21, 2018
    Publication date: December 27, 2018
    Applicant: THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
    Inventors: John Zachary SANBORN, David HAUSSLER
  • BAMBAM: PARALLEL COMPARATIVE ANALYSIS OF HIGH-THROUGHPUT SEQUENCING DATA
    Publication number: 20180365377
    Abstract: The present invention relates to methods for evaluating and/or predicting the outcome of a clinical condition, such as cancer, metastasis, AIDS, autism, Alzheimer's, and/or Parkinson's disorder. The methods can also be used to monitor and track changes in a patient's DNA and/or RNA during and following a clinical treatment regime. The methods may also be used to evaluate protein and/or metabolite levels that correlate with such clinical conditions. The methods are also of use to ascertain the probability outcome for a patient's particular prognosis.
    Type: Application
    Filed: August 21, 2018
    Publication date: December 20, 2018
    Applicant: THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
    Inventors: John Zachary SANBORN, David HAUSSLER
  • BAMBAM: PARALLEL COMPARATIVE ANALYSIS OF HIGH-THROUGHPUT SEQUENCING DATA
    Publication number: 20180357370
    Abstract: The present invention relates to methods for evaluating and/or predicting the outcome of a clinical condition, such as cancer, metastasis, AIDS, autism, Alzheimer's, and/or Parkinson's disorder. The methods can also be used to monitor and track changes in a patient's DNA and/or RNA during and following a clinical treatment regime. The methods may also be used to evaluate protein and/or metabolite levels that correlate with such clinical conditions. The methods are also of use to ascertain the probability outcome for a patient's particular prognosis.
    Type: Application
    Filed: August 21, 2018
    Publication date: December 13, 2018
    Applicant: THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
    Inventors: John Zachary SANBORN, David HAUSSLER
  • INTEGRATIVE PANOMIC APPROACH TO PHARMACOGENOMICS SCREENING
    Publication number: 20180357368
    Abstract: Complex genotypes, especially multiple single nucleotide variances, that may differentially distributed among alleles can be efficiently mapped in each allele of the gene using next generation sequencing of RNA transcripts from the alleles and the allele fraction information of RNA transcripts. Such reconstructed single nucleotide variances among alleles can be associated with the expected effectiveness of the cancer therapy to update or generate the patient's record or adjust the dose and schedule of the cancer therapy to reduce the undesirable effect of the cancer therapy.
    Type: Application
    Filed: June 7, 2018
    Publication date: December 13, 2018
    Inventors: Camille R. Schwartz, John Little, Charles Joseph Vaske, John Zachary Sanborn
  • BAMBAM: PARALLEL COMPARATIVE ANALYSIS OF HIGH-THROUGHPUT SEQUENCING DATA
    Publication number: 20180357369
    Abstract: The present invention relates to methods for evaluating and/or predicting the outcome of a clinical condition, such as cancer, metastasis, AIDS, autism, Alzheimer's, and/or Parkinson's disorder. The methods can also be used to monitor and track changes in a patient's DNA and/or RNA during and following a clinical treatment regime. The methods may also be used to evaluate protein and/or metabolite levels that correlate with such clinical conditions. The methods are also of use to ascertain the probability outcome for a patient's particular prognosis.
    Type: Application
    Filed: August 21, 2018
    Publication date: December 13, 2018
    Applicant: THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
    Inventors: John Zachary SANBORN, David HAUSSLER
  • BAMBAM: PARALLEL COMPARATIVE ANALYSIS OF HIGH-THROUGHPUT SEQUENCING DATA
    Publication number: 20180357371
    Abstract: The present invention relates to methods for evaluating and/or predicting the outcome of a clinical condition, such as cancer, metastasis, AIDS, autism, Alzheimer's, and/or Parkinson's disorder. The methods can also be used to monitor and track changes in a patient's DNA and/or RNA during and following a clinical treatment regime. The methods may also be used to evaluate protein and/or metabolite levels that correlate with such clinical conditions. The methods are also of use to ascertain the probability outcome for a patient's particular prognosis.
    Type: Application
    Filed: August 21, 2018
    Publication date: December 13, 2018
    Applicant: THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
    Inventors: John Zachary SANBORN, David HAUSSLER
  • Distributed system providing dynamic indexing and visualization of genomic data
    Patent number: 10140683
    Abstract: Systems and methods for dynamic visualization of genomic data are provided in which a genomic visualization system adapts presentation of information content according to scale-relevant annotations within a sequence object.
    Type: Grant
    Filed: December 7, 2012
    Date of Patent: November 27, 2018
    Inventors: Charles Joseph Vaske, John Zachary Sanborn, Stephen Charles Benz
  • SYSTEMS, METHODS, AND COMPOSITIONS FOR VIRAL-ASSOCIATED TUMORS
    Publication number: 20180322245
    Abstract: Contemplated systems and methods employ chimeric reference sequences that include a plurality of viral genome sequences to identify/quantify integration and co-amplification events. Most typically, the viral genome sequences are organized in the chimeric reference sequences as single chromosomes and the chimeric reference sequences are in BAM format.
    Type: Application
    Filed: July 11, 2018
    Publication date: November 8, 2018
    Inventors: John Zachary Sanborn, Charles Joseph Vaske, Stephen Charles Benz, Shahrooz Rabizadeh, Nicole Hensley, Patrick Soon-Shiong
  • SIGNATURE-HASH FOR MULTI-SEQUENCE FILES
    Publication number: 20180293348
    Abstract: A unique hash representing patient omics data is constructed using results for known SNP positions and their respective allele frequencies in the patient's omics data. In most preferred aspects, the known SNP positions are selected for specific factors (e.g., ethnicity, sex, etc.) and the allele fraction is represented in values of a non-linear scale. Typically, the hash comprises a header/metadata relating to the known SNP positions and non-linear scale and further includes the actual hash string.
    Type: Application
    Filed: March 28, 2018
    Publication date: October 11, 2018
    Inventors: John Zachary Sanborn, Stephen Charles Benz, Rahul Parulkar
  • Systems And Methods For High-Accuracy Variant Calling
    Publication number: 20180237949
    Abstract: Systems and methods for in silico prediction of HLA type of a patient are presented in which patient sequence reads and a reference sequence with known and distinct HLA alleles are used in a de Bruijn graph. A composite match score is then used to rank HLA alleles, thus providing a first HLA type. A second HLA type is identified by re-ranking using an adjusted composite match score.
    Type: Application
    Filed: August 25, 2016
    Publication date: August 23, 2018
    Inventor: John Zachary Sanborn
  • BAMBAM: PARALLEL COMPARATIVE ANALYSIS OF HIGH-THROUGHPUT SEQUENCING DATA
    Publication number: 20180157791
    Abstract: The present invention relates to methods for evaluating and/or predicting the outcome of a clinical condition, such as cancer, metastasis, AIDS, autism, Alzheimer's, and/or Parkinson's disorder. The methods can also be used to monitor and track changes in a patient's DNA and/or RNA during and following a clinical treatment regime. The methods may also be used to evaluate protein and/or metabolite levels that correlate with such clinical conditions. The methods are also of use to ascertain the probability outcome for a patient's particular prognosis.
    Type: Application
    Filed: June 8, 2017
    Publication date: June 7, 2018
    Inventors: John Zachary Sanborn, David Haussler
  • BAMBAM: PARALLEL COMPARATIVE ANALYSIS OF HIGH-THROUGHPUT SEQUENCING DATA
    Publication number: 20180144093
    Abstract: The present invention relates to methods for evaluating and/or predicting the outcome of a clinical condition, such as cancer, metastasis, AIDS, autism, Alzheimer's, and/or Parkinson's disorder. The methods can also be used to monitor and track changes in a patient's DNA and/or RNA during and following a clinical treatment regime. The methods may also be used to evaluate protein and/or metabolite levels that correlate with such clinical conditions. The methods are also of use to ascertain the probability outcome for a patient's particular prognosis.
    Type: Application
    Filed: November 9, 2017
    Publication date: May 24, 2018
    Inventors: David Haussler, John Zachary Sanborn
  • Healthcare Object Recognition Systems And Methods
    Publication number: 20180089782
    Abstract: Healthcare object (HCO) discriminator systems and methods are presented. Systems can obtain a digital representation of a scene via a sensor interface. An HCO discriminator platform analyzes the digital representation to discriminate objects within the scene as being associated with a type of HCO or as being unrelated to a type of HCO. Once the HCO recognition platform determines that a type of HCO is relevant, it instantiates an actual HCO. The HCO can be routed to one or more destinations based on routing rules generated from a template or based on the manner in which the objects in the scene were discriminated.
    Type: Application
    Filed: November 20, 2017
    Publication date: March 29, 2018
    Applicant: Nant Holdings IP, LLC
    Inventors: Patrick Soon-Shiong, John Zachary Sanborn, Stephen Charles Benz, Charles Joseph Vaske
  • BAMBAM: PARALLEL COMPARATIVE ANALYSIS OF HIGH-THROUGHPUT SEQUENCING DATA
    Publication number: 20180075185
    Abstract: The present invention relates to methods for evaluating and/or predicting the outcome of a clinical condition, such as cancer, metastasis, AIDS, autism, Alzheimer's, and/or Parkinson's disorder. The methods can also be used to monitor and track changes in a patient's DNA and/or RNA during and following a clinical treatment regime. The methods may also be used to evaluate protein and/or metabolite levels that correlate with such clinical conditions. The methods are also of use to ascertain the probability outcome for a patient's particular prognosis.
    Type: Application
    Filed: May 12, 2017
    Publication date: March 15, 2018
    Inventors: John Zachary Sanborn, DAVID HAUSSLER