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).

  • BAMBAM: parallel comparative analysis of high-throughput sequencing data
    Patent number: 10726945
    Abstract: A differential sequence object is constructed on the basis of alignment of sub-strings via incremental synchronization of sequence strings using known positions of the sub-strings relative to a reference genome sequence. An output file is then generated that comprises only relevant changes with respect to the reference genome.
    Type: Grant
    Filed: March 31, 2017
    Date of Patent: July 28, 2020
    Assignee: THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
    Inventors: John Zachary Sanborn, David Haussler
  • Systems And Methods For Genetic Analysis Of Metastases
    Publication number: 20200227137
    Abstract: Contemplated systems and methods use identification and classification of somatic single nucleotide variants found in a primary tumor and metastases to determine phylogeny of the metastases.
    Type: Application
    Filed: August 25, 2016
    Publication date: July 16, 2020
    Inventor: John Zachary Sanborn
  • Bambam: parallel comparative analysis of high-throughput sequencing data
    Patent number: 10706956
    Abstract: Methods are provided 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: Grant
    Filed: November 9, 2017
    Date of Patent: July 7, 2020
    Assignee: The Regents of the University of California
    Inventors: David Haussler, John Zachary Sanborn
  • SYSTEMS AND METHODS FOR COMPREHENSIVE ANALYSIS OF MOLECULAR PROFILES ACROSS MULTIPLE TUMOR AND GERMLINE EXOMES
    Publication number: 20200185053
    Abstract: Omics patient data are analyzed using sequences or diff objects of tumor and matched normal tissue to identify patient and disease specific mutations, using transcriptomic data to identify expression levels of the mutated genes, and pathway analysis based on the so obtained omic data to identify specific pathway characteristics for the diseased tissue. Most notably, many different tumors have shared pathway characteristics, and identification of a pathway characteristic of a tumor may thus indicate effective treatment options ordinarily not considered when tumor analysis is based on anatomical tumor type only.
    Type: Application
    Filed: January 2, 2020
    Publication date: June 11, 2020
    Inventors: Shahrooz Rabizadeh, John Zachary Sanborn, Charles Joseph Vaske, Stephen Charles Benz, Patrick Soon-Shiong
  • Systems and methods for comprehensive analysis of molecular profiles across multiple tumor and germline exomes
    Patent number: 10614910
    Abstract: Omics patient data are analyzed using sequences or diff objects of tumor and matched normal tissue to identify patient and disease specific mutations, using transcriptomic data to identify expression levels of the mutated genes, and pathway analysis based on the so obtained omic data to identify specific pathway characteristics for the diseased tissue. Most notably, many different tumors have shared pathway characteristics, and identification of a pathway characteristic of a tumor may thus indicate effective treatment options ordinarily not considered when tumor analysis is based on anatomical tumor type only.
    Type: Grant
    Filed: June 1, 2015
    Date of Patent: April 7, 2020
    Assignees: NANTOMICS, LLC, NANT HOLDINGS IP, LLC, FIVE3 GENOMICS, LLC
    Inventors: Shahrooz Rabizadeh, John Zachary Sanborn, Charles Joseph Vaske, Stephen Charles Benz, Patrick Soon-Shiong
  • SIGNATURE-HASH FOR MULTI-SEQUENCE FILES
    Publication number: 20200104285
    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: April 2, 2020
    Inventors: John Zachary SANBORN, Stephen Charles BENZ, Rahul PARULKAR
  • CANCER NEOEPITOPES
    Publication number: 20200093907
    Abstract: Certain universal neoepitopes and cancer specific neoepitopes and methods therefore are presented that may be used in immunotherapy and cancer diagnosis. Preferred therapeutic and diagnostic compositions include antibodies or fragments thereof that bind to neoepitopes on cancer cells.
    Type: Application
    Filed: September 13, 2019
    Publication date: March 26, 2020
    Inventors: Stephen Charles Benz, Andrew Nguyen, Charles Joseph Vaske, John Zachary Sanborn
  • TUMOR ANTIGENICITY PROCESSING AND PRESENTATION
    Publication number: 20200082906
    Abstract: Methods for targeting a tumor antigen for immunotherapy based on HLA allele type and the mutations present in the tumor antigen are presented. A patient's HLA allele type and a tumor antigen derived from a mutation in cancer driver gene can be matched with a majority allele type having a minimum affinity to the same tumor antigen or with those of a plurality of patients with a history of cancer treatment. Upon matching, a cancer treatment against the tumor antigen can be selected and administered to the patient to achieve a desired effect.
    Type: Application
    Filed: November 30, 2017
    Publication date: March 12, 2020
    Inventors: Andrew NGUYEN, John Zachary SANBORN, Charles Joseph VASKE, Shahrooz RABIZADEH, Kayvan NIAZI, Patrick SOON-SHIONG, Stephen Charles BENZ
  • SYSTEMS, METHODS, AND COMPOSITIONS FOR VIRAL-ASSOCIATED TUMORS
    Publication number: 20190392921
    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: September 5, 2019
    Publication date: December 26, 2019
    Applicants: FIVE3 GENOMICS, LLC, NANT HOLDINGS IP, LLC
    Inventors: John Zachary Sanborn, Charles Joseph Vaske, Stephen Charles Benz, Shahrooz Rabizadeh, Nicole Hensley, Patrick Soon-Shiong
  • HEALTHCARE OBJECT RECOGNITION, SYSTEMS AND METHODS
    Publication number: 20190325997
    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: July 2, 2019
    Publication date: October 24, 2019
    Inventors: Patrick Soon-Shiong, John Zachary Sanborn, Stephen Charles Benz, Charles Joseph Vaske
  • VIRAL NEOEPITOPES AND USES THEREOF
    Publication number: 20190287656
    Abstract: Contemplated antiviral/cancer treatments comprise analysis of neoepitopes from viral DNA that has integrated into the host genome, and design of immunotherapeutic agents against such neoepitopes.
    Type: Application
    Filed: May 24, 2019
    Publication date: September 19, 2019
    Inventors: Andrew Nguyen, John Zachary Sanborn, Stephen Charles Benz
  • INTEGRATIVE PANOMIC APPROACH TO PHARMACOGENOMICS SCREENING
    Publication number: 20190272892
    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: May 22, 2019
    Publication date: September 5, 2019
    Inventors: Camille R. Schwartz, John Little, Charles Joseph Vaske, John Zachary Sanborn
  • Healthcare object recognition systems and methods
    Patent number: 10388409
    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: Grant
    Filed: November 20, 2017
    Date of Patent: August 20, 2019
    Assignee: Nant Holdings IP, LLC
    Inventors: Patrick Soon-Shiong, John Zachary Sanborn, Stephen Charles Benz, Charles Joseph Vaske
  • IMMUNOTHERAPY MARKERS AND USES THEREFOR
    Publication number: 20190237196
    Abstract: Systems and methods for prediction of the treatment outcome for immune therapy are presented in which omics data of a patient tumor sample are used. Most typically, the omics data are processed to identify mutational signatures (especially APOBEC/POLE signatures), immune checkpoint expression, and MSI status as leading indicators to predict the treatment outcome for immune therapy. Such prediction advantageously integrates various parameters that would otherwise, when individually considered, skew prediction outcome.
    Type: Application
    Filed: August 25, 2017
    Publication date: August 1, 2019
    Inventors: Andrew Nguyen, John Zachary Sanborn, Shahrooz Rabizadeh
  • Viral neoepitopes and uses thereof
    Patent number: 10339274
    Abstract: Contemplated antiviral/cancer treatments comprise analysis of neoepitopes from viral DNA that has integrated into the host genome, and design of immunotherapeutic agents against such neoepitopes.
    Type: Grant
    Filed: October 12, 2016
    Date of Patent: July 2, 2019
    Assignee: NANTOMICS, LLC
    Inventors: Andrew Nguyen, Stephen Charles Benz, John Zachary Sanborn
  • Systems And Methods For Transmission And Pre-Processing Of Sequencing Data
    Publication number: 20190124135
    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: Application
    Filed: December 17, 2018
    Publication date: April 25, 2019
    Inventors: Stephen Charles Benz, John Zachary Sanborn, Charles Joseph Vaske
  • Systems and Methods For RNA Analysis In Functional Confirmation Of Cancer Mutations
    Publication number: 20190121937
    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: Application
    Filed: December 17, 2018
    Publication date: April 25, 2019
    Inventor: John Zachary Sanborn
  • BAMBAM: parallel comparative analysis of high-throughput sequencing data
    Patent number: 10268800
    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: Grant
    Filed: June 27, 2017
    Date of Patent: April 23, 2019
    Assignee: THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
    Inventors: John Zachary Sanborn, David Haussler
  • CANCER NEOEPITOPES
    Publication number: 20190099475
    Abstract: Certain universal neoepitopes and cancer specific neoepitopes and methods therefor are presented that may be used in immunotherapy and cancer diagnosis. Preferred therapeutic and diagnostic compositions include antibodies or fragments thereof that bind to neoepitopes on cancer cells.
    Type: Application
    Filed: April 8, 2016
    Publication date: April 4, 2019
    Inventors: Stephen Charles Benz, Andrew Nguyen, Charles Joseph Vaske, John Zachary Sanborn
  • Bambam: parallel comparative analysis of high-throughput sequencing data
    Patent number: 10249384
    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: Grant
    Filed: May 27, 2016
    Date of Patent: April 2, 2019
    Assignee: THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
    Inventors: John Zachary Sanborn, David Haussler