Patents by Inventor Helmy Eltoukhy

Helmy Eltoukhy 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).

  • METHODS AND SYSTEMS FOR DETECTING GENETIC VARIANTS
    Publication number: 20220145385
    Abstract: Disclosed herein in are methods and systems for determining genetic variants (e.g., copy number variation) in a polynucleotide sample. A method for determining copy number variations includes tagging double-stranded polynucleotides with duplex tags, sequencing polynucleotides from the sample and estimating total number of polynucleotides mapping to selected genetic loci. The estimate of total number of polynucleotides can involve estimating the number of double-stranded polynucleotides in the original sample for which no sequence reads are generated. This number can be generated using the number of polynucleotides for which reads for both complementary strands are detected and reads for which only one of the two complementary strands is detected.
    Type: Application
    Filed: December 28, 2021
    Publication date: May 12, 2022
    Inventors: AmirAli TALASAZ, Helmy ELTOUKHY, Stefanie Ann Ward MORTIMER
  • METHODS AND SYSTEMS FOR DETECTING GENETIC VARIANTS
    Publication number: 20220119880
    Abstract: Disclosed herein in are methods and systems for determining genetic variants (e.g., copy number variation) in a polynucleotide sample. A method for determining copy number variations includes tagging double-stranded polynucleotides with duplex tags, sequencing polynucleotides from the sample and estimating total number of polynucleotides mapping to selected genetic loci. The estimate of total number of polynucleotides can involve estimating the number of double-stranded polynucleotides in the original sample for which no sequence reads are generated. This number can be generated using the number of polynucleotides for which reads for both complementary strands are detected and reads for which only one of the two complementary strands is detected.
    Type: Application
    Filed: December 28, 2021
    Publication date: April 21, 2022
    Inventors: AmirAli TALASAZ, Helmy ELTOUKHY
  • Machine learning for somatic single nucleotide variant detection in cell-free tumor nucleic acid sequencing applications
    Patent number: 11302416
    Abstract: Systems and methods are disclosed to detect single-nucleotide variations (SNVs) from somatic sources in a cell-free biological sample of a subject by generating training data with class labels; in computer memory, generating a machine learning unit comprising one output for each of adenine (A), cytosine (C), guanine (G), and thymine (T) calls; training the machine learning unit; and applying the machine learning unit to detect the SNVs from somatic sources in the cell-free biological sample of the subject, wherein the cell-free biological sample comprises a mixture of nucleic acid molecules from somatic and germline sources.
    Type: Grant
    Filed: September 1, 2016
    Date of Patent: April 12, 2022
    Assignee: Guardant Health
    Inventors: Bahram Ghaffarzadeh Kermani, Helmy Eltoukhy
  • Cancer evolution detection and diagnostic
    Patent number: 11282610
    Abstract: The present disclosure provides methods for determining a probability that after any of a number of therapeutic interventions, an initial state of a subject, such as somatic cell mutational status of a subject with cancer, will develop a subsequent state. Such probabilities can be used to inform a health care provider as to particular courses of treatment to maximize probability of a desired outcome for the subject.
    Type: Grant
    Filed: September 3, 2020
    Date of Patent: March 22, 2022
    Assignee: GUARDANT HEALTH, INC.
    Inventors: Helmy Eltoukhy, AmirAli Talasaz
  • METHODS AND SYSTEMS FOR DETECTING GENETIC VARIANTS
    Publication number: 20220049299
    Abstract: Disclosed herein in are methods and systems for determining genetic variants (e.g., copy number variation) in a polynucleotide sample. A method for determining copy number variations includes tagging double-stranded polynucleotides with duplex tags, sequencing polynucleotides from the sample and estimating total number of polynucleotides mapping to selected genetic loci. The estimate of total number of polynucleotides can involve estimating the number of double-stranded polynucleotides in the original sample for which no sequence reads are generated. This number can be generated using the number of polynucleotides for which reads for both complementary strands are detected and reads for which only one of the two complementary strands is detected.
    Type: Application
    Filed: October 27, 2021
    Publication date: February 17, 2022
    Inventors: AmirAli TALASAZ, Helmy ELTOUKHY
  • METHODS FOR DETECTING SINGLE NUCLEOTIDE VARIANTS OR INDELS BY DEEP SEQUENCING
    Publication number: 20220049318
    Abstract: Disclosed herein are methods for use in detection of single nucleotide variants (SNVs) or indels. The methods may comprise enriching cell-free DNA molecules for a panel of genomic regions and deep sequencing the enriched cfDNA to detect the SNVs or indels.
    Type: Application
    Filed: October 21, 2021
    Publication date: February 17, 2022
    Inventors: Stefanie Ann Ward MORTIMER, AmirAli TALASAZ, Darya CHUDOVA, Helmy ELTOUKHY
  • METHODS AND SYSTEMS FOR DETECTING GENETIC VARIANTS
    Publication number: 20220049300
    Abstract: Disclosed herein in are methods and systems for determining genetic variants (e.g., copy number variation) in a polynucleotide sample. A method for determining copy number variations includes tagging double-stranded polynucleotides with duplex tags, sequencing polynucleotides from the sample and estimating total number of polynucleotides mapping to selected genetic loci. The estimate of total number of polynucleotides can involve estimating the number of double-stranded polynucleotides in the original sample for which no sequence reads are generated. This number can be generated using the number of polynucleotides for which reads for both complementary strands are detected and reads for which only one of the two complementary strands is detected.
    Type: Application
    Filed: October 27, 2021
    Publication date: February 17, 2022
    Inventors: AmirAli TALASAZ, Helmy ELTOUKHY, Stefanie Ann Ward MORTIMER
  • Methods to determine tumor gene copy number by analysis of cell-free DNA
    Patent number: 11242569
    Abstract: Methods are provided herein to improve automatic detection of copy number variation in nucleic acid samples. These methods provide improved approaches for determining baseline copy number of genetic loci within a sample, reduce variation due to features of genetic loci, sample preparation, and probe exhaustion.
    Type: Grant
    Filed: January 8, 2020
    Date of Patent: February 8, 2022
    Assignee: GUARDANT HEALTH, INC.
    Inventors: Helmy Eltoukhy, AmirAli Talasaz, Darya Chudova, Diana Abdueva
  • METHODS FOR COMPUTER PROCESSING SEQUENCE READS TO DETECT MOLECULAR RESIDUAL DISEASE
    Publication number: 20220025469
    Abstract: Disclosed herein are methods for use in detection of molecular residual disease. The methods may comprise deep sequencing a panel of genomic regions in cell-free DNA molecules and computer processing sequence reads to detect variants that are indicative of molecular residual disease.
    Type: Application
    Filed: July 2, 2021
    Publication date: January 27, 2022
    Inventors: Stefanie Ann Ward MORTIMER, AmirAli TALASAZ, Darya CHUDOVA, Helmy ELTOUKHY
  • DETECTION AND TREATMENT OF DISEASE EXHIBITING DISEASE CELL HETEROGENEITY AND SYSTEMS AND METHODS FOR COMMUNICATING TEST RESULTS
    Publication number: 20210395837
    Abstract: This disclosure provides, among other things, methods for generating and applying therapeutic interventions. The methods involve, for example, (a) sequencing polynucleotides from cancer cells from a subject; (b) identifying and quantifying somatic mutations in the polynucleotides; (c) developing a profile of tumor heterogeneity in the subject indicating the presence and relative quantity of a plurality of the somatic mutations in the polynucleotides, wherein different relative quantities indicates tumor heterogeneity; and (d) determining a therapeutic intervention for a cancer exhibiting the tumor heterogeneity, wherein the therapeutic intervention is effective against a cancer having the profile of tumor heterogeneity determined.
    Type: Application
    Filed: August 31, 2021
    Publication date: December 23, 2021
    Inventors: Helmy ELTOUKHY, AmirAli TALASAZ, Bahram Ghaffarzadeh KERMANI, Nnamdi IHUEGBU
  • METHODS AND SYSTEMS FOR DETECTING GENETIC VARIANTS
    Publication number: 20210395814
    Abstract: Disclosed herein in are methods and systems for determining genetic variants (e.g., copy number variation) in a polynucleotide sample. A method for determining copy number variations includes tagging double-stranded polynucleotides with duplex tags, sequencing polynucleotides from the sample and estimating total number of polynucleotides mapping to selected genetic loci. The estimate of total number of polynucleotides can involve estimating the number of double-stranded polynucleotides in the original sample for which no sequence reads are generated. This number can be generated using the number of polynucleotides for which reads for both complementary strands are detected and reads for which only one of the two complementary strands is detected.
    Type: Application
    Filed: August 24, 2021
    Publication date: December 23, 2021
    Inventors: AmirAli TALASAZ, Helmy ELTOUKHY
  • Methods and systems for detecting genetic variants
    Patent number: 11149307
    Abstract: Disclosed herein in are methods and systems for determining genetic variants (e.g., copy number variation) in a polynucleotide sample. A method for determining copy number variations includes tagging double-stranded polynucleotides with duplex tags, sequencing polynucleotides from the sample and estimating total number of polynucleotides mapping to selected genetic loci. The estimate of total number of polynucleotides can involve estimating the number of double-stranded polynucleotides in the original sample for which no sequence reads are generated. This number can be generated using the number of polynucleotides for which reads for both complementary strands are detected and reads for which only one of the two complementary strands is detected.
    Type: Grant
    Filed: February 4, 2021
    Date of Patent: October 19, 2021
    Assignee: GUARDANT HEALTH, INC.
    Inventors: AmirAli Talasaz, Helmy Eltoukhy, Stefanie Ann Ward Mortimer
  • Methods and systems for detecting genetic variants
    Patent number: 11149306
    Abstract: Disclosed herein in are methods and systems for determining genetic variants (e.g., copy number variation) in a polynucleotide sample. A method for determining copy number variations includes tagging double-stranded polynucleotides with duplex tags, sequencing polynucleotides from the sample and estimating total number of polynucleotides mapping to selected genetic loci. The estimate of total number of polynucleotides can involve estimating the number of double-stranded polynucleotides in the original sample for which no sequence reads are generated. This number can be generated using the number of polynucleotides for which reads for both complementary strands are detected and reads for which only one of the two complementary strands is detected.
    Type: Grant
    Filed: July 31, 2020
    Date of Patent: October 19, 2021
    Assignee: GUARDANT HEALTH, INC.
    Inventors: AmirAli Talasaz, Helmy Eltoukhy, Stefanie Ann Ward Mortimer
  • BIOSENSORS FOR BIOLOGICAL OR CHEMICAL ANALYSIS AND SYSTEMS AND METHODS FOR SAME
    Publication number: 20210318999
    Abstract: A biosensor is provided including a detection device and a flow cell mounted to the detection device. The detection device has a detector surface with a plurality of reaction sites. The detection device also includes a filter layer that is configured to at least one of (a) filter unwanted excitation light signals; (b) direct emission signals from a designated reaction site toward one or more associated light detectors that are configured to detect the emission signals from the designated reaction site; or (c) block or prevent detection of crosstalk emission signals from adjacent reaction sites.
    Type: Application
    Filed: June 25, 2021
    Publication date: October 14, 2021
    Inventors: Helmy A. Eltoukhy, Robert C. Kain, Wenyi Feng, Mark Pratt, Bernard Hirschbein, Poorya Sabounchi, Tarun Khurana
  • Methods and systems for detecting genetic variants
    Patent number: 11118221
    Abstract: Disclosed herein in are methods and systems for determining genetic variants (e.g., copy number variation) in a polynucleotide sample. A method for determining copy number variations includes tagging double-stranded polynucleotides with duplex tags, sequencing polynucleotides from the sample and estimating total number of polynucleotides mapping to selected genetic loci. The estimate of total number of polynucleotides can involve estimating the number of double-stranded polynucleotides in the original sample for which no sequence reads are generated. This number can be generated using the number of polynucleotides for which reads for both complementary strands are detected and reads for which only one of the two complementary strands is detected.
    Type: Grant
    Filed: January 7, 2020
    Date of Patent: September 14, 2021
    Assignee: GUARDANT HEALTH, INC.
    Inventors: AmirAli Talasaz, Stefanie Ann Ward Mortimer, Helmy Eltoukhy
  • Machine Learning for Somatic Single Nucleotide Variant Detection in Cell-free Tumor Nucleic acid Sequencing Applications
    Publication number: 20210265013
    Abstract: Systems and methods are disclosed to detect single-nucleotide variations (SNVs) from somatic sources in a cell-free biological sample of a subject by generating training data with class labels; in computer memory, generating a machine learning unit comprising one output for each of adenine (A), cytosine (C), guanine (G), and thymine (T) calls; training the machine learning unit; and applying the machine learning unit to detect the SNVs from somatic sources in the cell-free biological sample of the subject, wherein the cell-free biological sample comprises a mixture of nucleic acid molecules from somatic and germline sources.
    Type: Application
    Filed: February 17, 2021
    Publication date: August 26, 2021
    Inventors: Bahram Ghaffarzadeh Kermani, Helmy Eltoukhy
  • Biosensors for biological or chemical analysis and systems and methods for same
    Patent number: 11080248
    Abstract: A biosensor is provided including a detection device and a flow cell mounted to the detection device. The detection device has a detector surface with a plurality of reaction sites. The detection device also includes a filter layer that is configured to at least one of (a) filter unwanted excitation light signals; (b) direct emission signals from a designated reaction site toward one or more associated light detectors that are configured to detect the emission signals from the designated reaction site; or (c) block or prevent detection of crosstalk emission signals from adjacent reaction sites.
    Type: Grant
    Filed: June 1, 2018
    Date of Patent: August 3, 2021
    Assignee: ILLUMINA, INC.
    Inventors: Helmy A. Eltoukhy, Robert C. Kain, Wenyi Feng, Mark Pratt, Bernard Hirschbein, Poorya Sabounchi, Tarun Khurana
  • Methods for multi-resolution analysis of cell-free nucleic acids
    Patent number: 11062791
    Abstract: The present disclosure provides a method for enriching for multiple genomic regions using a first bait set that selectively hybridizes to a first set of genomic regions of a nucleic acid sample and a second bait set that selectively hybridizes to a second set of genomic regions of the nucleic acid sample. These bait set panels can selectively enrich for one or more nucleosome-associated regions of a genome, said nucleosome-associated regions comprising genomic regions having one or more genomic base positions with differential nucleosomal occupancy, wherein the differential nucleosomal occupancy is characteristic of a cell or tissue type of origin or disease state.
    Type: Grant
    Filed: December 18, 2019
    Date of Patent: July 13, 2021
    Assignee: GUARDANT HEALTH, INC.
    Inventors: Darya Chudova, Helmy Eltoukhy, Stefanie Ann Ward Mortimer, Diana Abdueva
  • METHODS AND SYSTEMS FOR DETECTING GENETIC VARIANTS
    Publication number: 20210164037
    Abstract: Disclosed herein in are methods and systems for determining genetic variants (e.g., copy number variation) in a polynucleotide sample. A method for determining copy number variations includes tagging double-stranded polynucleotides with duplex tags, sequencing polynucleotides from the sample and estimating total number of polynucleotides mapping to selected genetic loci. The estimate of total number of polynucleotides can involve estimating the number of double-stranded polynucleotides in the original sample for which no sequence reads are generated. This number can be generated using the number of polynucleotides for which reads for both complementary strands are detected and reads for which only one of the two complementary strands is detected.
    Type: Application
    Filed: February 4, 2021
    Publication date: June 3, 2021
    Inventors: AmirAli TALASAZ, Helmy ELTOUKHY, Stefanie Ann Ward MORTIMER
  • METHODS AND COMPOSITIONS FOR NUCLEIC ACID SEQUENCING
    Publication number: 20210139978
    Abstract: The present disclosure provides methods and systems for detecting multiple different nucleotides in a sample. In particular, the disclosure provides for detection of multiple different nucleotides in a sample utilizing fewer detection moieties than the number of nucleotides being detected and/or fewer imaging events than the number of nucleotides being detected.
    Type: Application
    Filed: January 20, 2021
    Publication date: May 13, 2021
    Inventors: Robert C. Kain, Xiaohai Liu, Wenyi Feng, Bernard Hirschbein, Helmy A. Eltoukhy, Xiaolin Wu, Geoffrey Paul Smith, Jonathan Mark Boutell, Thomas Joseph, Randall Smith, Min-Jui Richard Shen, Carolyn Tregidgo, Kay Klausing