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).

  • CANCER EVOLUTION DETECTION AND DIAGNOSTIC
    Publication number: 20210050072
    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: Application
    Filed: September 3, 2020
    Publication date: February 18, 2021
    Inventors: Helmy ELTOUKHY, AmirAli TALASAZ
  • DETECTION AND TREATMENT OF DISEASE EXHIBITING DISEASE CELL HETEROGENEITY AND SYSTEMS AND METHODS FOR COMMUNICATING TEST RESULTS
    Publication number: 20210040565
    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 21, 2020
    Publication date: February 11, 2021
    Inventors: Helmy ELTOUKHY, AmirAli TALASAZ, Bahram Ghaffarzadeh KERMANI, Nnamdi IHUEGBU
  • Methods and compositions for nucleic acid sequencing
    Patent number: 10900077
    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: Grant
    Filed: May 7, 2019
    Date of Patent: January 26, 2021
    Assignee: ILLUMINA, INC.
    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
  • Methods and systems for detecting genetic variants
    Patent number: 10883139
    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 8, 2018
    Date of Patent: January 5, 2021
    Assignee: GUARDANT HEALTH, INC.
    Inventors: Helmy Eltoukhy, AmirAli Talasaz, Stefanie Ann Ward Mortimer
  • POPULATION BASED TREATMENT RECOMMENDER USING CELL FREE DNA
    Publication number: 20200395100
    Abstract: Systems and methods are disclosed for generating a therapeutic response predict or detecting a disease, by: using a genetic analyzer to generate genetic information; receiving into computer memory a training dataset comprising, for each of a plurality of individuals having a disease, (1) genetic information from the individual generated at first time point and (2) treatment response of the individual to one or more therapeutic interventions determined at a second, later, time point; and implementing a machine learning algorithm using the dataset to generate at least one computer implemented classification algorithm, wherein the classification algorithm, based on genetic information from a subject, predicts therapeutic response of the subject to a therapeutic intervention.
    Type: Application
    Filed: August 26, 2020
    Publication date: December 17, 2020
    Inventors: Helmy ELTOUKHY, AmirAli TALASAZ
  • METHODS AND SYSTEMS FOR DETECTING GENETIC VARIANTS
    Publication number: 20200362405
    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: July 31, 2020
    Publication date: November 19, 2020
    Inventors: AmirAli TALASAZ, Helmy ELTOUKHY, Stefanie Ann Ward MORTIMER
  • Methods and systems for detecting genetic variants
    Patent number: 10801063
    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: October 14, 2019
    Date of Patent: October 13, 2020
    Assignee: GUARDANT HEALTH, INC.
    Inventors: Helmy Eltoukhy, AmirAli Talasaz, Stefanie Ann Ward Mortimer
  • METHODS FOR MULTI-RESOLUTION ANALYSIS OF CELL-FREE NUCLEIC ACIDS
    Publication number: 20200185060
    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: Application
    Filed: December 18, 2019
    Publication date: June 11, 2020
    Inventors: Darya CHUDOVA, Helmy ELTOUKHY, Stefanie Ann Ward MORTIMER
  • METHODS TO DETERMINE TUMOR GENE COPY NUMBER BY ANALYSIS OF CELL-FREE DNA
    Publication number: 20200140960
    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: Application
    Filed: January 8, 2020
    Publication date: May 7, 2020
    Inventors: Helmy Eltoukhy, AmirAli Talasaz, Darya Chudova, Diana Abdueva
  • METHODS AND SYSTEMS FOR DETECTING GENETIC VARIANTS
    Publication number: 20200123602
    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 14, 2019
    Publication date: April 23, 2020
    Inventors: Helmy ELTOUKHY, AmirAli Talasaz, Stefanie Ann Ward Mortimer
  • METHODS AND SYSTEMS FOR DETECTING CONTAMINATION BETWEEN SAMPLES
    Publication number: 20200071754
    Abstract: Provided herein are various methods and related systems for detecting the presence/absence of contamination of a first sample with a second sample. In some embodiments, for example, the methods include (a) sequencing a set of polynucleotides to produce a plurality of sequencing reads, (b) aligning the plurality of sequencing reads to a reference sequence, (c) grouping the plurality of sequencing reads into a plurality of families, (d) generating family identifiers for the plurality of families, (e) screening for a set of shared family identifiers, (f) determining a quantitative measure of the set of shared family identifiers, and (g) classifying the first sample as being contaminated or not contaminated with the second sample based on the quantitative measure of the shared family identifiers.
    Type: Application
    Filed: August 30, 2019
    Publication date: March 5, 2020
    Inventors: Darya CHUDOVA, Helmy ELTOUKHY, Stephen FAIRCLOUGH, Narsi RAJAGOPALAN, Marcin SIKORA
  • METHODS AND SYSTEMS FOR ANALYZING NUCLEIC ACID MOLECULES
    Publication number: 20190390253
    Abstract: The disclosure provides methods for processing nucleic acid populations containing different forms (e.g., RNA and DNA, single-stranded or double-stranded) and/or extents of modification (e.g., cytosine methylation, association with proteins). These methods accommodate multiple forms and/or modifications of nucleic acid in a sample, such that sequence information can be obtained for multiple forms. The methods also preserve the identity of multiple forms or modified states through processing and analysis, such that analysis of sequence can be combined with epigenetic analysis.
    Type: Application
    Filed: June 24, 2019
    Publication date: December 26, 2019
    Inventors: Andrew KENNEDY, Stefanie Ann Ward MORTIMER, Helmy ELTOUKHY, AmirAli TALASAZ, Diana ABDUEVA, Matthew SCHULTZ
  • PORTABLE GENETIC DETECTION AND ANALYSIS SYSTEM AND METHOD
    Publication number: 20190367965
    Abstract: A portable detector is disclosed for detecting certain analytes of interest, such as genetic material (e.g., nucleic acids). The detector includes a reading component for the detection of the analytes, and control circuitry for controlling operation of the reading component. Processing circuitry may be included to perform both primary analysis of acquired data, and where desired, secondary analysis. Where desired, some or all of the computationally intensive tasks may be off-loaded to enhance the portability and speed of the device. The device may incorporate various types of interface, technologies for reading and analysis, positioning system interfaces, and so forth. A number of exemplary use cases and methods are also disclosed.
    Type: Application
    Filed: August 14, 2019
    Publication date: December 5, 2019
    Inventors: Robert C. Kain, Min-Jui Richard Shen, John A. Moon, Helmy A. Eltoukhy
  • MICRODEVICES AND BIOSENSOR CARTRIDGES FOR BIOLOGICAL OR CHEMICAL ANALYSIS AND SYSTEMS AND METHODS FOR THE SAME
    Publication number: 20190351414
    Abstract: A flow cell including inlet and outlet ports in fluid communication with each other through a flow channel that extends therebetween. The flow channel includes a diffuser region and a field region that is located downstream from the diffuser region. The field region of the flow channel directs fluid along reaction sites where desired reactions occur. The fluid flows through the diffuser region in a first flow direction and through the field region in a second flow direction. The first and second flow directions being substantially perpendicular.
    Type: Application
    Filed: August 1, 2019
    Publication date: November 21, 2019
    Inventors: Helmy A. Eltoukhy, Tarun Khurana, Behnam Javanmardi, Poorya Sabounchi, Majid Aghababazadeh
  • SYSTEMS AND METHODS TO DETECT RARE MUTATIONS AND COPY NUMBER VARIATION
    Publication number: 20190316185
    Abstract: The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.
    Type: Application
    Filed: April 19, 2019
    Publication date: October 17, 2019
    Inventors: AmirAli TALASAZ, HELMY ELTOUKHY, Stefanie Ann Ward MORTIMER
  • Portable genetic detection and analysis system and method
    Patent number: 10428367
    Abstract: A portable detector is disclosed for detecting certain analytes of interest, such as genetic material (e.g., nucleic acids). The detector includes a reading component for the detection of the analytes, and control circuitry for controlling operation of the reading component. Processing circuitry may be included to perform both primary analysis of acquired data, and where desired, secondary analysis. Where desired, some or all of the computationally intensive tasks may be off-loaded to enhance the portability and speed of the device. The device may incorporate various types of interface, technologies for reading and analysis, positioning system interfaces, and so forth. A number of exemplary use cases and methods are also disclosed.
    Type: Grant
    Filed: July 13, 2016
    Date of Patent: October 1, 2019
    Assignee: ILLUMINA, INC.
    Inventors: Robert C. Kain, Min-Jui Richard Shen, John A. Moon, Helmy A. Eltoukhy
  • Microdevices and biosensor cartridges for biological or chemical analysis and systems and methods for the same
    Patent number: 10406519
    Abstract: A flow cell including inlet and outlet ports in fluid communication with each other through a flow channel that extends therebetween. The flow channel includes a diffuser region and a field region that is located downstream from the diffuser region. The field region of the flow channel directs fluid along reaction sites where desired reactions occur. The fluid flows through the diffuser region in a first flow direction and through the field region in a second flow direction. The first and second flow directions being substantially perpendicular.
    Type: Grant
    Filed: March 26, 2018
    Date of Patent: September 10, 2019
    Assignee: ILLUMINA, INC.
    Inventors: Helmy A. Eltoukhy, Tarun Khurana, Behnam Javanmardi, Poorya Sabounchi, Majid Aghababazadeh
  • METHODS AND COMPOSITIONS FOR NUCLEIC ACID SEQUENCING
    Publication number: 20190264279
    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: May 7, 2019
    Publication date: August 29, 2019
    Applicant: Illumina, Inc.
    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
  • Methods and compositions for nucleic acid sequencing
    Patent number: 10287629
    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: Grant
    Filed: July 12, 2016
    Date of Patent: May 14, 2019
    Assignee: Illumina, Inc.
    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
  • METHODS FOR EARLY DETECTION OF CANCER
    Publication number: 20190085406
    Abstract: Disclosed herein are methods, compositions, and devices for use in early detection of cancer. The methods include sequencing a panel of regions in cell-free nucleic acid molecules and detecting one or more tumor markers that are indicative of a cancer.
    Type: Application
    Filed: April 14, 2017
    Publication date: March 21, 2019
    Inventors: Stefanie Ann Ward MORTIMER, AmirAli TALASAZ, Darya CHUDOVA, HELMY ELTOUKHY, Andrew KENNEDY