公开(公告)号：US20200115739A1

公开(公告)日：2020-04-16

申请号：US16593653

申请日：2019-10-04

Applicant: GUARDANT HEALTH, INC.

Inventor： AmirAli TALASAZ ,  Stefanie Ann Ward MORTIMER

IPC: C12Q1/6827 ,  G16B30/00 ,  C12Q1/6806

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.

公开(公告)号：US20200087735A1

公开(公告)日：2020-03-19

申请号：US16575128

申请日：2019-09-18

Applicant: GUARDANT HEALTH, INC.

Inventor： AmirAli TALASAZ

IPC: C12Q1/6886 ,  C12Q1/6874 ,  C12Q1/6806 ,  C12N15/10 ,  C12Q1/6869 ,  G16B30/00

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.

公开(公告)号：US20190390253A1

公开(公告)日：2019-12-26

申请号：US16450918

申请日：2019-06-24

Applicant: Guardant Health, Inc.

Inventor： Andrew KENNEDY ,  Stefanie Ann Ward MORTIMER ,  Helmy ELTOUKHY ,  AmirAli TALASAZ ,  Diana ABDUEVA ,  Matthew SCHULTZ

IPC: C12Q1/6806 ,  C12Q1/6886 ,  C12Q1/6874 ,  C12N15/10

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.

公开(公告)号：US20190005194A1

公开(公告)日：2019-01-03

申请号：US16075105

申请日：2017-02-02

Applicant: GUARDANT HEALTH, INC.

Inventor： HELMY ELTOUKHY ,  AmirAli TALASAZ

IPC: G06F19/24 ,  G06F19/18

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.

公开(公告)号：US20180300456A1

公开(公告)日：2018-10-18

申请号：US15766765

申请日：2016-10-07

Applicant: GUARDANT HEALTH, INC.

Inventor： HELMY ELTOUKHY ,  AmirAli TALASAZ

IPC: G06F19/28 ,  G06F19/24 ,  G16H20/00

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.

公开(公告)号：US20180223374A1

公开(公告)日：2018-08-09

申请号：US15872831

申请日：2018-01-16

Applicant: Guardant Health, Inc.

Inventor： AmirAli TALASAZ ,  HELMY ELTOUKHY

IPC: C12Q1/6886 ,  C12Q1/6806 ,  G06F19/22 ,  C12Q1/6874 ,  C12N15/10 ,  C12Q1/6869

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.

公开(公告)号：US20250002993A1

公开(公告)日：2025-01-02

申请号：US18812385

申请日：2024-08-22

Applicant: GUARDANT HEALTH, INC.

Inventor： AmirAli TALASAZ ,  Helmy ELTOUKHY ,  Stefanie Ann Ward MORTIMER

IPC: C12Q1/6869 ,  C12Q1/6886 ,  G16B15/00

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.

公开(公告)号：US20240409979A1

公开(公告)日：2024-12-12

申请号：US18770271

申请日：2024-07-11

Applicant: GUARDANT HEALTH, INC.

Inventor： Andrew KENNEDY ,  Stefanie Ann Ward MORTIMER ,  Helmy ELTOUKHY ,  AmirAli TALASAZ ,  DIANA ABDUEVA

IPC: C12Q1/6806 ,  C12N15/10 ,  C12Q1/6874 ,  C12Q1/6886

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.

公开(公告)号：US20240279714A1

公开(公告)日：2024-08-22

申请号：US18625882

申请日：2024-04-03

Applicant: GUARDANT HEALTH, INC.

Inventor： Andrew KENNEDY ,  Stefanie Ann Ward MORTIMER ,  Helmy ELTOUKHY ,  AmirAli TALASAZ ,  DIANA ABDUEVA

IPC: C12Q1/6806 ,  C12N15/10 ,  C12Q1/6874 ,  C12Q1/6886

CPC classification number: C12Q1/6806 ,  C12N15/1065 ,  C12Q1/6874 ,  C12Q1/6886 ,  C12Q2600/154

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.

公开(公告)号：US20240240247A1

公开(公告)日：2024-07-18

申请号：US18538986

申请日：2023-12-13

Applicant: GUARDANT HEALTH, INC.

Inventor： AmirAli TALASAZ ,  Helmy ELTOUKHY ,  Stefanie Ann Ward MORTIMER

IPC: C12Q1/6869 ,  C12Q1/6886 ,  G16B15/00

CPC classification number: C12Q1/6869 ,  C12Q1/6886 ,  C12Q2535/122 ,  C12Q2600/158 ,  G16B15/00

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.