公开(公告)号：US11952616B2

公开(公告)日：2024-04-09

申请号：US18061898

申请日：2022-12-05

Applicant: GUARDANT HEALTH, INC.

Inventor： Andrew Kennedy ,  Stefanie Ann Ward Mortimer ,  Helmy Eltoukhy ,  AmirAli Talasaz ,  Diana Abdueva

IPC: C12Q1/68 ,  C12N15/10 ,  C12Q1/6806 ,  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：US11827942B2

公开(公告)日：2023-11-28

申请号：US18156890

申请日：2023-01-19

Applicant: GUARDANT HEALTH, INC.

Inventor： Stefanie Ann Ward Mortimer ,  AmirAli Talasaz ,  Darya Chudova ,  Helmy Eltoukhy

IPC: C12Q1/6886 ,  G16B30/10 ,  G16H50/30 ,  C12M1/00 ,  C12Q1/6869 ,  C12Q1/6806 ,  G16H50/20 ,  G01N33/574 ,  C12M1/34 ,  G16B20/20

CPC classification number: C12Q1/6886 ,  C12M1/00 ,  C12M1/34 ,  C12Q1/6806 ,  C12Q1/6869 ,  G01N33/57407 ,  G16B20/20 ,  G16B30/10 ,  G16H50/20 ,  G16H50/30 ,  C12Q2600/118 ,  C12Q2600/154 ,  C12Q2600/156 ,  C12Q2600/166

Abstract: Disclosed herein are methods, compositions, and devices for use in the early detection of cancer. The methods include preparing cell-free nucleic acid molecules from a subject for sequencing, sequencing a panel of regions in the cell-free nucleic acid molecules, and detecting one or more markers that are indicative of a cancer.

公开(公告)号：US11667967B2

公开(公告)日：2023-06-06

申请号：US17563816

申请日：2021-12-28

Applicant: GUARDANT HEALTH, INC.

Inventor： AmirAli Talasaz ,  Helmy Eltoukhy

IPC: C12P19/34 ,  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.

公开(公告)号：US11667959B2

公开(公告)日：2023-06-06

申请号：US17396097

申请日：2021-08-06

Applicant: GUARDANT HEALTH, INC.

Inventor： AmirAli Talasaz ,  Stefanie Ann Ward Mortimer

IPC: C12Q1/6827 ,  C12Q1/6806 ,  G16B30/00 ,  C12Q1/6869

CPC classification number: C12Q1/6827 ,  C12Q1/6806 ,  G16B30/00 ,  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：US20220356527A1

公开(公告)日：2022-11-10

申请号：US17552728

申请日：2021-12-16

Applicant: GUARDANT HEALTH, INC.

Inventor： Helmy Eltoukhy ,  AmirAli Talasaz ,  Darya Chudova ,  Diana Abdueva

IPC: C12Q1/6886 ,  G16B30/00 ,  C12Q1/6809 ,  G16B99/00 ,  G16B30/10 ,  G16B20/10 ,  C12Q1/6874

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.

公开(公告)号：US11434531B2

公开(公告)日：2022-09-06

申请号：US17410903

申请日：2021-08-24

Applicant: GUARDANT HEALTH, INC.

Inventor： AmirAli Talasaz ,  Helmy Eltoukhy

IPC: C12P19/34 ,  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：US11242556B2

公开(公告)日：2022-02-08

申请号：US17069535

申请日：2020-10-13

Applicant: GUARDANT HEALTH, INC.

Inventor： AmirAli Talasaz ,  Stefanie Ann Ward Mortimer

IPC: C12Q1/6827 ,  C12Q1/6806 ,  G16B30/00 ,  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：US11091796B2

公开(公告)日：2021-08-17

申请号：US17069559

申请日：2020-10-13

Applicant: GUARDANT HEALTH, INC.

Inventor： AmirAli Talasaz ,  Stefanie Ann Ward Mortimer

IPC: C12Q1/6827 ,  C12Q1/6806 ,  G16B30/00 ,  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：US11001899B1

公开(公告)日：2021-05-11

申请号：US17152529

申请日：2021-01-19

Applicant: GUARDANT HEALTH, INC.

Inventor： AmirAli Talasaz

IPC: C12P19/34 ,  C12Q1/6886 ,  G16B30/00 ,  C12Q1/6806 ,  C12N15/10 ,  C12Q1/6874 ,  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：US10883139B2

公开(公告)日：2021-01-05

申请号：US15892178

申请日：2018-02-08

Applicant: Guardant Health, Inc.

Inventor： Helmy Eltoukhy ,  AmirAli Talasaz ,  Stefanie Ann Ward Mortimer

IPC: C12P19/34 ,  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.