公开(公告)号：US20240425915A1

公开(公告)日：2024-12-26

申请号：US18813477

申请日：2024-08-23

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：US20240233868A9

公开(公告)日：2024-07-11

申请号：US18482779

申请日：2023-10-06

Applicant: GUARDANT HEALTH, INC.

Inventor： Darya CHUDOVA ,  Helmy ELTOUKHY ,  Stefanie Ann Ward MORTIMER ,  Diana ABDUEVA

IPC: G16B30/00 ,  C12Q1/6806 ,  C12Q1/6827 ,  G16B5/00 ,  G16B25/10 ,  G16B40/30

CPC classification number: G16B30/00 ,  C12Q1/6806 ,  C12Q1/6827 ,  G16B5/00 ,  G16B25/10 ,  G16B40/30 ,  C12Q2535/122 ,  C12Q2537/159

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.

公开(公告)号：US20240182977A1

公开(公告)日：2024-06-06

申请号：US18436821

申请日：2024-02-08

Applicant: GUARDANT HEALTH, INC.

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

IPC: C12Q1/6886 ,  C12M1/00 ,  C12M1/34 ,  C12Q1/6806 ,  C12Q1/6855 ,  C12Q1/6869 ,  G01N33/574 ,  G16B20/20 ,  G16B30/10 ,  G16H50/20 ,  G16H50/30

CPC classification number: C12Q1/6886 ,  C12M1/00 ,  C12M1/34 ,  C12Q1/6806 ,  C12Q1/6855 ,  C12Q1/6869 ,  G01N33/57407 ,  G16B20/20 ,  G16B30/10 ,  G16H50/20 ,  G16H50/30 ,  C12Q2600/118 ,  C12Q2600/154 ,  C12Q2600/156 ,  C12Q2600/158 ,  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：US20240087680A1

公开(公告)日：2024-03-14

申请号：US18503392

申请日：2023-11-07

Applicant: GUARDANT HEALTH, INC.

Inventor： Darya CHUDOVA ,  Helmy ELTOUKHY ,  Stefanie Ann Ward MORTIMER ,  DIANA ABDUEVA

IPC: G16B30/00 ,  C12Q1/6806 ,  C12Q1/6827 ,  G16B5/00 ,  G16B25/10 ,  G16B40/30

CPC classification number: G16B30/00 ,  C12Q1/6806 ,  C12Q1/6827 ,  G16B5/00 ,  G16B25/10 ,  G16B40/30 ,  C12Q2535/122 ,  C12Q2537/159

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.

公开(公告)号：US20230141527A1

公开(公告)日：2023-05-11

申请号：US17809540

申请日：2022-06-28

Applicant: GUARDANT HEALTH, INC.

Inventor： Andrew KENNEDY ,  Stefanie Ann Ward MORTIMER ,  AmirAli TALASAZ ,  Darya CHUDOVA ,  Helmy ELTOUKHY ,  Oliver ZILL ,  Richard B. LANMAN ,  Rebecca NAGY ,  Christine LEE ,  Kimberley BANKS

IPC: C12Q1/6806 ,  C12Q1/6855 ,  C12Q1/6886

CPC classification number: C12Q1/6806 ,  C12Q1/6855 ,  C12Q1/6886 ,  C12Q2600/156 ,  C12Q2600/158

Abstract: Methods of preparing double-stranded nucleic acids with single-stranded overhangs for amplification and sequencing are disclosed. Contacting a blunt-ended double-stranded nucleic acid molecules with Taq results in non-templated directed addition of a single nucleotide to the 3′ ends of the nucleic acid with A added most frequently followed by G followed by C and T. G tailing is sufficiently frequent that the efficiency of ligation of nucleic acid molecules to adapters can be significantly increased by including adapters tailed with T and C. The ligation efficiency can be increased even further with blunted-ended adapters to ligate to blunt-ended nucleic acid molecules that failed to undergo tailing.

公开(公告)号：US20220380842A1

公开(公告)日：2022-12-01

申请号：US17810103

申请日：2022-06-30

Applicant: GUARDANT HEALTH, INC.

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

IPC: C12Q1/6869 ,  C12Q1/6886

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：US20220145385A1

公开(公告)日：2022-05-12

申请号：US17563781

申请日：2021-12-28

Applicant: GUARDANT HEALTH, INC.

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

IPC: C12Q1/6869 ,  C12Q1/6886

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：US20210395814A1

公开(公告)日：2021-12-23

申请号：US17410903

申请日：2021-08-24

Applicant: GUARDANT HEALTH, INC.

Inventor： AmirAli TALASAZ ,  Helmy ELTOUKHY

IPC: C12Q1/6869 ,  C12Q1/6886

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：US20240153593A1

公开(公告)日：2024-05-09

申请号：US18358388

申请日：2023-07-25

Applicant: GUARDANT HEALTH, INC.

Inventor： Helmy ELTOUKHY ,  AmirAli TALASAZ

IPC: G16B50/20 ,  C12Q1/6883 ,  G16B40/00 ,  G16B40/20 ,  G16B40/30 ,  G16B50/00 ,  G16H20/00 ,  G16H50/30

CPC classification number: G16B50/20 ,  C12Q1/6883 ,  G16B40/00 ,  G16B40/20 ,  G16B40/30 ,  G16B50/00 ,  G16H20/00 ,  G16H50/30 ,  C12Q1/6886

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：US20240043922A1

公开(公告)日：2024-02-08

申请号：US18491071

申请日：2023-10-20

Applicant: GUARDANT HEALTH, INC.

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

IPC: C12Q1/6869 ,  C12Q1/6886

CPC classification number: 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.