公开(公告)号：US20240167100A1

公开(公告)日：2024-05-23

申请号：US18457770

申请日：2023-08-29

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：US20240136014A1

公开(公告)日：2024-04-25

申请号：US18482779

申请日：2023-10-05

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：US20230313315A1

公开(公告)日：2023-10-05

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

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：US20230083814A1

公开(公告)日：2023-03-16

申请号：US18047979

申请日：2022-10-19

Applicant: GUARDANT HEALTH, INC.

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

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

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：US20220325360A1

公开(公告)日：2022-10-13

申请号：US17837375

申请日：2022-06-10

Applicant: GUARDANT HEALTH, INC.

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

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

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.

公开(公告)号：US20220186323A1

公开(公告)日：2022-06-16

申请号：US17688762

申请日：2022-03-07

Applicant: GUARDANT HEALTH, INC.

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

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

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.

公开(公告)号：US20220098671A1

公开(公告)日：2022-03-31

申请号：US17387830

申请日：2021-07-28

Applicant: GUARDANT HEALTH, INC.

Inventor： Katie Julia QUINN ,  Elena HELMAN ,  Darya CHUDOVA

IPC: C12Q1/6886 ,  G16B20/40 ,  G16B20/20 ,  G16B20/10

Abstract: Provided herein are methods for detecting tumor mutational burden (TMB) in subjects. In one aspect, the methods include determining observed mutational counts from sequence information obtained from nucleic acids in samples from the subjects and determining a tumor fraction and/or a coverage of the nucleic acids to generate sequencing parameters. The methods also include determining an expected mutational fraction and/or an expected distribution of the expected mutational fraction given the sequencing parameters to generate an expected result, and adjusting the observed mutational count given the expected result to generate an adjusted result, thereby detecting the TMB in the subject. Other aspects are directed to methods of selecting customized therapies for treating cancer in subjects, and methods of treating cancer in subjects. Yet other aspects include related systems and computer readable media used to detect TMB in subjects.

公开(公告)号：US20200370129A1

公开(公告)日：2020-11-26

申请号：US16917582

申请日：2020-06-30

Applicant: GUARDANT HEALTH, INC.

Inventor： Katie Julia QUINN ,  Elena HELMAN ,  Darya CHUDOVA

IPC: C12Q1/6886

Abstract: Provided herein are methods for detecting tumor mutational burden (TMB) in subjects. In one aspect, the methods include determining observed mutational counts from sequence information obtained from nucleic acids in samples from the subjects and determining a tumor fraction and/or a coverage of the nucleic acids to generate sequencing parameters. The methods also include determining an expected mutational fraction and/or an expected distribution of the expected mutational fraction given the sequencing parameters to generate an expected result, and adjusting the observed mutational count given the expected result to generate an adjusted result, thereby detecting the TMB in the subject. Other aspects are directed to methods of selecting customized therapies for treating cancer in subjects, and methods of treating cancer in subjects. Yet other aspects include related systems and computer readable media used to detect TMB in subjects.

公开(公告)号：US20200273538A1

公开(公告)日：2020-08-27

申请号：US16803680

申请日：2020-02-27

Applicant: GUARDANT HEALTH, INC.

Inventor： Catalin BARBACIORU ,  Marcin SIKORA ,  Darya CHUDOVA

IPC: G16B20/20

Abstract: The disclosure relates to computer technology for precision diagnosis of various states of genetic material such as a gene sequenced from cell-free DNA in a sample. The state may include a somatic homozygous deletion, a somatic heterozygous deletion, a copy number variation, or other states. A computer system may generate competing probabilistic models that each output a probability that the genetic material is in a certain state. Each model may be trained on a training sample set to output a probability that the genetic material is in a respective state. In some embodiments, the computer system may use various probabilistic distributions to generate the models. For example, the computer system may use a beta-binomial distribution, a binomial distribution, a normal (also referred to as “Gaussian”) distribution, or other type of probabilistic modeling techniques.