公开(公告)号：US20240233871A9

公开(公告)日：2024-07-11

申请号：US18308171

申请日：2023-04-27

Applicant: GUARDANT HEALTH, INC.

Inventor： Justin I. ODEGAARD ,  Marcin SIKORA ,  Aliaksandr ARTSIOMENKA

IPC: G16B30/10

CPC classification number: G16B30/10

Abstract: Methods, systems, and compositions for non-invasively detecting and/or monitoring therapeutic nucleic acid constructs in a sample comprising cell-free nucleic acids from a subject. Detection of therapeutic nucleic acid constructs in samples comprising cell-free nucleic acids allows for verifying therapeutic nucleic acid construct administration, determining the persistence or biological efficacy of the therapeutic nucleic acid construct, and/or ascertaining the efficacy of the therapy in the subject.

公开(公告)号：US20210363586A1

公开(公告)日：2021-11-25

申请号：US16907034

申请日：2019-08-30

Applicant: GUARDANT HEALTH, INC.

Inventor： Aliaksandr ARTSIOMENKA ,  Marcin SIKORA ,  Catalin BARBACIORU ,  Darya CHUDOVA ,  Martina I. LEFTEROVA

IPC: C12Q1/6886 ,  G16B20/20 ,  G16B30/10 ,  G16B40/20

Abstract: Provided herein are methods for determining the microsatellite instability status of samples. In one aspect, the methods include quantifying a number of different repeat lengths present at each of a plurality of microsatellite loci from sequence information to generate a site score for each of the plurality of the microsatellite loci. The methods also include comparing the site score of a given microsatellite locus to a site specific trained threshold for the given microsatellite locus for each of the plurality of the microsatellite loci and calling the given microsatellite locus as being unstable when the site score of the given microsatellite locus exceeds the site specific trained threshold for the given microsatellite locus to generate a microsatellite instability score, which includes a number of unstable microsatellite loci from the plurality of the microsatellite loci.

公开(公告)号：US20190287648A1

公开(公告)日：2019-09-19

申请号：US16352722

申请日：2019-03-13

Applicant: GUARDANT HEALTH, INC.

Inventor： Justin I. ODEGAARD ,  Marcin SIKORA ,  Aliaksandr ARTSIOMENKA

IPC: G16B30/10

Abstract: Methods, systems, and compositions for non-invasively detecting and/or monitoring therapeutic nucleic acid constructs in a sample comprising cell-free nucleic acids from a subject. Detection of therapeutic nucleic acid constructs in samples comprising cell-free nucleic acids allows for verifying therapeutic nucleic acid construct administration, determining the persistence or biological efficacy of the therapeutic nucleic acid construct, and/or ascertaining the efficacy of the therapy in the subject.

公开(公告)号：US20220344004A1

公开(公告)日：2022-10-27

申请号：US17691049

申请日：2022-03-09

Applicant: GUARDANT HEALTH, INC.

Inventor： Catalin BARBACIORU ,  Darya CHUDOVA ,  Aliaksandr ARTSIOMENKA ,  Daniel GAILE ,  Hao WANG

IPC: G16B30/10 ,  G16B20/20 ,  G16B20/10

Abstract: In implementations described herein, information derived from a sample that is derived from off-target sequences can be used to determine estimates for the copy number of tumor cells and/or the tumor fraction of a sample. Additionally, information derived from the presence of germline SNPs can be used to determine estimates for at least one of the copy number of tumor cells or the tumor fraction of a sample.

公开(公告)号：US20210398610A1

公开(公告)日：2021-12-23

申请号：US17162897

申请日：2021-01-29

Applicant: GUARDANT HEALTH, INC.

Inventor： Aliaksandr ARTSIOMENKA ,  Aaron Isaac HARDIN ,  Stephen FAIRCLOUGH ,  Marcin SIKORA ,  Catalin BARBACIORU

IPC: G16B20/20 ,  G16H10/40 ,  G16H50/70 ,  G16H20/10

Abstract: Provided herein are methods of making negative predictions. In some aspects, methods of determining that a first target nucleic acid variant is absent at a first genetic locus in a cell-free nucleic acid (cfNA) sample obtained from a subject having a given cancer type at least partially using a computer are provided. Certain of these methods include determining that the first target nucleic acid variant is not detected in the cfNA sample obtained from the subject, generating, by the computer, at least one tumor fraction based value; generating, by the computer, at least one mutual exclusivity value; and determining that the first target nucleic acid variant is absent at the first genetic locus in the cfNA sample using the tumor fraction based value and/or the mutual exclusivity value. Additional methods and related systems and computer readable media are also provided.

公开(公告)号：US20240247319A1

公开(公告)日：2024-07-25

申请号：US18500890

申请日：2023-11-02

Applicant: GUARDANT HEALTH, INC.

Inventor： Aliaksandr ARTSIOMENKA ,  Marcin Pawel SIKORA ,  Catalin BARBACIORU ,  Darya CHUDOVA ,  Martina I. LEFTEROVA

IPC: C12Q1/6886 ,  G16B20/20 ,  G16B30/10 ,  G16B40/20

CPC classification number: C12Q1/6886 ,  G16B20/20 ,  G16B30/10 ,  G16B40/20

Abstract: Provided herein are methods for determining the microsatellite instability status of samples. In one aspect, the methods include quantifying a number of different repeat lengths present at each of a plurality of microsatellite loci from sequence information to generate a site score for each of the plurality of the microsatellite loci. The methods also include comparing the site score of a given microsatellite locus to a site specific trained threshold for the given microsatellite locus for each of the plurality of the microsatellite loci and calling the given microsatellite locus as being unstable when the site score of the given microsatellite locus exceeds the site specific trained threshold for the given microsatellite locus to generate a microsatellite instability score, which includes a number of unstable microsatellite loci from the plurality of the microsatellite loci.

公开(公告)号：US20240136017A1

公开(公告)日：2024-04-25

申请号：US18308171

申请日：2023-04-26

Applicant: GUARDANT HEALTH, INC.

Inventor： Justin I. ODEGAARD ,  Marcin SIKORA ,  Aliaksandr ARTSIOMENKA

IPC: G16B30/10

CPC classification number: G16B30/10

Abstract: Methods, systems, and compositions for non-invasively detecting and/or monitoring therapeutic nucleic acid constructs in a sample comprising cell-free nucleic acids from a subject. Detection of therapeutic nucleic acid constructs in samples comprising cell-free nucleic acids allows for verifying therapeutic nucleic acid construct administration, determining the persistence or biological efficacy of the therapeutic nucleic acid construct, and/or ascertaining the efficacy of the therapy in the subject.

公开(公告)号：US20230416843A1

公开(公告)日：2023-12-28

申请号：US18456362

申请日：2023-08-25

Applicant: GUARDANT HEALTH, INC.

Inventor： Aliaksandr ARTSIOMENKA ,  Marcin SIKORA ,  Catalin BARBACIORU ,  Darya CHUDOVA ,  Martina I. LEFTEROVA

IPC: C12Q1/6886 ,  G16B30/10 ,  G16B20/20 ,  G16B40/20

CPC classification number: C12Q1/6886 ,  G16B30/10 ,  G16B20/20 ,  G16B40/20

Abstract: Provided herein are methods for determining the microsatellite instability status of samples. In one aspect, the methods include quantifying a number of different repeat lengths present at each of a plurality of microsatellite loci from sequence information to generate a site score for each of the plurality of the microsatellite loci. The methods also include comparing the site score of a given microsatellite locus to a site specific trained threshold for the given microsatellite locus for each of the plurality of the microsatellite loci and calling the given microsatellite locus as being unstable when the site score of the given microsatellite locus exceeds the site specific trained threshold for the given microsatellite locus to generate a microsatellite instability score, which includes a number of unstable microsatellite loci from the plurality of the microsatellite loci.