公开(公告)号：US20240327926A1

公开(公告)日：2024-10-03

申请号：US18607277

申请日：2024-03-15

Applicant: Foundation Medicine, Inc.

Inventor： Geoffrey Alan OTTO ,  Michelle NAHAS ,  Doron LIPSON

IPC: C12Q1/6886 ,  C12N15/10 ,  C12Q1/6806 ,  G16B25/00 ,  G16B25/10 ,  G16B30/00 ,  G16B30/10 ,  G16B45/00

CPC classification number: C12Q1/6886 ,  C12N15/1065 ,  C12Q1/6806 ,  G16B25/00 ,  G16B25/10 ,  G16B30/00 ,  G16B30/10 ,  G16B45/00 ,  C12Q2600/156 ,  C12Q2600/158 ,  C12Q2600/16

Abstract: Methods of evaluating or providing a clonal profile of a subject interval, e.g., a subgenomic interval, or an expressed subgenomic interval (or of a cell containing the same), in a subject, are disclosed.

公开(公告)号：US20190025308A1

公开(公告)日：2019-01-24

申请号：US16041363

申请日：2018-07-20

Applicant: Genentech, Inc. ,  Foundation Medicine, Inc.

Inventor： Craig Anthony CUMMINGS ,  Yan LI ,  Sarah Margaret PAUL ,  Erica Beth SCHLEIFMAN ,  David SHAMES ,  David FABRIZIO ,  Daniel LIEBER ,  Geoffrey Alan OTTO ,  Mark KENNEDY ,  Travis CLARK ,  Doron LIPSON ,  Jie HE ,  Shan ZHONG

IPC: G01N33/574 ,  C07K16/28 ,  G16H50/70 ,  G16H50/50 ,  G16H50/30 ,  G16H50/20 ,  G06F17/30 ,  C07K14/735 ,  A61P35/00

Abstract: The present invention provides therapeutic, diagnostic, and prognostic methods for cancer. The invention provides methods of treating a cancer, methods of determining whether an individual having a cancer is likely to respond to a treatment including an immune checkpoint inhibitor (e.g., a PD-L1 axis binding antagonist), methods of predicting responsiveness of an individual having a cancer to a treatment including an immune checkpoint inhibitor (e.g., a PD-L1 axis binding antagonist), methods of selecting a therapy for an individual having a cancer, methods of providing a prognosis for an individual having a cancer, and methods of monitoring a response of an individual having a cancer, based on a blood tumor mutational burden (bTMB) score or a maximum somatic allele frequency (MSAF) from a sample (e.g., a whole blood sample, a plasma sample, a serum sample, or a combination thereof) from the individual.

公开(公告)号：US20240288430A1

公开(公告)日：2024-08-29

申请号：US18513107

申请日：2023-11-17

Applicant: Genentech, Inc. ,  Foundation Medicine, Inc.

Inventor： Craig Anthony CUMMINGS ,  Yan LI ,  Sarah Margaret SHAGAN ,  Erica Beth SCHLEIFMAN ,  David SHAMES ,  David FABRIZIO ,  Daniel LIEBER ,  Geoffrey Alan OTTO ,  Mark KENNEDY ,  Travis CLARK ,  Doron LIPSON ,  Jie HE ,  Shan ZHONG

IPC: G01N33/574 ,  A61K39/00 ,  A61P35/00 ,  C07K14/735 ,  C07K16/28 ,  C12Q1/68 ,  C12Q1/6883 ,  G06F16/28 ,  G16H50/20 ,  G16H50/30 ,  G16H50/50 ,  G16H50/70

CPC classification number: G01N33/574 ,  A61P35/00 ,  C07K14/70535 ,  C07K16/2827 ,  C07K16/2896 ,  C12Q1/68 ,  C12Q1/6883 ,  G01N33/57492 ,  G06F16/285 ,  G16H50/20 ,  G16H50/30 ,  G16H50/50 ,  G16H50/70 ,  A61K2039/505 ,  A61K2039/55 ,  C07K2317/24 ,  C12Q2600/156 ,  G01N2333/70532 ,  G01N2800/52

Abstract: The present invention provides therapeutic, diagnostic, and prognostic methods for cancer. The invention provides methods of treating a cancer, methods of determining whether an individual having a cancer is likely to respond to a treatment including an immune checkpoint inhibitor (e.g., a PD-L1 axis binding antagonist), methods of predicting responsiveness of an individual having a cancer to a treatment including an immune checkpoint inhibitor (e.g., a PD-L1 axis binding antagonist), methods of selecting a therapy for an individual having a cancer, methods of providing a prognosis for an individual having a cancer, and methods of monitoring a response of an individual having a cancer, based on a blood tumor mutational burden (bTMB) score or a maximum somatic allele frequency (MSAF) from a sample (e.g., a whole blood sample, a plasma sample, a serum sample, or a combination thereof) from the individual.

公开(公告)号：US20230148412A1

公开(公告)日：2023-05-11

申请号：US17812415

申请日：2022-07-13

Applicant: Foundation Medicine, Inc.

Inventor： Doron LIPSON ,  Geoffrey Alan OTTO ,  Alexander Nevin PARKER ,  Philip James STEPHENS ,  Sean R. DOWNING ,  Mirna JAROSZ ,  Mikhail G. SHAPIRO ,  Roman YELENSKY

IPC: C12Q1/6827 ,  C12Q1/6874 ,  G16B20/10 ,  G16B30/10 ,  G16B20/20 ,  G16B20/00 ,  G16B30/00

CPC classification number: C12Q1/6827 ,  C12Q1/6874 ,  G16B20/10 ,  G16B30/10 ,  G16B20/20 ,  G16B20/00 ,  G16B30/00 ,  C12Q1/6886

Abstract: A method of analyzing a tumor sample comprising:



(a) acquiring a library comprising a plurality of tumor members from a tumor sample;
(b) contacting the library with a bait set to provide selected members;
(c) acquiring a read for a subgenomic interval from a tumor member from said library;
(d) aligning said read; and
(e) assigning a nucleotide value (e.g., calling a mutation) from said read for the preselected nucleotide position, thereby analyzing said tumor sample.