公开(公告)号：US11421265B2

公开(公告)日：2022-08-23

申请号：US16245301

申请日：2019-01-11

Applicant: FOUNDATION MEDICINE, INC.

Inventor： Doron Lipson ,  Geoffrey Alan Otto ,  Alexander Nevin Parker ,  Philip James Stephens ,  Sean R. Downing ,  Mima Jarosz ,  Mikhail G. Shapiro ,  Roman Yelensky

IPC: C12Q1/6827 ,  C12Q1/6874 ,  C12Q1/6886 ,  G16B20/10 ,  G16B30/10 ,  G16B20/20 ,  G16B20/00 ,  G16B30/00

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.

公开(公告)号：US20190119733A1

公开(公告)日：2019-04-25

申请号：US16178101

申请日：2018-11-01

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

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.

公开(公告)号：US20170356053A1

公开(公告)日：2017-12-14

申请号：US15529237

申请日：2015-12-04

Applicant: FOUNDATION MEDICINE, INC.

Inventor： Geoffrey Alan Otto ,  Michelle Nahas ,  Doron Lipson

IPC: C12Q1/68 ,  G06F19/20 ,  C12N15/10 ,  G06F19/26 ,  G06F19/22

CPC classification number: C12Q1/6886 ,  C12N15/1065 ,  C12Q1/6806 ,  C12Q2600/156 ,  C12Q2600/158 ,  C12Q2600/16 ,  G16B25/00 ,  G16B30/00 ,  G16B45/00 ,  C12Q2535/122 ,  C12Q2537/159 ,  C12Q2563/131

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：US12180540B2

公开(公告)日：2024-12-31

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 ,  C12Q1/6886 ,  G16B20/00 ,  G16B20/10 ,  G16B20/20 ,  G16B30/00 ,  G16B30/10

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.

公开(公告)号：US11959141B2

公开(公告)日：2024-04-16

申请号：US15529237

申请日：2015-12-04

Applicant: FOUNDATION MEDICINE, INC.

Inventor： Geoffrey Alan Otto ,  Michelle Nahas ,  Doron Lipson

IPC: C12Q1/68 ,  C12N15/10 ,  C12Q1/6806 ,  C12Q1/6886 ,  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 ,  C12Q1/6806 ,  C12Q2535/122 ,  C12Q2537/159 ,  C12Q2563/131

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：US11674962B2

公开(公告)日：2023-06-13

申请号：US16041363

申请日：2018-07-20

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

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：US11136619B2

公开(公告)日：2021-10-05

申请号：US16178101

申请日：2018-11-01

Applicant: FOUNDATION MEDICINE, INC.

Inventor： Doron Lipson ,  Geoffrey Alan Otto ,  Alexander Nevin Parker ,  Philip James Stephens ,  Sean R. Downing ,  Mima Jarosz ,  Mikhail G. Shapiro ,  Roman Yelensky

IPC: C12Q1/6827 ,  C12Q1/6874 ,  C12Q1/6886 ,  G16B20/00 ,  G16B30/00

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.

公开(公告)号：US11118213B2

公开(公告)日：2021-09-14

申请号：US15897824

申请日：2018-02-15

Applicant: FOUNDATION MEDICINE, INC.

Inventor： Doron Lipson ,  Geoffrey Alan Otto ,  Alexander N. Parker ,  Philip James Stephens ,  Sean R. Downing ,  Mirna Jarosz ,  Mikhail G. Shapiro ,  Roman Yelensky

IPC: C12Q1/6827 ,  C12Q1/6874 ,  C12Q1/6886 ,  G16B20/00 ,  G16B30/00

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.

公开(公告)号：US20200149097A1

公开(公告)日：2020-05-14

申请号：US16437974

申请日：2019-06-11

Applicant: FOUNDATION MEDICINE, INC.

Inventor： Geoffrey Alan Otto ,  Travis Clark ,  Doron Lipson ,  Daniel Lieber ,  David Fabrizio

IPC: C12Q1/6848 ,  C12N15/10 ,  C12Q1/6827 ,  C12Q1/6886 ,  C12Q1/6853

Abstract: Compositions and methods of evaluating genomic alterations in a sample are disclosed.

公开(公告)号：US20190136301A1

公开(公告)日：2019-05-09

申请号：US16245301

申请日：2019-01-11

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

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.