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：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：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.

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：US20200020430A1

公开(公告)日：2020-01-16

申请号：US16579500

申请日：2019-09-23

Applicant: FOUNDATION MEDICINE, INC.

Inventor： Helena Futscher de Deus ,  Rachel Lauren Erlich ,  Ronald David Collette ,  Alexander Nevin Parker ,  Michael Pellini ,  Gary Palmer ,  Mary Patricia Lancelotta ,  Matthew J. Hawryluk ,  Philip James Stephens ,  Eric Karl Neumann

IPC: G16H10/60

Abstract: A system for managing genomic information includes a processor to collect and store biomarker data, receive and store patient-specific pathology information, generate a graph-based data structure of complex data elements arranged into a walkable graph representation that includes at least one of a disease alteration group association (DAGA) element representing a relationship between a disease and an alteration group (AG), at least one of a disease therapy association (DTA) element representing a relationship between a disease and a therapy for treating the disease, and a therapy genomic effect (TGE) element representing a relationship between a gene and a known effect of a therapy on the gene. The processor follows links in the walkable graph representation to determine at least one inferred path, generates inferential matches to actionable items based on an accumulated trust score of the at least one inferred path, and determines a treatment decision for a cancer patient.

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.