公开(公告)号：US20250059585A1

公开(公告)日：2025-02-20

申请号：US18720536

申请日：2022-12-15

Applicant: Foundation Medicine, Inc.

Inventor： Christine Marie MALBOEUF ,  Daniela Beatriz MUNAFO

IPC: C12Q1/6806 ,  C12N15/10 ,  C40B50/00

Abstract: The present disclosure provides methods of detecting analytes such as RNA and/or DNA, extracting analytes such as RNA and/or DNA, improving library construction for nucleic acid sequencing, and reducing the level of embedding agent in analyte samples such as RNA and/or DNA samples that are extracted from embedded samples such as paraffin-embedded samples.

公开(公告)号：US20250051840A1

公开(公告)日：2025-02-13

申请号：US18722508

申请日：2022-12-28

Applicant: Foundation Medicine, Inc.

Inventor： Yexun WANG ,  Nicole Jacinda LAMBERT ,  Becky WONG ,  Yu ZHENG ,  Haleigh WOOD

IPC: C12Q1/6869 ,  C12Q1/6855 ,  C12Q1/6881 ,  C12Q1/6886

Abstract: Provided herein are methods related to detecting genetic and epigenetic information in a single workflow, as well as methods of treatment, uses, systems, and computer readable storage media related thereto. These methods allow, e.g., for detection of genetic variants and epigenetic modifications (e.g., methylation level) in a single workflow and/or from a single sample (e.g., a DNA sample).

公开(公告)号：US20240420799A1

公开(公告)日：2024-12-19

申请号：US18718989

申请日：2022-12-06

Applicant: Foundation Medicine, Inc.

Inventor： Yanmei HUANG ,  Jason D. HUGHES

IPC: G16B20/20 ,  C12Q1/6806 ,  C12Q1/6855 ,  C12Q1/6874 ,  C12Q1/6886 ,  G16B20/10 ,  G16H20/10 ,  G16H50/20

Abstract: Methods for determining the reliability of a prediction of somatic or germline origin for a variant sequence in a sample from a subject are described. The methods comprise determining a tumor fraction metric that characterizes a tumor fraction of the sample based on the sequence read data; determining a copy number metric for a variant sequence present in the sample based on the sequence read data; generating a reliability parameter for predicting somatic or germline origin for the variant sequence based on the tumor fraction metric and the copy number metric; and comparing the reliability parameter to a predetermined threshold to determine if the prediction of somatic or germline origin for the variant sequence is reliable.

公开(公告)号：US12087453B2

公开(公告)日：2024-09-10

申请号：US17885412

申请日：2022-08-10

Applicant: Foundation Medicine, Inc.

Inventor： Michael Pellini ,  Gary Palmer ,  Mary Patricia Lancelotta ,  Matthew J. Hawryluk ,  Vincent A. Miller

IPC: G16H70/60 ,  G16B30/00 ,  G16H10/20 ,  G16H10/60 ,  G16H15/00 ,  G16H20/10 ,  G16H50/20

CPC classification number: G16H70/60 ,  G16B30/00 ,  G16H10/20 ,  G16H10/60 ,  G16H15/00 ,  G16H20/10 ,  G16H50/20

Abstract: Provided are systems and methods for capturing outcome information associated with various cancer treatments. The system facilitates capture and analysis of cancer treatment information and associated outcome information. The treatment and outcome information can include genomic analysis and information on treatment of different cancers. The system can store and analyze any one or more of: tumor type, genomic alterations (e.g., genes and associated alterations, gene sequence mutations, alterations, amplifications, deletions, etc.), and treatment data (including, for example, treatments targeted to specific genes and/or genomic alterations). Users of the outcome system can supply and use the treatment and outcome information to facilitate diagnosis and therapy decisions. User interfaces within the system can be configured to allow users to easily locate outcome information associated with particular treatments of tumors having certain genomic alterations.

公开(公告)号：US20240110230A1

公开(公告)日：2024-04-04

申请号：US18276223

申请日：2022-02-09

Applicant: Foundation Medicine, Inc.

Inventor： Jeffrey ROSS

IPC: C12Q1/6827 ,  A61K45/06 ,  A61P35/00

CPC classification number: C12Q1/6827 ,  A61K45/06 ,  A61P35/00 ,  G01N2800/52

Abstract: The present disclosure provides biomarkers associated with cancers, such as urothelial bladder cancer, non-small cell lung cancer, and renal cell carcinoma, as well as methods, kits and reagents for detecting such biomarkers. The disclosure also provides methods for evaluating, identifying, assessing, and/or treating an individual having a cancer, such as a urothelial bladder cancer, non-small cell lung cancer, and renal cell carcinoma.

公开(公告)号：US20240062916A1

公开(公告)日：2024-02-22

申请号：US18039921

申请日：2021-12-02

Applicant: Foundation Medicine, Inc.

Inventor： Leah COMMENT ,  Giovanni PARMIGIANI

IPC: G16H70/20 ,  C12Q1/6855 ,  G16B20/00

CPC classification number: G16H70/20 ,  C12Q1/6855 ,  G16B20/00

Abstract: Methods and systems for determining an expected disease treatment outcome upon treating a subject, methods and devices for selecting a treatment option for the subject, and methods of treating a subject for a disease, are described herein. The method can include receiving a plurality of subject characteristics for the subject; accessing a tree-based model corresponding to a treatment option for the disease, wherein the tree-based model is generated based on a plurality of prior patient characteristics and an associated treatment outcome for the corresponding treatment option; and determining from the plurality of subject characteristics and the tree-based model, an expected treatment outcome for the subject if the subject were treated with the corresponding treatment option.

公开(公告)号：US11578372B2

公开(公告)日：2023-02-14

申请号：US16683575

申请日：2019-11-14

Applicant: FOUNDATION MEDICINE, INC.

Inventor： Matthew J. Hawryluk ,  Doron Lipson ,  Vincent A. Miller ,  Philip James Stephens

IPC: C12Q1/6886 ,  C12N15/113 ,  C12N9/12 ,  C07K14/47 ,  A61K31/519 ,  A61K31/553 ,  A61K45/06

Abstract: Novel NTRK1 fusion molecules, detection reagents, and uses and kits for evaluating, identifying, assessing and/or treating a subject having a cancer are disclosed.

公开(公告)号：US11566282B2

公开(公告)日：2023-01-31

申请号：US15294695

申请日：2016-10-15

Applicant: Integrated DNA Technologies, Inc. ,  Foundation Medicine, Inc.

Inventor： Mark Aaron Behlke ,  John Robert Havens ,  Mirna Jarosz ,  Zachary Zwirko ,  Doron Lipson ,  Frank Soo Juhn

IPC: C12Q1/68 ,  C12Q1/6874 ,  C12Q1/6869 ,  C12Q1/6886 ,  C12N15/10 ,  C12Q1/6876

Abstract: The invention is directed to modified oligonucleotide compositions and methods for selectively reducing unwanted nucleic acid contaminants and enriching for desired nucleic acid targets from complex genomic nucleic acid mixtures for sequencing applications. The modified oligonucleotide compositions include one or more modified groups that increase the Tm of the resultant oligonucleotide composition.

公开(公告)号：US20220096483A1

公开(公告)日：2022-03-31

申请号：US17344777

申请日：2021-06-10

Applicant: FOUNDATION MEDICINE, INC. ,  UCL BUSINESS LTD

Inventor： Chris Hendrik Boshoff ,  Timothy Robert Fenton ,  Matthias Alexander Lechner ,  Philip James Stephens ,  Matthew J. Hawryluk ,  Garrett Michael Frampton ,  Roman Yelensky

IPC: A61K31/519 ,  C12Q1/70 ,  A61K31/506 ,  A61K31/454 ,  A61K31/52 ,  A61K31/404 ,  A61K31/4196 ,  A61K31/282 ,  A61K31/337 ,  A61K31/513 ,  A61K39/395 ,  A61K31/436 ,  A61K31/05 ,  A61K31/4709 ,  A61K31/496 ,  A61K31/5377 ,  A61K31/352 ,  A61N5/00 ,  C12Q1/6886 ,  A61K31/366 ,  A61K31/505 ,  A61K31/555 ,  A61K33/243 ,  A61K33/24 ,  A61K31/439 ,  A61K31/4745 ,  C07K16/28 ,  C12Q1/6883 ,  G01N33/571 ,  A61N5/10

Abstract: Methods of treating a head and neck cancer are disclosed.

公开(公告)号：US20220002818A1

公开(公告)日：2022-01-06

申请号：US17377231

申请日：2021-07-15

Applicant: Foundation Medicine, Inc.

Inventor： Maureen T. CRONIN ,  Doron LIPSON ,  Roman YELENSKY

IPC: C12Q1/6886 ,  C07K14/47 ,  C12N9/12 ,  A61K31/4545 ,  C07K16/40 ,  G01N33/50 ,  G01N33/574

Abstract: Novel ALK and NTRK1 fusion molecules and uses are disclosed.