Patents by Inventor Philip James Stephens

Philip James Stephens has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).

  • Patent number: 12274699
    Abstract: Methods and compositions for treating cholangiocarcinoma.
    Type: Grant
    Filed: June 30, 2023
    Date of Patent: April 15, 2025
    Assignee: Foundation Medicine, Inc.
    Inventors: Siraj Mahamed Ali, Matthew J. Hawryluk, Jie He, Doron Lipson, Vincent A. Miller, Jeffrey S. Ross, Philip James Stephens
  • Patent number: 12239648
    Abstract: Novel RET fusion molecules and uses are disclosed.
    Type: Grant
    Filed: August 4, 2022
    Date of Patent: March 4, 2025
    Assignee: Foundation Medicine, Inc.
    Inventors: Sean R. Downing, Matthew J. Hawryluk, Doron Lipson, Alexander N. Parker, Philip James Stephens
  • Patent number: 12180540
    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.
    Type: Grant
    Filed: July 13, 2022
    Date of Patent: December 31, 2024
    Assignee: Foundation Medicine, Inc.
    Inventors: Doron Lipson, Geoffrey Alan Otto, Alexander Nevin Parker, Philip James Stephens, Sean R. Downing, Mirna Jarosz, Mikhail G. Shapiro, Roman Yelensky
  • Patent number: 12116638
    Abstract: Novel mutant ESR1 molecules and uses are disclosed.
    Type: Grant
    Filed: February 16, 2022
    Date of Patent: October 15, 2024
    Assignee: Foundation Medicine, Inc.
    Inventors: Maureen T. Cronin, Garrett Michael Frampton, Doron Lipson, Vincent A. Miller, Gary Palmer, Jeffrey S. Ross, Philip James Stephens, Roman Yelensky
  • Patent number: 11771698
    Abstract: Methods and compositions for treating cholangiocarcinoma.
    Type: Grant
    Filed: March 17, 2021
    Date of Patent: October 3, 2023
    Assignee: Foundation Medicine, Inc.
    Inventors: Siraj Mahamed Ali, Matthew J. Hawryluk, Jie He, Doron Lipson, Vincent A. Miller, Jeffrey S. Ross, Philip James Stephens
  • Patent number: 11766439
    Abstract: Methods of treating a head and neck cancer are disclosed.
    Type: Grant
    Filed: June 10, 2021
    Date of Patent: September 26, 2023
    Assignees: FOUNDATION MEDICINE, INC., UCL BUSINESS LTD
    Inventors: Chris Hendrik Boshoff, Timothy Robert Fenton, Matthias Alexander Lechner, Philip James Stephens, Matthew J. Hawryluk, Garrett Michael Frampton, Roman Yelensky
  • Patent number: 11725247
    Abstract: Methods and compositions for treating cancer such as melanomas are disclosed.
    Type: Grant
    Filed: February 27, 2017
    Date of Patent: August 15, 2023
    Assignees: FOUNDATION MEDICINE, INC., VANDERBILT UNIVERSITY
    Inventors: Garrett Michael Frampton, Roman Yelensky, James Xin Sun, Douglas Buckner Johnson, Christine Marie Lovly, Jeffrey Alan Sosman, David Fabrizio, Philip James Stephens, Vincent A. Miller
  • Patent number: 11578372
    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.
    Type: Grant
    Filed: November 14, 2019
    Date of Patent: February 14, 2023
    Assignee: Foundation Medicine, Inc.
    Inventors: Matthew J. Hawryluk, Doron Lipson, Vincent A. Miller, Philip James Stephens
  • Patent number: 11421265
    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.
    Type: Grant
    Filed: January 11, 2019
    Date of Patent: August 23, 2022
    Assignee: FOUNDATION MEDICINE, INC.
    Inventors: Doron Lipson, Geoffrey Alan Otto, Alexander Nevin Parker, Philip James Stephens, Sean R. Downing, Mima Jarosz, Mikhail G. Shapiro, Roman Yelensky
  • Publication number: 20220096483
    Abstract: Methods of treating a head and neck cancer are disclosed.
    Type: Application
    Filed: June 10, 2021
    Publication date: March 31, 2022
    Inventors: Chris Hendrik Boshoff, Timothy Robert Fenton, Matthias Alexander Lechner, Philip James Stephens, Matthew J. Hawryluk, Garrett Michael Frampton, Roman Yelensky
  • Patent number: 11286532
    Abstract: Novel mutant ESR1 molecules and uses are disclosed.
    Type: Grant
    Filed: January 22, 2018
    Date of Patent: March 29, 2022
    Assignee: FOUNDATION MEDICINE, INC.
    Inventors: Maureen T. Cronin, Garrett Michael Frampton, Doron Lipson, Vincent A. Miller, Gary Palmer, Jeffrey S. Ross, Philip James Stephens, Roman Yelensky
  • Patent number: 11158425
    Abstract: Various embodiments provide interfaces to access genomic testing information and incorporate it into daily physician practice. According to one aspect, a graph-based data model is used that may be used to organizes and revise precision medicine knowledge. In one example structure, gene states are abstracted into alteration groups, where alteration groups are built using reverse engineering actionable information and storing that information within the graph-based data structure. Volumes of genomic alterations and associated information (e.g., journal articles, clinical trial information, therapies, etc.) are analyzed and synthesized into actionable information items viewable on an alteration system in a graph-based data format. According to one embodiment, the system can be configured to focus practitioners on discrete portions of the alteration information on which they can act.
    Type: Grant
    Filed: August 19, 2014
    Date of Patent: October 26, 2021
    Assignee: FOUNDATION MEDICINE, INC.
    Inventors: Helena Futscher de Deus, Rachel Lauren Erbach, Ronald David Collette, Alexander N. Parker, Michael Pellini, Gary Palmer, Mary Pat Lancelotta, Matthew J. Hawryluk, Philip James Stephens, Eric Karl Neumann
  • Patent number: 11136619
    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.
    Type: Grant
    Filed: November 1, 2018
    Date of Patent: October 5, 2021
    Assignee: Foundation Medicine, Inc.
    Inventors: Doron Lipson, Geoffrey Alan Otto, Alexander Nevin Parker, Philip James Stephens, Sean R. Downing, Mima Jarosz, Mikhail G. Shapiro, Roman Yelensky
  • Patent number: 11118213
    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.
    Type: Grant
    Filed: February 15, 2018
    Date of Patent: September 14, 2021
    Assignee: Foundation Medicine, Inc.
    Inventors: Doron Lipson, Geoffrey Alan Otto, Alexander N. Parker, Philip James Stephens, Sean R. Downing, Mirna Jarosz, Mikhail G. Shapiro, Roman Yelensky
  • Patent number: 11058687
    Abstract: Methods of treating a head and neck cancer are disclosed.
    Type: Grant
    Filed: October 16, 2019
    Date of Patent: July 13, 2021
    Assignees: FOUNDATION MEDICINE, INC., UCL BUSINESS LTD
    Inventors: Chris Hendrik Boshoff, Timothy Robert Fenton, Matthias Alexander Lechner, Philip James Stephens, Matthew J. Hawryluk, Garrett Michael Frampton, Roman Yelensky
  • Patent number: 10980804
    Abstract: Methods and compositions for treating cholangiocarcinoma.
    Type: Grant
    Filed: January 17, 2014
    Date of Patent: April 20, 2021
    Assignee: FOUNDATION MEDICINE, INC.
    Inventors: Siraj Mahamed Ali, Matthew J. Hawryluk, Jie He, Doron Lipson, Vincent A. Miller, Jeffrey S. Ross, Philip James Stephens
  • Publication number: 20200299775
    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.
    Type: Application
    Filed: November 14, 2019
    Publication date: September 24, 2020
    Inventors: Matthew J. Hawryluk, Doron Lipson, Vincent A. Miller, Philip James Stephens
  • Publication number: 20200294668
    Abstract: Various embodiments provide interfaces to access genomic testing information and incorporate it into daily physician practice. In some embodiments, presentation of genomic alteration data is simplified and/or coupled with contextual applications. Volumes of genomic alterations and associated information (e.g., journal articles, clinical trial information, therapies, etc.) are analyzed and synthesized into actionable information items viewable on an alteration system. According to one embodiment, the system can be configured to focus practitioners on discrete portions of the alteration information on which they can act. According to other aspects, curated information is provided on the system to enable practitioners to make informed decisions regarding the implications of the presence of specific genomic alterations.
    Type: Application
    Filed: February 18, 2020
    Publication date: September 17, 2020
    Inventors: Michael Pellini, Gary Palmer, Mary Patricia Lancelotta, Matthew J. Hawryluk, Philip James Stephens
  • Publication number: 20200281930
    Abstract: Methods of treating a head and neck cancer are disclosed.
    Type: Application
    Filed: October 16, 2019
    Publication date: September 10, 2020
    Inventors: Chris Hendrik Boshoff, Timothy Robert Fenton, Matthias Alexander Lechner, Philip James Stephens, Matthew J. Hawryluk, Garrett Michael Frampton, Roman Yelensky
  • Publication number: 20200020430
    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.
    Type: Application
    Filed: September 23, 2019
    Publication date: January 16, 2020
    Inventors: 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