Patents by Inventor Sean R. Downing

Sean R. Downing 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).

  • KIF5B-RET FUSION MOLECULES AND USES THEREOF
    Publication number: 20230241065
    Abstract: Novel RET fusion molecules and uses are disclosed.
    Type: Application
    Filed: August 4, 2022
    Publication date: August 3, 2023
    Applicant: FOUNDATION MEDICINE, INC.
    Inventors: Sean R. DOWNING, Matthew J. HAWRYLUK, Doron LIPSON, Alexander N. PARKER, Philip James STEPHENS
  • OPTIMIZATION OF MULTIGENE ANALYSIS OF TUMOR SAMPLES
    Publication number: 20230148412
    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: Application
    Filed: July 13, 2022
    Publication date: May 11, 2023
    Applicant: 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
  • Optimization of multigene analysis of tumor samples
    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
  • Optimization of multigene analysis of tumor samples
    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
  • Optimization of multigene analysis of tumor samples
    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
  • OPTIMIZATION OF MULTIGENE ANALYSIS OF TUMOR SAMPLES
    Publication number: 20190136301
    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: Application
    Filed: January 11, 2019
    Publication date: May 9, 2019
    Inventors: Doron Lipson, Geoffrey Alan Otto, Alexander Nevin Parker, Philip James Stephens, Sean R. Downing, Mirna Jarosz, Mikhail G. Shapiro, Roman Yelensky
  • OPTIMIZATION OF MULTIGENE ANALYSIS OF TUMOR SAMPLES
    Publication number: 20190119733
    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: Application
    Filed: November 1, 2018
    Publication date: April 25, 2019
    Inventors: Doron Lipson, Geoffrey Alan Otto, Alexander Nevin Parker, Philip James Stephens, Sean R. Downing, Mirna Jarosz, Mikhail G. Shapiro, Roman Yelensky
  • OPTIMIZATION OF MULTIGENE ANALYSIS OF TUMOR SAMPLES
    Publication number: 20190032118
    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: Application
    Filed: February 15, 2018
    Publication date: January 31, 2019
    Inventors: Doron Lipson, Geoffrey Alan Otto, Alexander N. Parker, Philip James Stephens, Sean R. Downing, Mirna Jarosz, Mikhail G. Shapiro, Roman Yelensky
  • NOVEL KIF5B-RET FUSION MOLECULES AND USES THEREOF
    Publication number: 20180280391
    Abstract: Novel RET fusion molecules and uses are disclosed.
    Type: Application
    Filed: December 12, 2017
    Publication date: October 4, 2018
    Inventors: Sean R. Downing, Matthew J. Hawryluk, Doron Lipson, Alexander N. Parker, Philip James Stephens
  • KIF5B-RET fusion molecules and uses thereof
    Patent number: 9884060
    Abstract: Novel RET fusion molecules and uses are disclosed. In one embodiment, a KIF5B-RET fusion includes an in-frame fusion of an exon of KIF5B (e.g., one or more exons encoding a kinesin motor domain or a fragment thereof) and an exon of RET (e.g., one or more exons encoding a RET tyrosine kinase domain or a fragment thereof). For example, the KIF5B-RET fusion can include an in-frame fusion of at least exon 15 of KIF5B or a fragment thereof (e.g., exons 1-15 of KIF5B or a fragment thereof) with at least exon 12 of RET or a fragment thereof (e.g., exons 12-20 of RET or a fragment thereof).
    Type: Grant
    Filed: February 17, 2016
    Date of Patent: February 6, 2018
    Assignee: FOUNDATION MEDICINE, INC.
    Inventors: Sean R. Downing, Matthew J. Hawryluk, Doron Lipson, Alexander N. Parker, Philip James Stephens
  • NOVEL KIF5B-RET FUSION MOLECULES AND USES THEREOF
    Publication number: 20170014413
    Abstract: Novel RET fusion molecules and uses are disclosed. In one embodiment, a KIF5B-RET fusion includes an in-frame fusion of an exon of KIF5B (e.g., one or more exons encoding a kinesin motor domain or a fragment thereof) and an exon of RET (e.g., one or more exons encoding a RET tyrosine kinase domain or a fragment thereof). For example, the KIF5B-RET fusion can include an in-frame fusion of at least exon 15 of KIF5B or a fragment thereof (e.g., exons 1-15 of KIF5B or a fragment thereof) with at least exon 12 of RET or a fragment thereof (e.g., exons 12-20 of RET or a fragment thereof).
    Type: Application
    Filed: February 17, 2016
    Publication date: January 19, 2017
    Inventors: Sean R. Downing, Matthew J. Hawryluk, Doron Lipson, Alexander N. Parker, Philip James Stephens
  • Optimization of multigene analysis of tumor samples
    Patent number: 9340830
    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: December 29, 2011
    Date of Patent: May 17, 2016
    Assignee: FOUNDATION MEDICINE, INC.
    Inventors: Doron Lipson, Geoffrey Alan Otto, Alexander N. Parker, Philip James Stephens, Sean R. Downing, Mima Jarosz, Mikhail G. Shapiro, Roman Yelensky
  • KIF5B-RET fusion molecules and uses thereof
    Patent number: 9297011
    Abstract: Novel RET fusion molecules and uses are disclosed.
    Type: Grant
    Filed: February 23, 2014
    Date of Patent: March 29, 2016
    Assignee: FOUNDATION MEDICINE, INC.
    Inventors: Sean R. Downing, Matthew J. Hawryluk, Doron Lipson, Alexander N. Parker, Philip James Stephens
  • NOVEL KIF5B-RET FUSION MOLECULES AND USES THEREOF
    Publication number: 20140243390
    Abstract: Novel RET fusion molecules and uses are disclosed.
    Type: Application
    Filed: February 23, 2014
    Publication date: August 28, 2014
    Applicant: FOUNDATION MEDICINE, INC.
    Inventors: Sean R. Downing, Matthew J. Hawryluk, Doron Lipson, Alexander N. Parker, Philip James Stephens
  • OPTIMIZATION OF MULTIGENE ANALYSIS OF TUMOR SAMPLES
    Publication number: 20120208706
    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: Application
    Filed: December 29, 2011
    Publication date: August 16, 2012
    Applicant: FOUNDATION MEDICINE, INC.
    Inventors: Sean R. Downing, Mirna Jarosz, Doron Lipson, Geoffrey Alan Otto, Alexander N. Parker, Mikhail G. Shapiro, Philip James Stephens, Roman Yelensky