Patents by Inventor Roman Yelensky

Roman Yelensky 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).

  • Publication number: 20190279742
    Abstract: A method for identifying neoantigens that are likely to be presented on a surface of tumor cells of a subject. Peptide sequences of tumor neoantigens are obtained by sequencing the tumor cells of the subject. The peptide sequence of each of the neoantigens is associated with one or more k-mer blocks of a plurality of k-mer blocks of the nucleotide sequencing data of the subject; The peptide sequences and the associated k-mer blocks are input into a machine-learned presentation model to generate presentation likelihoods for the tumor neoantigens, each presentation likelihood representing the likelihood that a neoantigen is presented by an MHC allele on the surfaces of the tumor cells of the subject. A subset of the neoantigens is selected based on the presentation likelihoods.
    Type: Application
    Filed: May 3, 2019
    Publication date: September 12, 2019
    Inventors: Brendan Bulik-Sullivan, Thomas Francis Boucher, Roman Yelensky
  • Publication number: 20190233897
    Abstract: Novel mutant ESR1 molecules and uses are disclosed.
    Type: Application
    Filed: September 5, 2018
    Publication date: August 1, 2019
    Inventors: Maureen T. Cronin, Garrett Michael Frampton, Doron Lipson, Vincent A. Miller, Gary Palmer, Jeffrey S. Ross, Philip James Stephens, Roman Yelensky
  • Publication number: 20190219586
    Abstract: The present invention provides therapeutic and diagnostic methods and compositions for cancer, for example, lung cancer (e.g., NSCLC), bladder cancer (e.g., UC), kidney cancer (e.g., RCC), breast cancer (e.g., TNBC), or melanoma. The invention provides methods of treating cancer (e.g., lung cancer (e.g., NSCLC), bladder cancer (e.g., UC), kidney cancer (e.g., RCC), breast cancer (e.g., TNBC), or melanoma), methods of determining whether a patient suffering from cancer (e.g., lung cancer (e.g., NSCLC), bladder cancer (e.g., UC), kidney cancer (e.g., RCC), breast cancer (e.g., TNBC), or melanoma) is likely to respond to treatment comprising a PD-L1 axis binding antagonist, methods of predicting responsiveness of a patient suffering from cancer (e.g., lung cancer (e.g., NSCLC), bladder cancer (e.g., UC), kidney cancer (e.g., RCC), breast cancer (e.g., TNBC), or melanoma) to treatment comprising a PD-L1 axis binding antagonist, and methods of selecting a therapy for a patient suffering from cancer (e.g.
    Type: Application
    Filed: April 1, 2019
    Publication date: July 18, 2019
    Inventors: David Fabrizio, Garrett M. Frampton, Priti Hegde, Marcin Kowanetz, David Shames, Philip J. Stephens, James Xin Sun, Roman Yelensky, Wei Zou
  • 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
  • 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
  • Publication number: 20190085403
    Abstract: Methods and compositions for treating cancer such as melanomas are disclosed.
    Type: Application
    Filed: February 27, 2017
    Publication date: March 21, 2019
    Inventors: Garrett Michael Frampton, Roman Yelensky, James Xin Sun, Douglas Buckner Johnson, Christine Marie Lovly, Jeffrey Alan Sosman
  • Publication number: 20190065675
    Abstract: Disclosed herein is a system and methods for determining the alleles, neoantigens, and vaccine composition as determined on the basis of an individual's tumor mutations. Also disclosed are systems and methods for obtaining high quality sequencing data from a tumor. Further, described herein are systems and methods for identifying somatic changes in polymorphic genome data. Finally, described herein are unique cancer vaccines.
    Type: Application
    Filed: June 6, 2018
    Publication date: February 28, 2019
    Inventors: Roman Yelensky, Adnan Derti, Brendan Bulik-Sullivan, Jennifer Busby
  • 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
  • Publication number: 20190034585
    Abstract: Disclosed herein is a system and methods for determining the alleles, neoantigens, and vaccine composition as determined on the basis of an individual's tumor mutations. Also disclosed are systems and methods for obtaining high quality sequencing data from a tumor. Further, described herein are systems and methods for identifying somatic changes in polymorphic genome data. Finally, described herein are unique cancer vaccines.
    Type: Application
    Filed: September 11, 2018
    Publication date: January 31, 2019
    Inventors: Roman Yelensky, Adnan Derti, Brendan Bulik-Sullivan, Jennifer Busby
  • Publication number: 20180371099
    Abstract: The present invention provides therapeutic and diagnostic methods and compositions for cancer, for example, bladder cancer. The invention provides methods of treating bladder cancer, methods of determining whether a patient suffering from bladder cancer is likely to respond to treatment comprising a PD-L1 axis binding antagonist, methods of predicting responsiveness of a patient suffering from bladder cancer to treatment comprising a PD-L1 axis binding antagonist, and methods of selecting a therapy for a patient suffering from bladder cancer, based on somatic mutation levels of genes of the invention (e.g., somatic mutation levels in a tumor sample obtained from the patient).
    Type: Application
    Filed: August 28, 2018
    Publication date: December 27, 2018
    Inventors: Richard BOURGON, David FABRIZIO, Gregg FINE, Garrett M. FRAMPTON, Priti HEGDE, Sanjeev MARIATHASAN, Philip J. STEPHENS, James Xin SUN, Roman YELENSKY
  • Publication number: 20180363066
    Abstract: Methods of evaluating tumor mutational burden in a sample, e.g., a tumor sample or a sample derived from a tumor, from a subject, are disclosed.
    Type: Application
    Filed: August 28, 2018
    Publication date: December 20, 2018
    Inventors: Zachary R. Chalmers, Caitlin F. Connelly, David Fabrizio, Garrett Michael Frampton, Priti Hegde, Marcin Kowanetz, Philip J. Stephens, James Xin Sun, Roman Yelensky
  • Publication number: 20180346992
    Abstract: Novel ALK and NTRK1 fusion molecules and uses are disclosed.
    Type: Application
    Filed: May 14, 2018
    Publication date: December 6, 2018
    Inventors: Maureen T. Cronin, Doron Lipson, Roman Yelensky
  • Publication number: 20180338977
    Abstract: Methods of treating a head and neck cancer are disclosed.
    Type: Application
    Filed: January 17, 2018
    Publication date: November 29, 2018
    Inventors: Chris Hendrik Boshoff, Timothy Robert Fenton, Matthias Alexander Lechner, Philip James Stephens, Matthew J. Hawryluk, Garrett Michael Frampton, Roman Yelensky
  • Publication number: 20180330055
    Abstract: Disclosed herein is a system and methods for determining the alleles, neoantigens, and vaccine composition as determined on the basis of an individual's tumor mutations. Also disclosed are systems and methods for obtaining high quality sequencing data from a tumor. Further, described herein are systems and methods for identifying somatic changes in polymorphic genome data. Finally, described herein are unique cancer vaccines.
    Type: Application
    Filed: July 19, 2018
    Publication date: November 15, 2018
    Inventors: Roman Yelensky, Adnan Derti, Brendan Bulik-Sullivan, Jennifer Busby
  • Publication number: 20180320238
    Abstract: Novel mutant ESR1 molecules and uses are disclosed.
    Type: Application
    Filed: January 22, 2018
    Publication date: November 8, 2018
    Inventors: Maureen T. Cronin, Garrett Michael Frampton, Doron Lipson, Vincent A. Miller, Gary Palmer, Jeffrey S. Ross, Philip James Stephens, Roman Yelensky
  • Patent number: 10093983
    Abstract: Novel mutant ESR1 molecules and uses are disclosed.
    Type: Grant
    Filed: June 29, 2015
    Date of Patent: October 9, 2018
    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: 10055540
    Abstract: Disclosed herein is a system and methods for determining the alleles, neoantigens, and vaccine composition as determined on the basis of an individual's tumor mutations. Also disclosed are systems and methods for obtaining high quality sequencing data from a tumor. Further, described herein are systems and methods for identifying somatic changes in polymorphic genome data. Finally, described herein are unique cancer vaccines.
    Type: Grant
    Filed: March 22, 2017
    Date of Patent: August 21, 2018
    Assignee: Gritstone Oncology, Inc.
    Inventors: Roman Yelensky, Adnan Derti, Brendan Bulik-Sullivan, Jennifer Busby
  • Publication number: 20180218113
    Abstract: Methods and systems for analyzing genetic variants are disclosed.
    Type: Application
    Filed: September 19, 2017
    Publication date: August 2, 2018
    Inventors: James Xin Sun, Roman Yelensky
  • Patent number: 10000814
    Abstract: Novel ALK and NTRK1 fusion molecules and uses are disclosed.
    Type: Grant
    Filed: April 21, 2014
    Date of Patent: June 19, 2018
    Assignee: FOUNDATION MEDICINE, INC.
    Inventors: Maureen T. Cronin, Doron Lipson, Roman Yelensky
  • Patent number: 9907798
    Abstract: Methods of treating a head and neck cancer are disclosed.
    Type: Grant
    Filed: July 1, 2016
    Date of Patent: March 6, 2018
    Assignees: FOUNDATION MEDICINE, INC., UCL Business PLC
    Inventors: Chris Hendrik Boshoff, Timothy Robert Fenton, Matthias Alexander Lechner, Philip James Stephens, Matthew J. Hawryluk, Garrett Michael Frampton, Roman Yelensky