Patents by Inventor Geoffrey Alan Otto
Geoffrey Alan Otto 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).
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Patent number: 11959141Abstract: Methods of evaluating or providing a clonal profile of a subject interval, e.g., a subgenomic interval, or an expressed subgenomic interval (or of a cell containing the same), in a subject, are disclosed.Type: GrantFiled: December 4, 2015Date of Patent: April 16, 2024Assignee: Foundation Medicine, Inc.Inventors: Geoffrey Alan Otto, Michelle Nahas, Doron Lipson
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Patent number: 11674962Abstract: The present invention provides therapeutic, diagnostic, and prognostic methods for cancer. The invention provides methods of treating a cancer, methods of determining whether an individual having a cancer is likely to respond to a treatment including an immune checkpoint inhibitor (e.g., a PD-L1 axis binding antagonist), methods of predicting responsiveness of an individual having a cancer to a treatment including an immune checkpoint inhibitor (e.g., a PD-L1 axis binding antagonist), methods of selecting a therapy for an individual having a cancer, methods of providing a prognosis for an individual having a cancer, and methods of monitoring a response of an individual having a cancer, based on a blood tumor mutational burden (bTMB) score or a maximum somatic allele frequency (MSAF) from a sample (e.g., a whole blood sample, a plasma sample, a serum sample, or a combination thereof) from the individual.Type: GrantFiled: July 20, 2018Date of Patent: June 13, 2023Assignees: Genentech, Inc., Foundation Medicine, Inc.Inventors: Craig Anthony Cummings, Yan Li, Sarah Margaret Shagan, Erica Beth Schleifman, David Shames, David Fabrizio, Daniel Lieber, Geoffrey Alan Otto, Mark Kennedy, Travis Clark, Doron Lipson, Jie He, Shan Zhong
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Publication number: 20230148412Abstract: 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: ApplicationFiled: July 13, 2022Publication date: May 11, 2023Applicant: 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
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Patent number: 11421265Abstract: 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: GrantFiled: January 11, 2019Date of Patent: August 23, 2022Assignee: 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
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Patent number: 11136619Abstract: 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: GrantFiled: November 1, 2018Date of Patent: October 5, 2021Assignee: 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
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Patent number: 11118213Abstract: 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: GrantFiled: February 15, 2018Date of Patent: September 14, 2021Assignee: 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
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Publication number: 20200149097Abstract: Compositions and methods of evaluating genomic alterations in a sample are disclosed.Type: ApplicationFiled: June 11, 2019Publication date: May 14, 2020Applicants: FOUNDATION MEDICINE, INC., FOUNDATION MEDICINE, INC.Inventors: Geoffrey Alan Otto, Travis Clark, Doron Lipson, Daniel Lieber, David Fabrizio
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Publication number: 20190136301Abstract: 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: ApplicationFiled: January 11, 2019Publication date: May 9, 2019Inventors: Doron Lipson, Geoffrey Alan Otto, Alexander Nevin Parker, Philip James Stephens, Sean R. Downing, Mirna Jarosz, Mikhail G. Shapiro, Roman Yelensky
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Publication number: 20190119733Abstract: 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: ApplicationFiled: November 1, 2018Publication date: April 25, 2019Inventors: Doron Lipson, Geoffrey Alan Otto, Alexander Nevin Parker, Philip James Stephens, Sean R. Downing, Mirna Jarosz, Mikhail G. Shapiro, Roman Yelensky
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Publication number: 20190032118Abstract: 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: ApplicationFiled: February 15, 2018Publication date: January 31, 2019Inventors: Doron Lipson, Geoffrey Alan Otto, Alexander N. Parker, Philip James Stephens, Sean R. Downing, Mirna Jarosz, Mikhail G. Shapiro, Roman Yelensky
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Publication number: 20190025308Abstract: The present invention provides therapeutic, diagnostic, and prognostic methods for cancer. The invention provides methods of treating a cancer, methods of determining whether an individual having a cancer is likely to respond to a treatment including an immune checkpoint inhibitor (e.g., a PD-L1 axis binding antagonist), methods of predicting responsiveness of an individual having a cancer to a treatment including an immune checkpoint inhibitor (e.g., a PD-L1 axis binding antagonist), methods of selecting a therapy for an individual having a cancer, methods of providing a prognosis for an individual having a cancer, and methods of monitoring a response of an individual having a cancer, based on a blood tumor mutational burden (bTMB) score or a maximum somatic allele frequency (MSAF) from a sample (e.g., a whole blood sample, a plasma sample, a serum sample, or a combination thereof) from the individual.Type: ApplicationFiled: July 20, 2018Publication date: January 24, 2019Inventors: Craig Anthony CUMMINGS, Yan LI, Sarah Margaret PAUL, Erica Beth SCHLEIFMAN, David SHAMES, David FABRIZIO, Daniel LIEBER, Geoffrey Alan OTTO, Mark KENNEDY, Travis CLARK, Doron LIPSON, Jie HE, Shan ZHONG
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Publication number: 20170356053Abstract: Methods of evaluating or providing a clonal profile of a subject interval, e.g., a subgenomic interval, or an expressed subgenomic interval (or of a cell containing the same), in a subject, are disclosed.Type: ApplicationFiled: December 4, 2015Publication date: December 14, 2017Inventors: Geoffrey Alan Otto, Michelle Nahas, Doron Lipson
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Patent number: 9340830Abstract: 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: GrantFiled: December 29, 2011Date of Patent: May 17, 2016Assignee: 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
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Publication number: 20120208706Abstract: 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: ApplicationFiled: December 29, 2011Publication date: August 16, 2012Applicant: 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