Patents by Inventor Alexander N. Parker
Alexander N. Parker 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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Publication number: 20230241065Abstract: Novel RET fusion molecules and uses are disclosed.Type: ApplicationFiled: August 4, 2022Publication date: August 3, 2023Applicant: FOUNDATION MEDICINE, INC.Inventors: Sean R. DOWNING, Matthew J. HAWRYLUK, Doron LIPSON, Alexander N. PARKER, Philip James STEPHENS
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Patent number: 11158425Abstract: 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: GrantFiled: August 19, 2014Date of Patent: October 26, 2021Assignee: 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
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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: 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: 20180280391Abstract: Novel RET fusion molecules and uses are disclosed.Type: ApplicationFiled: December 12, 2017Publication date: October 4, 2018Inventors: Sean R. Downing, Matthew J. Hawryluk, Doron Lipson, Alexander N. Parker, Philip James Stephens
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Patent number: 9884060Abstract: 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: GrantFiled: February 17, 2016Date of Patent: February 6, 2018Assignee: FOUNDATION MEDICINE, INC.Inventors: Sean R. Downing, Matthew J. Hawryluk, Doron Lipson, Alexander N. Parker, Philip James Stephens
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Publication number: 20170014413Abstract: 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: ApplicationFiled: February 17, 2016Publication date: January 19, 2017Inventors: Sean R. Downing, Matthew J. Hawryluk, Doron Lipson, Alexander N. Parker, Philip James Stephens
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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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Patent number: 9297011Abstract: Novel RET fusion molecules and uses are disclosed.Type: GrantFiled: February 23, 2014Date of Patent: March 29, 2016Assignee: FOUNDATION MEDICINE, INC.Inventors: Sean R. Downing, Matthew J. Hawryluk, Doron Lipson, Alexander N. Parker, Philip James Stephens
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Publication number: 20150046191Abstract: 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: ApplicationFiled: August 19, 2014Publication date: February 12, 2015Inventors: Helena Futscher de Deus, Rachel Lauren Erlich, Ronald David Collette, Alexander N. Parker, Michael Pellini, Gary Palmer, Mary Pat Lancelotta, Matthew J. Hawryluk, Philip James Stephens, Eric Karl Neumann, Jeffrey B. Collemer
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Publication number: 20150046180Abstract: 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: ApplicationFiled: August 19, 2014Publication date: February 12, 2015Inventors: Helena Futscher de Deus, Rachel Lauren Erlich, Ronald David Collette, Alexander N. Parker, Michael Pellini, Gary Palmer, Mary Pat Lancelotta, Matthew J. Hawryluk, Philip James Stephens, Eric Karl Neumann
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Publication number: 20140243390Abstract: Novel RET fusion molecules and uses are disclosed.Type: ApplicationFiled: February 23, 2014Publication date: August 28, 2014Applicant: FOUNDATION MEDICINE, INC.Inventors: Sean R. Downing, Matthew J. Hawryluk, Doron Lipson, Alexander N. Parker, Philip James Stephens
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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
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Publication number: 20080076120Abstract: The present invention is directed to the identification of predictive genotypes, e.g., predictive single nucleotide polymorphisms (SNPs), and markers that can be used to determine whether a patient having a CC-Chemokine Receptor 2 (CCR-2) mediated disorders is likely to be responsive or non-responsive to a therapeutic regimen. For example, the present invention is directed, in part, to the use of certain individual and/or combinations of SNPs, wherein the expression of particular alleles at particular SNPs, or combinations of alleles at loci in linkage disequilibrium with a particular SNP, correlate with responsiveness or non-responsiveness to a therapeutic regimen. The present invention is also directed to the use of certain individual and/or combinations of predictive markers which correlate with responsiveness or non-responsiveness to a therapeutic regimen.Type: ApplicationFiled: September 14, 2006Publication date: March 27, 2008Inventors: Debra D. Donaldson, Alexander N. Parker
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Patent number: 6274317Abstract: An auto allele caller executed in a computer system for identifying alleles from a trace is described. The auto allele caller applies a typical shape of an allele for a marker to the trace to identify potential allele calls that match to the typical shape of the allele at the marker and assigns a quality factor to the allele calls.Type: GrantFiled: November 2, 1998Date of Patent: August 14, 2001Assignee: Millennium Pharmaceuticals, Inc.Inventors: Martha J. Hiller, John W. Martin, Alexander N. Parker, Richard A. Nicoletti, Christopher R. Page