Patents by Inventor Charles M. Perou
Charles M. Perou 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: 20240018597Abstract: The present disclosure provides a method for generating a calculated cancer signature for a cancer-related phenotype based on copy number alterations (CNAs) in a patient sample. The calculated cancer signature may correspond to a somatic mutation, an mRNA expression signature, or a protein expression signature. The disclosure also provides a method treating a patient using the calculated cancer phenotype. In addition, the disclosure provides a method for generating a calculated signature based on CNAs to replicate a cancer phenotype.Type: ApplicationFiled: October 9, 2020Publication date: January 18, 2024Inventors: Charles M. Perou, Joel S. Parker, Youli Xia, Cheng Fan
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Patent number: 11851715Abstract: Methods and compositions are provided for determining a pan-cancer clustering of cluster assignment (COCA) subtype of a cancer in an individual by detecting the expression level of at least one classifier biomarker selected from a group of classifier biomarkers for COCA subtypes. Also provided herein are methods and compositions for determining the response of an individual with a COCA subtype to a therapy such as immunotherapy.Type: GrantFiled: August 17, 2022Date of Patent: December 26, 2023Assignees: GeneCentric Therapeutics, Inc., The University of North Carolina at Chapel HillInventors: Greg Mayhew, Hawazin Faruki, Myla Lai-Goldman, Charles M. Perou, Joel S. Parker
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Publication number: 20230395263Abstract: Methods are provided for determining a subtype of head and neck squamous cell carcinoma (HNSCC) of an individual by detecting the expression level of at least one subtype classifier selected from a group of genes that are relevant for determining HNSCC subtypes. Also provided herein are methods for determining a suitable treatment and predicting the overall survival and the likelihood of metastasis for the HNSCC patients according to their subtypes.Type: ApplicationFiled: August 24, 2023Publication date: December 7, 2023Inventors: Myla LAI-GOLDMAN, Hawazin FARUKI, Gregory MAYHEW, Charles M. PEROU, David Neil HAYES, Jose ZEVALLOS
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Publication number: 20230272476Abstract: The present invention provides methods for classifying and for evaluating the prognosis of a subject having breast cancer are provided. The methods include prediction of breast cancer subtype using a supervised algorithm trained to stratify subjects on the basis of breast cancer intrinsic subtype. The prediction model is based on the gene expression profile of the intrinsic genes listed in Table 1. Further provided are compositions and methods for predicting outcome or response to therapy of a subject diagnosed with or suspected of having breast cancer. These methods are useful for guiding or determining treatment options for a subject afflicted with breast cancer. Methods of the invention further include means for evaluating gene expression profiles, including microarrays and quantitative polymerase chain reaction assays, as well as kits comprising reagents for practicing the methods of the invention.Type: ApplicationFiled: September 29, 2022Publication date: August 31, 2023Inventors: Sean M. Ferree, James J. Storhoff, Joel S. Parker, Charles M. Perou, Matthew J. Ellis, Philip S. Bernard, Torsten O. Nielsen
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Publication number: 20230250484Abstract: Methods for classifying and for evaluating the prognosis of a subject having breast cancer are provided. The methods include prediction of breast cancer subtype using a supervised algorithm trained to stratify subjects on the basis of breast cancer intrinsic subtype. The prediction model is based on the gene expression profile of the intrinsic genes listed in Table 1. This prediction model can be used to accurately predict the intrinsic subtype of a subject diagnosed with or suspected of having breast cancer. Further provided are compositions and methods for predicting outcome or response to therapy of a subject diagnosed with or suspected of having breast cancer. These methods are useful for guiding or determining treatment options for a subject afflicted with breast cancer.Type: ApplicationFiled: January 23, 2023Publication date: August 10, 2023Inventors: Charles M. Perou, Joel S. Parker, James Stephen Marron, Andrew Nobel, Philip S. Bernard, Matthew J. Ellis, Elaine Mardis, Torsten O. Nielson, Maggie Chon U. Cheang
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Publication number: 20230037765Abstract: Methods and compositions are provided for determining a pan-cancer clustering of cluster assignment (COCA) subtype of a cancer in an individual by detecting the expression level of at least one classifier biomarker selected from a group of classifier biomarkers for COCA subtypes. Also provided herein are methods and compositions for determining the response of an individual with a COCA subtype to a therapy such as immunotherapy.Type: ApplicationFiled: August 17, 2022Publication date: February 9, 2023Inventors: Greg MAYHEW, Hawazin FARUKI, Myla LAI-GOLDMAN, Charles M. PEROU, Joel S. PARKER
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Publication number: 20220213563Abstract: Methods for classifying and for evaluating the prognosis of a subject having breast cancer are provided. The methods include prediction of breast cancer subtype using a supervised algorithm trained to stratify subjects on the basis of breast cancer intrinsic subtype. The prediction model is based on the gene expression profile of the intrinsic genes listed in Table 1. This prediction model can be used to accurately predict the intrinsic subtype of a subject diagnosed with or suspected of having breast cancer. Further provided are compositions and methods for predicting outcome or response to therapy of a subject diagnosed with or suspected of having breast cancer. These methods are useful for guiding or determining treatment options for a subject afflicted with breast cancer.Type: ApplicationFiled: March 23, 2022Publication date: July 7, 2022Inventors: Charles M. Perou, Joel S. Parker, James Stephen Marron, Andrew Nobel, Philip S. Bernard, Matthew J. Ellis, Elaine Mardis, Torsten O. Nielson, Maggie Chon U. Cheang
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Publication number: 20200392581Abstract: This new method relates to the development of a chemoendocrine score (CES), based on the known analysis PAM50 for predicting whether a patient with breast cancer will respond to chemotherapy or to endocrine therapy, specifically in a patient with HR+/HER2? breast cancer beyond the risk of recurrence (ROR) and PAM50 intrinsic subtypes. Specifically, the clinical utility of this CES predictor is based on the intermediate PAM50 ROR group, the proportion of each CES group (sensitive to endocrine therapy, intermediate, and sensitive to chemotherapy) being greater than 25%.Type: ApplicationFiled: November 27, 2017Publication date: December 17, 2020Inventors: Aleix Prat, Charles M. Perou, Emilio Alba Conejo
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Publication number: 20200332368Abstract: The present invention provides methods for classifying and for evaluating the prognosis of a subject having breast cancer are provided. The methods include prediction of breast cancer subtype using a supervised algorithm trained to stratify subjects on the basis of breast cancer intrinsic subtype. The prediction model is based on the gene expression profile of the intrinsic genes listed in Table 1. Further provided are compositions and methods for predicting outcome or response to therapy of a subject diagnosed with or suspected of having breast cancer. These methods are useful for guiding or determining treatment options for a subject afflicted with breast cancer. Methods of the invention further include means for evaluating gene expression profiles, including microarrays and quantitative polymerase chain reaction assays, as well as kits comprising reagents for practicing the methods of the invention.Type: ApplicationFiled: February 14, 2020Publication date: October 22, 2020Inventors: Sean M. Ferree, James J. Storhoff, Joel S. Parker, Charles M. Perou, Matthew J. Ellis, Phillip S. Bernard, Torsten O. Nielsen
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Publication number: 20200040407Abstract: Methods for classifying and for evaluating the prognosis of a subject having breast cancer are provided. The methods include prediction of breast cancer subtype using a supervised algorithm trained to stratify subjects on the basis of breast cancer intrinsic subtype. The prediction model is based on the gene expression profile of the intrinsic genes listed in Table 1. This prediction model can be used to accurately predict the intrinsic subtype of a subject diagnosed with or suspected of having breast cancer. Further provided are compositions and methods for predicting outcome or response to therapy of a subject diagnosed with or suspected of having breast cancer. These methods are useful for guiding or determining treatment options for a subject afflicted with breast cancer.Type: ApplicationFiled: October 18, 2019Publication date: February 6, 2020Inventors: Charles M. PEROU, Joel S. PARKER, James Stephen MARRON, Andrew NOBEL, Philip S. BERNARD, Matthew J. ELLIS, Elaine MARDIS, Torsten O. NIELSEN, Maggie Chon U. CHEANG
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Publication number: 20190264290Abstract: Methods for classifying and for evaluating the prognosis of a subject having breast cancer are provided. The methods include prediction of breast cancer subtype using a supervised algorithm trained to stratify subjects on the basis of breast cancer intrinsic subtype. The prediction model is based on the gene expression profile of the intrinsic genes listed in Table 1. This prediction model can be used to accurately predict the intrinsic subtype of a subject diagnosed with or suspected of having breast cancer. Further provided are compositions and methods for predicting outcome or response to therapy of a subject diagnosed with or suspected of having breast cancer. These methods are useful for guiding or determining treatment options for a subject afflicted with breast cancer.Type: ApplicationFiled: March 14, 2019Publication date: August 29, 2019Inventors: Charles M. PEROU, Joel S. PARKER, James Stephen MARRON, Andrew NOBEL, Philip S. BERNARD, Matthew J. ELLIS, Elaine MARDIS, Torsten O. NIELSEN, Maggie Chon U. CHEANG, Robert A. PALAIS
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Patent number: 10196687Abstract: Compositions and methods useful in determining the major morphological types of lung cancer are provided. The methods include detecting expression of at least one gene or biomarker in a sample at the protein or nucleic level. The expression of the gene or biomarker can be indicative of the lung tumor subtype as well as prognostic and predictive for therapeutic response. The compositions and methods provided herein are suited for analysis of gene or biomarker expression at the protein or nucleic acid level in paraffin-embedded tissues.Type: GrantFiled: November 22, 2016Date of Patent: February 5, 2019Assignee: University of North Carolina at Chapel HillInventors: David N. Hayes, Charles M. Perou, Philip Bernard
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Publication number: 20170298414Abstract: Compositions and methods useful in determining the major morphological types of lung cancer are provided. The methods include detecting expression of at least one gene or biomarker in a sample. The expression of the gene or biomarker is indicative of the lung tumor subtype. The compositions include subsets of genes that are monitored for gene expression. The gene expression is capable of distinguishing between normal lung parenchyma and the major morphological types of lung cancer. The gene expression and somatic mutation data are useful in developing a complete classification of lung cancer that is prognostic and predictive for therapeutic response. The methods are suited for analysis of paraffin-embedded tissues. Methods of the invention include means for monitoring gene or biomarker expression including PCR and antibody-based detection. The biomarkers of the invention are genes and/or proteins that are selectively expressed at a high or low level in certain tumor subtypes.Type: ApplicationFiled: November 22, 2016Publication date: October 19, 2017Inventors: David N. Hayes, Charles M. Perou, Philip Bernard
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Patent number: 9631239Abstract: Methods for classifying and for evaluating the prognosis of a subject having breast cancer are provided. The methods include prediction of breast cancer subtype using a supervised algorithm trained to stratify subjects on the basis of breast cancer intrinsic subtype. The prediction model is based on the gene expression profile of the intrinsic genes listed in Table 1. This prediction model can be used to accurately predict the intrinsic subtype of a subject diagnosed with or suspected of having breast cancer. Further provided are compositions and methods for predicting outcome or response to therapy of a subject diagnosed with or suspected of having breast cancer. These methods are useful for guiding or determining treatment options for a subject afflicted with breast cancer.Type: GrantFiled: June 1, 2009Date of Patent: April 25, 2017Assignees: University of Utah Research Foundation, British Columbia Cancer Agency Branch, Washington University, University of North Carolina at Chapel HillInventors: Charles M. Perou, Joel S. Parker, James Stephen Marron, Andrew Nobel, Philip S. Bernard, Matthew Ellis, Elaine Mardis, Torsten O. Nielsen, Maggie Cheang
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Publication number: 20170044618Abstract: Disclosed are compositions and methods related intrinsic gene sets and methods and compositions related to detecting and classifying cancer.Type: ApplicationFiled: February 12, 2016Publication date: February 16, 2017Inventors: Matthew J. ELLIS, Philip S. BERNARD, Robert A. PALAIS, Charles M. PEROU
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Publication number: 20160168645Abstract: Methods for classifying and for evaluating the prognosis of a subject having breast cancer are provided. The methods include prediction of breast cancer subtype using a supervised algorithm trained to stratify subjects on the basis of breast cancer intrinsic subtype. The prediction model is based on the gene expression profile of the intrinsic genes listed in Table 1. This prediction model can be used to accurately predict the intrinsic subtype of a subject diagnosed with or suspected of having breast cancer. Further provided are compositions and methods for predicting outcome or response to therapy of a subject diagnosed with or suspected of having breast cancer. These methods are useful for guiding or determining treatment options for a subject afflicted with breast cancer.Type: ApplicationFiled: November 3, 2015Publication date: June 16, 2016Inventors: Charles M. PEROU, Joel S. Parker, James S. Marron, Andrew Nobel, Philip S. Bernard, Matthew Ellis, Elaine Mardis, Torsten O. Nielsen, Maggie Cheang
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Publication number: 20160153051Abstract: Methods for classifying and for evaluating the prognosis of a subject having breast cancer are provided. The methods include prediction of breast cancer subtype using a supervised algorithm trained to stratify subjects on the basis of breast cancer intrinsic subtype. The prediction model is based on the gene expression profile of the intrinsic genes listed in Table 1. This prediction model can be used to accurately predict the intrinsic subtype of a subject diagnosed with or suspected of having breast cancer. Further provided are compositions and methods for predicting outcome or response to therapy of a subject diagnosed with or suspected of having breast cancer. These methods are useful for guiding or determining treatment options for a subject afflicted with breast cancer.Type: ApplicationFiled: November 3, 2015Publication date: June 2, 2016Inventors: Charles M. PEROU, Joel S. Parker, James S. Marron, Andrew Nobel, Philip S. Bernard, Matthew Ellis, Elaine Mardis, Torsten O. Nielsen, Maggie Cheang
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Publication number: 20160017438Abstract: The application describes methods for screening subjects with breast cancer to determine if the breast cancer will be responsive to a breast cancer therapy including a taxane or a taxane derivative. The application also describes methods for treating subjects with breast cancer by screening them for the likelihood of the effectiveness of treating the cancer with a therapy including a taxane or a taxane derivative and administering the therapy in subjects when it is found that a taxane or a taxane derivative is likely to be effective.Type: ApplicationFiled: August 17, 2015Publication date: January 21, 2016Inventors: Charles M. Perou, Philip S. Bernard, Torsten O. Nielsen, Matthew J. Ellis, Joel S. Parker, Miguel Martin, Eva Carrasco, Rosalia Caballero
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Publication number: 20150344962Abstract: Methods for diagnosing and for evaluating the prognosis of a cancer patient, particularly a breast cancer patient, are provided. The methods include determining expression levels of at least five biomarkers in a body sample including a cancer cell from the patient, where expression levels of the biomarkers are indicative of cancer prognosis. Overexpression of the biomarkers of the invention is indicative of a poor prognosis. In some embodiments, the body sample is a breast tissue sample, particularly a primary breast tumor sample. The methods of the invention can be used in combination with assessment of conventional clinical factors and permit a more accurate evaluation of breast cancer prognosis.Type: ApplicationFiled: February 24, 2015Publication date: December 3, 2015Inventors: Charles M. Perou, Zhiyuan Hu
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Patent number: 9181588Abstract: The application describes methods for screening subjects with breast cancer to determine if the breast cancer will be responsive to a breast cancer therapy including a taxane or a taxane derivative. The application also describes methods for treating subjects with breast cancer by screening them for the likelihood of the effectiveness of treating the cancer with a therapy including a taxane or a taxane derivative and administering the therapy in subjects when it is found that a taxane or a taxane derivative is likely to be effective.Type: GrantFiled: November 30, 2012Date of Patent: November 10, 2015Assignees: The University of Utah Research Foundation, British Columbia Cancer Agency Branch, Washington University, The University of North Carolina at Chapel Hill, Bioclassifier, LLCInventors: Charles M. Perou, Philip S. Bernard, Torsten O. Nielsen, Matthew J. Ellis, Joel S. Parker, Miguel Martin, Eva Carrasco, Rosalia Caballero