Patents by Inventor Francois Collin
Francois Collin 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: 20240026459Abstract: Disclosed herein are methods for identifying patients with pancreatic cancer and subjects at risk for developing pancreatic cancer, methods for monitoring a patient with an identified pancreatic lesion, methods for evaluating the effectiveness of a treatment used for a patient with pancreatic cancer, and methods for selecting a therapy for treating pancreatic cancer in a particular patient. The invention makes use of hydroxymethylation biomarkers, which in combination with one or more clinical parameters and optionally one or more additional types of biomarkers and/or patient-specific risk factors, exhibit a hydroxymethylation level that correlates with pancreatic cancer. Kits and other methods of use are also provided.Type: ApplicationFiled: February 2, 2023Publication date: January 25, 2024Inventors: Samuel Levy, Patrick A. Arensdorf, Chin-Jen Ku, Francois Collin
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Publication number: 20230352144Abstract: Disclosed herein are systems, kits, and methods for classifying the status of a transplant based on expression levels of a plurality of genes from a biological sample of a transplant recipient. The status of a transplant may be classified based on a predictive rejection classification including, but not limited to, antibody-mediated rejection (ABMR), T-cell mediated rejection (TCMR), mixed ABMR+TCMR, and no rejection. The predictive rejection classification may be assigned based on probability rejection scores, and a probability rejection score may be assigned to each rejection label. In some embodiments, the rejection label having the highest probability rejection score amongst the plurality of rejection labels may be assigned as the predictive rejection classification. Non-limiting rejection labels may include ABMR, TCMR, mixed ABMR+TCMR, and no rejection. The probability rejection score of each rejection label may be generated based on a plurality of sets of weights and expression levels of genes.Type: ApplicationFiled: April 28, 2023Publication date: November 2, 2023Inventors: Hao ZHANG, Francois COLLIN, Steven STONE, Kunbin QU
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Publication number: 20230223111Abstract: Described herein are methods such as multi-omic methods for assessing a disease such as cancer. The multi-omic methods may integrate proteomic, transcriptomic, genomic, lipidomic, or metabolomic data. The method screening diseases or disease states. Also described herein are methods for screening for diseases or disease states from biological samples. The methods may include assessing whether a nodule, mass, or cyst is cancerous.Type: ApplicationFiled: February 3, 2023Publication date: July 13, 2023Inventors: Philip Ma, Bruce Wilcox, Francois Collin, Chinmay Belthangady, Mi Yang, Manoj Khadka, Manway Liu, John Blume, Robert S. Langer, JR., Ehdieh Khaledian
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Publication number: 20230187028Abstract: Described herein are methods such as multi-omic methods for assessing a disease such as cancer. The multi-omic methods may integrate proteomic, transcriptomic, genomic, lipidomic, or metabolomic data. The method screening diseases or disease states. Also described herein are methods for screening for diseases or disease states from biological samples. The methods may include assessing whether a nodule, mass, or cyst is cancerous.Type: ApplicationFiled: January 5, 2023Publication date: June 15, 2023Inventors: Philip Ma, Bruce Wilcox, Francois Collin, Chinmay Belthangady, Mi Yang, Manoj Khadka, Manway Liu, John Blume, Robert S. Langer, JR., Ehdieh Khaledian
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Publication number: 20230095582Abstract: A method is provided for probabilistically assigning a tissue of origin to a nucleic acid in a sample, e.g., DNA in a cell-free fluid sample obtained from a human subject. A hydroxymethylation profile is generated for the sample DNA and then compared across a reference data set of hydroxymethylation profile vectors, where each hydroxymethylation profile vector identifies the hydroxymethylation profile at a specific reference locus, the tissue-specific gene associated with the reference locus, and the tissue with which the gene and reference locus are associated. A tissue of origin can be probabilistically assigned to the sample nucleic acid using the results of the comparison. Other methods of use are also provided.Type: ApplicationFiled: May 9, 2022Publication date: March 30, 2023Inventors: Chin-Jen Ku, Francois Collin, Patrick A. Arensdorf, Samuel Levy
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Publication number: 20220328129Abstract: Described herein are methods such as multi-omic methods for assessing a disease such as cancer. The multi-omic methods may integrate proteomic, transcriptomic, genomic, lipidomic, or metabolomic data. The method screening diseases or disease states. Also described herein are methods for screening for diseases or disease states from biological samples. The methods may include assessing whether a nodule, mass, or cyst is cancerous.Type: ApplicationFiled: March 30, 2022Publication date: October 13, 2022Inventors: Philip Ma, Bruce Wilcox, Francois Collin, Chinmay Belthangady, Mi Yang, Manoj Khadka, Manway Liu, John Blume, Robert S. Langer, JR., Ehdieh Khaledian
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Publication number: 20220328134Abstract: Described herein are methods such as multi-omic methods for assessing a disease such as cancer. The multi-omic methods may integrate proteomic, transcriptomic, genomic, lipidomic, or metabolomic data. The method screening diseases or disease states. Also described herein are methods for screening for diseases or disease states from biological samples. The methods may include assessing whether a nodule, mass, or cyst is cancerous.Type: ApplicationFiled: March 30, 2022Publication date: October 13, 2022Inventors: Philip Ma, Bruce Wilcox, Francois Collin, Chinmay Belthangady, Mi Yang, Manoj Khadka, Manway Liu, John Blume, Robert S. Langer, Jr., Ehdieh Khaledian
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Publication number: 20210108274Abstract: Disclosed herein are methods for identifying patients likely to have pancreatic ductal adenocarcinoma (PDAC) and patients likely to be at risk for developing PDAC. Related methods are also provided that pertain to patient monitoring, treatment evaluation, and an improved multi-cancer test., as are kits that are suitable for carrying out the aforementioned methods. The invention makes use of hydroxymethylation biomarkers, which in combination with one or more clinical parameters and optionally one or more additional types of biomarkers and/or patient-specific risk factors, exhibit a hydroxymethylation level that correlates with the presence of or risk of developing PDAC.Type: ApplicationFiled: December 22, 2020Publication date: April 15, 2021Applicant: Bluestar Genomics, Inc.Inventors: Patrick A. Arensdorf, Samuel Levy, Chin-Jen Ku, Francois Collin, Gulfem Guler
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Publication number: 20210062275Abstract: The present invention provides methods to determine the prognosis and appropriate treatment for patients diagnosed with cancer, based on the expression levels of one or more biomarkers. More particularly, the invention relates to the identification of genes, or sets of genes, able to distinguish breast cancer patients with a good clinical prognosis from those with a bad clinical prognosis. The invention further provides methods for providing a personalized genomics report for a cancer patient. The inventions also relates to computer systems and software for data analysis using the prognostic and statistical methods disclosed herein.Type: ApplicationFiled: September 11, 2020Publication date: March 4, 2021Applicant: GENOMIC HEALTH, INC.Inventors: Joffre B. BAKER, Maureen T. CRONIN, Francois COLLIN, Mei-Lan LIU
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Publication number: 20200263257Abstract: The present invention relates to biomarkers associated with breast cancer prognosis. These biomarkers include coding transcripts and their expression products, as well as non-coding transcripts, and are useful for predicting the likelihood of breast cancer recurrence in a breast cancer patient. The present invention also relates to a novel method of identifying intergenic sequences that correlate with a clinical outcome.Type: ApplicationFiled: February 7, 2020Publication date: August 20, 2020Applicant: GENOMIC HEALTH, INC.Inventors: Joffre B. BAKER, Dominick SINICROPI, Robert J. PELHAM, Michael R. CRAGER, Francois COLLIN, James C. STEPHANS, Mei-Lan LIU, John D. MORLAN, Kunbin QU
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Publication number: 20200123616Abstract: Disclosed herein are methods for identifying patients with pancreatic cancer and subjects at risk for developing pancreatic cancer, methods for monitoring a patient with an identified pancreatic lesion, methods for evaluating the effectiveness of a treatment used for a patient with pancreatic cancer, and methods for selecting a therapy for treating pancreatic cancer in a particular patient. The invention makes use of hydroxymethylation biomarkers, which in combination with one or more clinical parameters and optionally one or more additional types of biomarkers and/or patient-specific risk factors, exhibit a hydroxymethylation level that correlates with pancreatic cancer. Kits and other methods of use are also provided.Type: ApplicationFiled: September 19, 2019Publication date: April 23, 2020Applicant: Bluestar Genomics, Inc.Inventors: Patrick A. Arensdorf, Samuel Levy, Chin-Jen Ku, Francois Collin
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Publication number: 20200105367Abstract: The present invention provides methods for incorporating transcript chromosomal locus information for identification of biomarkers of disease recurrence risk.Type: ApplicationFiled: September 27, 2019Publication date: April 2, 2020Applicant: Genomic Health, Inc.Inventors: Michael C. Kiefer, Francois Collin, Samuel Levy, Joffre B. Baker, Michael R. Crager, Mark R. Segal
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Publication number: 20200010880Abstract: A method is provided for probabilistically assigning a tissue of origin to a nucleic acid in a sample, e.g., DNA in a cell-free fluid sample obtained from a human subject. A hydroxymethylation profile is generated for the sample DNA and then compared across a reference data set of hydroxymethylation profile vectors, where each hydroxymethylation profile vector identifies the hydroxymethylation profile at a specific reference locus, the tissue-specific gene associated with the reference locus, and the tissue with which the gene and reference locus are associated. A tissue of origin can be probabilistically assigned to the sample nucleic acid using the results of the comparison. Other methods of use are also provided.Type: ApplicationFiled: June 24, 2019Publication date: January 9, 2020Applicant: Bluestar Genomics, Inc.Inventors: Chin-Jen Ku, Francois Collin, Patrick A. Arensdorf, Samuel Levy
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Publication number: 20190256923Abstract: The present invention relates to biomarkers associated with breast cancer prognosis. These biomarkers include coding transcripts and their expression products, as well as non-coding transcripts, and are useful for predicting the likelihood of breast cancer recurrence in a breast cancer patient. The present invention also relates to a novel method of identifying intergenic sequences that correlate with a clinical outcome.Type: ApplicationFiled: January 17, 2019Publication date: August 22, 2019Applicant: GENOMIC HEALTH, INC.Inventors: Joffre B. BAKER, Dominick SINICROPI, Robert J. PELHAM, Michael R. CRAGER, Francois COLLIN, James C. STEPHANS, Mei-Lan LIU, John D. MORLAN, Kunbin QU
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Publication number: 20190241967Abstract: The present invention provides methods to determine the prognosis and appropriate treatment for patients diagnosed with cancer, based on the expression levels of one or more biomarkers. More particularly, the invention relates to the identification of genes, or sets of genes, able to distinguish breast cancer patients with a good clinical prognosis from those with a bad clinical prognosis. The invention further provides methods for providing a personalized genomics report for a cancer patient. The inventions also relates to computer systems and software for data analysis using the prognostic and statistical methods disclosed herein.Type: ApplicationFiled: January 9, 2019Publication date: August 8, 2019Applicant: GENOMIC HEALTH, INC.Inventors: Joffre B. BAKER, Maureen T. CRONIN, Francois COLLIN, Mei-Lan LIU
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Publication number: 20180365283Abstract: A system is designed for processing instructions in real time during a session. This system comprises: a preloader for obtaining reference data relating to the instructions, the reference data indicating the current values of each specified resource account data file, and the preloader being arranged to read the reference data for a plurality of received instructions in parallel from a master database; an enriched instruction queue for queuing the instructions together with their respective preloaded reference data; an execution engine for determining sequentially whether each received instruction can be executed under the present values of the relevant resource account files and for each executable instruction to generate an updating command; and an updater, responsive to the updating command from the execution engine (for updating the master database with the results of each executable instruction, the operation of the plurality of updaters being decoupled from the operation of the execution engine.Type: ApplicationFiled: June 19, 2018Publication date: December 20, 2018Applicant: Euroclear SA/NVInventors: Henri Petit, Jean-Francois Collin, Nicolas Marechal, Christine Deloge
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Patent number: 10025809Abstract: A system is designed for processing instructions in real time during a session. This system comprises: a preloader for obtaining reference data relating to the instructions, the reference data indicating the current values of each specified resource account data file, and the preloader being arranged to read the reference data for a plurality of received instructions in parallel from a master database; an enriched instruction queue for queuing the instructions together with their respective preloaded reference data; an execution engine for determining sequentially whether each received instruction can be executed under the present values of the relevant resource account files and for each executable instruction to generate an updating command; and an updater, responsive to the updating command from the execution engine (for updating the master database with the results of each executable instruction, the operation of the plurality of updaters being decoupled from the operation of the execution engine.Type: GrantFiled: November 20, 2013Date of Patent: July 17, 2018Assignee: Euroclear SA/NVInventors: Henri Petit, Jean-Francois Collin, Nicolas Marechal, Christine Deloge
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Publication number: 20170211154Abstract: The present invention provides methods to determine the prognosis and appropriate treatment for patients diagnosed with cancer, based on the expression levels of one or more biomarkers. More particularly, the invention relates to the identification of genes, or sets of genes, able to distinguish breast cancer patients with a good clinical prognosis from those with a bad clinical prognosis. The invention further provides methods for providing a personalized genomics report for a cancer patient. The inventions also relates to computer systems and software for data analysis using the prognostic and statistical methods disclosed herein.Type: ApplicationFiled: February 3, 2017Publication date: July 27, 2017Applicant: GENOMIC HEALTH, INC.Inventors: Joffre B. BAKER, Maureen T. CRONIN, Francois COLLIN, Mei-Lan LIU
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Publication number: 20160259881Abstract: The present invention provides methods for incorporating transcript chromosomal locus information for identification of biomarkers of disease recurrence risk.Type: ApplicationFiled: October 28, 2014Publication date: September 8, 2016Inventors: Michael C. Kiefer, Francois Collin, Samuel Levy, Joffre B. Baker, Michael R. Crager, Mark R. Segal
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Publication number: 20160222463Abstract: The present invention relates to biomarkers associated with breast cancer prognosis. These biomarkers include coding transcripts and their expression products, as well as non-coding transcripts, and are useful for predicting the likelihood of breast cancer recurrence in a breast cancer patient, The present invention also relates to a novel method of identifying intergenic sequences that correlate with a clinical outcome.Type: ApplicationFiled: January 29, 2016Publication date: August 4, 2016Applicant: GENOMIC HEALTH, INC.Inventors: Joffre B. BAKER, Dominick S. SINICROPI, Robert J. PELHAM, Michael R. CRAGER, Francois COLLIN, James C. STEPHANS, Mei-Lan LIU, John D. MORLAN, Kunbin QU