Patents by Inventor Patrick A. Arensdorf

Patrick A. Arensdorf 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: 20240026459
    Abstract: 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: Application
    Filed: February 2, 2023
    Publication date: January 25, 2024
    Inventors: Samuel Levy, Patrick A. Arensdorf, Chin-Jen Ku, Francois Collin
  • Publication number: 20230235380
    Abstract: Methods are provided for the epigenetic analysis of cell-free DNA using organic boranes to convert oxidized 5-methylcytosine residues in the cell-free DNA to dihydrouracil (DHU) residues. Cell-free DNA is contacted with an organic borane selected to successively bring about reduction, deamination, and decarboxylation of oxidized 5-methylcytosine residues such as 5-carboxylcytosine and 5-formylcytosine, resulting in DHU residues in place thereof. Following amplification, the treated cell-free DNA is sequenced, with the DHU residues read as thymine residues. Reaction mixtures, kits and additional methods are also provided, as are related methods for the epigenetic analysis of DNA, including cell-free DNA.
    Type: Application
    Filed: March 30, 2023
    Publication date: July 27, 2023
    Inventors: Patrick A. Arensdorf, Damek Spacek
  • Patent number: 11634748
    Abstract: Methods are provided for the epigenetic analysis of cell-free DNA using organic boranes to convert oxidized 5-methylcytosine residues in the cell-free DNA to dihydrouracil (DHU) residues. Cell-free DNA is contacted with an organic borane selected to successively bring about reduction, deamination, and decarboxylation of oxidized 5-methylcytosine residues such as 5-carboxymethylcytosine and 5-formylcytosine, resulting in DHU residues in place thereof. Following amplification, the treated cell-free DNA is sequenced, with the DHU residues read as thymine residues. Reaction mixtures, kits and additional methods are also provided, as are related methods for the epigenetic analysis of DNA, including cell-free DNA.
    Type: Grant
    Filed: February 13, 2019
    Date of Patent: April 25, 2023
    Assignee: CLEARNOTE HEALTH, INC.
    Inventors: Patrick A. Arensdorf, Damek Spacek
  • Publication number: 20230095582
    Abstract: 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: Application
    Filed: May 9, 2022
    Publication date: March 30, 2023
    Inventors: Chin-Jen Ku, Francois Collin, Patrick A. Arensdorf, Samuel Levy
  • Patent number: 11274335
    Abstract: Methods are provided for the epigenetic analysis of cell-free DNA using organic boranes to convert oxidized 5-methylcytosine residues in the cell-free DNA to dihydrouracil (DHU) residues. Cell-free DNA is contacted with an organic borane selected to successively bring about reduction, deamination, and decarboxylation of oxidized 5-methylcytosine residues such as 5-carboxylcytosine and 5-formylcytosine, resulting in DHU residues in place thereof. Following amplification, the treated cell-free DNA is sequenced, with the DHU residues read as thymine residues. Reaction mixtures, kits and additional methods are also provided, as are related methods for the epigenetic analysis of DNA, including cell-free DNA.
    Type: Grant
    Filed: December 10, 2020
    Date of Patent: March 15, 2022
    Assignee: BLUESTAR GENOMICS, INC.
    Inventors: Patrick A. Arensdorf, Damek Spacek
  • Publication number: 20210378698
    Abstract: Described here are paranasal sinus devices for treating paranasal sinus conditions. The devices include a cavity member, ostial member, and nasal portion. One or more of the cavity member, ostial member, and nasal portion may deliver an active agent for sustained release to treat the paranasal sinus condition. Exemplary paranasal sinus conditions are sinus inflammation due to functional endoscopic sinus surgery (FESS) and rhinosinusitis.
    Type: Application
    Filed: August 17, 2021
    Publication date: December 9, 2021
    Inventors: Donald J. EATON, Thomas R. TICE, David B. DOWNIE, Patrick A. ARENSDORF, Rodney A. BRENNEMAN, Danielle L. CLAY
  • Publication number: 20210380971
    Abstract: The invention provides a method for the analysis of a biological sample to determine multiple types of information therefrom in a streamlined, combined workflow, where all information is obtained in a sequencing-based analysis. The information includes the presence and concentration of specific plasma proteins in a blood sample; the number, location, and types of histone modifications associated with cell-free DNA obtained from the same sample; the sequence of cfRNA and cfDNA in the cell-free DNA sample; and epigenetic information pertaining to the cell-free DNA, such as hydroxymethylation and methylation profiles, i.e., the distribution of 5-hydroxymethylcytosine (5hmC) and 5-methylcytosine (5mC) residues, respectively. The invention additionally pertains to a classical sequencing-based method for analyzing a biological sample to determine one or more non-classical sequence features of the sample.
    Type: Application
    Filed: October 3, 2019
    Publication date: December 9, 2021
    Applicant: Bluestar Genomics, Inc.
    Inventors: Patrick A. Arensdorf, Damek Spacek, Christopher E. Ellison, Samuel Levy
  • Patent number: 11123091
    Abstract: Described here are paranasal sinus devices for treating paranasal sinus conditions. The devices include a cavity member, ostial member, and nasal portion. One or more of the cavity member, ostial member, and nasal portion may deliver an active agent for sustained release to treat the paranasal sinus condition. Exemplary paranasal sinus conditions are sinus inflammation due to functional endoscopic sinus surgery (FESS) and rhinosinusitis.
    Type: Grant
    Filed: January 25, 2017
    Date of Patent: September 21, 2021
    Assignee: Intersect ENT, Inc.
    Inventors: Donald J. Eaton, Thomas R. Tice, David B. Downie, Patrick A. Arensdorf, Rodney A. Brenneman, Danielle L. Clay
  • Publication number: 20210262009
    Abstract: Methods are provided for the epigenetic analysis of cell-free DNA using organic boranes to convert oxidized 5-methylcytosine residues in the cell-free DNA to dihydrouracil (DHU) residues. Cell-free DNA is contacted with an organic borane selected to successively bring about reduction, deamination, and decarboxylation of oxidized 5-methylcytosine residues such as 5-carboxylcytosine and 5-formylcytosine, resulting in DHU residues in place thereof. Following amplification, the treated cell-free DNA is sequenced, with the DHU residues read as thymine residues. Reaction mixtures, kits and additional methods are also provided, as are related methods for the epigenetic analysis of DNA, including cell-free DNA.
    Type: Application
    Filed: December 10, 2020
    Publication date: August 26, 2021
    Applicant: Bluestar Genomics, Inc.
    Inventors: Patrick A. Arensdorf, Damek Spacek
  • Publication number: 20210108274
    Abstract: 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: Application
    Filed: December 22, 2020
    Publication date: April 15, 2021
    Applicant: Bluestar Genomics, Inc.
    Inventors: Patrick A. Arensdorf, Samuel Levy, Chin-Jen Ku, Francois Collin, Gulfem Guler
  • Publication number: 20200123616
    Abstract: 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: Application
    Filed: September 19, 2019
    Publication date: April 23, 2020
    Applicant: Bluestar Genomics, Inc.
    Inventors: Patrick A. Arensdorf, Samuel Levy, Chin-Jen Ku, Francois Collin
  • Publication number: 20200024643
    Abstract: Methods are provided for the epigenetic analysis of cell-free DNA using organic boranes to convert oxidized 5-methylcytosine residues in the cell-free DNA to dihydrouracil (DHU) residues. Cell-free DNA is contacted with an organic borane selected to successively bring about reduction, deamination, and decarboxylation of oxidized 5-methylcytosine residues such as 5-carboxymethylcytosine and 5-formylcytosine, resulting in DHU residues in place thereof. Following amplification, the treated cell-free DNA is sequenced, with the DHU residues read as thymine residues. Reaction mixtures, kits and additional methods are also provided, as are related methods for the epigenetic analysis of DNA, including cell-free DNA.
    Type: Application
    Filed: February 13, 2019
    Publication date: January 23, 2020
    Applicant: Bluestar Genomics, Inc.
    Inventors: Patrick A. Arensdorf, Damek Spacek, Chunxiao Song
  • Publication number: 20200010880
    Abstract: 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: Application
    Filed: June 24, 2019
    Publication date: January 9, 2020
    Applicant: Bluestar Genomics, Inc.
    Inventors: Chin-Jen Ku, Francois Collin, Patrick A. Arensdorf, Samuel Levy
  • Publication number: 20180275140
    Abstract: Disclosed are methods of identifying subjects with osteoporosis or osteopenia, subjects at risk for developing osteoporosis, osteopenia, and bone fractures, methods of evaluating the effectiveness of osteoporosis treatments in subjects with osteoporosis or osteopenia, and methods of selecting therapies for treating osteoporosis or osteopenia, using biomarkers.
    Type: Application
    Filed: November 28, 2017
    Publication date: September 27, 2018
    Inventors: Mickey S. Urdea, Michael P. McKenna, Patrick A. Arensdorf
  • Publication number: 20170261520
    Abstract: Disclosed are methods of identifying subjects with arteriovascular disease, subjects at risk for developing arteriovascular disease, methods of differentially diagnosing diseases associated with arteriovascular disease from other diseases or within sub-classifications of arteriovascular disease, methods of evaluating the risk of arteriovascular events in patients with arteriovascular disease, methods of evaluating the effectiveness of treatments in subjects with arteriovascular disease, and methods of selecting therapies for treating arteriovascular disease.
    Type: Application
    Filed: May 23, 2017
    Publication date: September 14, 2017
    Inventors: Mickey S. Urdea, Michael P. McKenna, Patrick A. Arensdorf
  • Publication number: 20170205430
    Abstract: Disclosed are methods of identifying subjects with osteoporosis or osteopenia, subjects at risk for developing osteoporosis, osteopenia, and bone fractures, methods of evaluating the effectiveness of osteoporosis treatments in subjects with osteoporosis or osteopenia, and methods of selecting therapies for treating osteoporosis or osteopenia, using biomarkers.
    Type: Application
    Filed: April 5, 2017
    Publication date: July 20, 2017
    Inventors: Mickey S. Urdea, Michael P. McKenna, Patrick A. Arensdorf
  • Patent number: 9689880
    Abstract: Disclosed are methods of identifying subjects with arteriovascular disease, subjects at risk for developing arteriovascular disease, methods of differentially diagnosing diseases associated with arteriovascular disease from other diseases or within sub-classifications of arteriovascular disease, methods of evaluating the risk of arteriovascular events in patients with arteriovascular disease, methods of evaluating the effectiveness of treatments in subjects with arteriovascular disease, and methods of selecting therapies for treating arteriovascular disease.
    Type: Grant
    Filed: May 5, 2015
    Date of Patent: June 27, 2017
    Assignee: TRUE HEALTH IP LLC
    Inventors: Mickey S. Urdea, Michael P. McKenna, Patrick A. Arensdorf
  • Publication number: 20170128093
    Abstract: Described here are paranasal sinus devices for treating paranasal sinus conditions. The devices include a cavity member, ostial member, and nasal portion. One or more of the cavity member, ostial member, and nasal portion may deliver an active agent for sustained release to treat the paranasal sinus condition. Exemplary paranasal sinus conditions are sinus inflammation due to functional endoscopic sinus surgery (FESS) and rhinosinusitis.
    Type: Application
    Filed: January 25, 2017
    Publication date: May 11, 2017
    Inventors: Donald J. EATON, Thomas R. TICE, David B. DOWNIE, Patrick A. ARENSDORF, Rodney A. BRENNEMAN, Danielle L. BIGGS
  • Patent number: 9585681
    Abstract: Described here are paranasal sinus devices for treating paranasal sinus conditions. The devices include a cavity member, ostial member, and nasal portion. One or more of the cavity member, ostial member, and nasal portion may deliver an active agent for sustained release to treat the paranasal sinus condition. Exemplary paranasal sinus conditions are sinus inflammation due to functional endoscopic sinus surgery (FESS) and rhinosinusitis.
    Type: Grant
    Filed: September 15, 2010
    Date of Patent: March 7, 2017
    Assignee: Intersect ENT, Inc.
    Inventors: Donald J. Eaton, Thomas R. Tice, David B. Downie, Patrick A. Arensdorf, Rodney A. Brenneman, Danielle L. Biggs
  • Publication number: 20150346218
    Abstract: Disclosed are methods of identifying subjects with arteriovascular disease, subjects at risk for developing arteriovascular disease, methods of differentially diagnosing diseases associated with arteriovascular disease from other diseases or within sub-classifications of arteriovascular disease, methods of evaluating the risk of arteriovascular events in patients with arteriovascular disease, methods of evaluating the effectiveness of treatments in subjects with arteriovascular disease, and methods of selecting therapies for treating arteriovascular disease.
    Type: Application
    Filed: May 5, 2015
    Publication date: December 3, 2015
    Inventors: Mickey S. Urdea, Michael P. McKenna, Patrick A. Arensdorf