Patents by Inventor Martin Moorhead

Martin Moorhead 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: 20220170910
    Abstract: Provided herein is a high-throughput method for screening and identifying regulatory elements that provide selective expression in a particular cell type of interest. Also provided are nucleic acid compositions used in the high-throughput screening method.
    Type: Application
    Filed: March 20, 2020
    Publication date: June 2, 2022
    Inventors: Kartik Ramamoorthi, Anne Tanenhaus, Sirika Wood, Martin Moorhead, Stephanie Tagliatela, Jerry S. Chen, Raghavendra Hosur
  • Patent number: 10526650
    Abstract: The invention is directed to sequence-based profiling of populations of nucleic acids by multiplex amplification and attachment of one or more sequence tags to target nucleic acids and/or copies thereof followed by high-throughput sequencing of the amplification product. In some embodiments, the invention includes successive steps of primer extension, removal of unextended primers and addition of new primers either for amplification (for example by PCR) or for additional primer extensions. Some embodiments of the invention are directed to minimal residual disease (MRD) analysis of patients being treated for cancer. Sequence tags incorporated into sequence reads provide an efficient means for determining clonotypes and at the same time provide a convenient means for detecting carry-over contamination from other samples of the same patient or from samples of a different patient which were tested in the same laboratory.
    Type: Grant
    Filed: August 2, 2018
    Date of Patent: January 7, 2020
    Assignee: Adaptive Biotechnologies Corporation
    Inventors: Thomas Asbury, Kieran Hervold, Chitra Kotwaliwale, Malek Faham, Martin Moorhead, Li Weng, Tobias Wittkop, Jianbiao Zheng
  • Publication number: 20190040462
    Abstract: The invention is directed to sequence-based profiling of populations of nucleic acids by multiplex amplification and attachment of one or more sequence tags to target nucleic acids and/or copies thereof followed by high-throughput sequencing of the amplification product. In some embodiments, the invention includes successive steps of primer extension, removal of unextended primers and addition of new primers either for amplification (for example by PCR) or for additional primer extensions. Some embodiments of the invention are directed to minimal residual disease (MRD) analysis of patients being treated for cancer. Sequence tags incorporated into sequence reads provide an efficient means for determining clonotypes and at the same time provide a convenient means for detecting carry-over contamination from other samples of the same patient or from samples of a different patient which were tested in the same laboratory.
    Type: Application
    Filed: August 2, 2018
    Publication date: February 7, 2019
    Inventors: Thomas Asbury, Kieran Hervold, Chitra Kotwaliwale, Malek Faham, Martin Moorhead, Li Weng, Tobias Wittkop, Jianbiao Zheng
  • Patent number: 10077473
    Abstract: The invention is directed to sequence-based profiling of populations of nucleic acids by multiplex amplification and attachment of one or more sequence tags to target nucleic acids and/or copies thereof followed by high-throughput sequencing of the amplification product. In some embodiments, the invention includes successive steps of primer extension, removal of unextended primers and addition of new primers either for amplification (for example by PCR) or for additional primer extensions. Some embodiments of the invention are directed to minimal residual disease (MRD) analysis of patients being treated for cancer. Sequence tags incorporated into sequence reads provide an efficient means for determining clonotypes and at the same time provide a convenient means for detecting carry-over contamination from other samples of the same patient or from samples of a different patient which were tested in the same laboratory.
    Type: Grant
    Filed: June 1, 2017
    Date of Patent: September 18, 2018
    Assignee: Adaptive Biotechnologies Corp.
    Inventors: Thomas Asbury, Kieran Hervold, Chitra Kotwaliwale, Malek Faham, Martin Moorhead, Li Weng, Tobias Wittkop, Jianbiao Zheng
  • Publication number: 20170335390
    Abstract: The invention is directed to sequence-based profiling of populations of nucleic acids by multiplex amplification and attachment of one or more sequence tags to target nucleic acids and/or copies thereof followed by high-throughput sequencing of the amplification product. In some embodiments, the invention includes successive steps of primer extension, removal of unextended primers and addition of new primers either for amplification (for example by PCR) or for additional primer extensions. Some embodiments of the invention are directed to minimal residual disease (MRD) analysis of patients being treated for cancer. Sequence tags incorporated into sequence reads provide an efficient means for determining clonotypes and at the same time provide a convenient means for detecting carry-over contamination from other samples of the same patient or from samples of a different patient which were tested in the same laboratory.
    Type: Application
    Filed: June 1, 2017
    Publication date: November 23, 2017
    Inventors: Thomas Asbury, Kieran Hervold, Chitra Kotwaliwale, Malek Faham, Martin Moorhead, Li Weng, Tobias Wittkop, Jianbiao Zheng
  • Patent number: 9708657
    Abstract: The invention is directed to sequence-based profiling of populations of nucleic acids by multiplex amplification and attachment of one or more sequence tags to target nucleic acids anchor copies thereof followed by high-throughput sequencing of the amplification product. In some embodiments, the invention includes successive steps of primer extension, removal of unextended primers and addition of new primers either for amplification (for example by PCR) or for additional primer extension. Some embodiments of the invention are directed to minimal residual disease (MRD) analysis of patients being treated for cancer. Sequence tags incorporated into sequence reads provide an efficient means for determining clonotypes and at the same time provide a convenient means for detecting carry-over contamination from other samples of the same patient or from samples of a different patient which were tested in the same laboratory.
    Type: Grant
    Filed: June 27, 2014
    Date of Patent: July 18, 2017
    Assignee: Adaptive Biotechnologies Corp.
    Inventors: Thomas Asbury, Kieran Hervold, Chitra Kotwaliwale, Malek Faham, Martin Moorhead, Li Weng, Tobias Wittkop, Jianbiao Zheng
  • Publication number: 20170191132
    Abstract: The invention includes a method for determining the disease status of an individual suffering from ankylosing spondylitis by monitoring the individual's T-cell repertoire for the presence and/or level of clonotypes encoding T-cell receptor chains with segments identical to ant or related to the peptide LCASSLEASGSSYNEQFFGPGTRLTV (SEQ ID NO: 1) or the peptide VYFCASSDSSGSTDTQYFGPGTRLTV (SEQ ID NO: 2). The invention also includes therapeutic antibodies specific for these peptides for ameliorating the effects ankylosing spondylitis.
    Type: Application
    Filed: February 3, 2017
    Publication date: July 6, 2017
    Inventors: Malek Faham, Victoria Carlton, Martin Moorhead, Jianbiao Zheng, Thomas Asbury
  • Patent number: 9528160
    Abstract: The invention is directed to a method of selecting disease-correlated clonotypes that have a reduced likelihood of producing a false positive signal of relapse when, used to monitor minimal residual disease. In accordance with the invention, candidate correlating clonotype are obtained from a patient, the rarity of each is determined either by comparison with a clonotype database or a clonotype model, and one or more of the rarest of such clonotypes are used to monitor the minimal residual disease.
    Type: Grant
    Filed: March 15, 2013
    Date of Patent: December 27, 2016
    Assignee: Adaptive Biotechnolgies Corp.
    Inventors: Francois Pepin, Malek Faham, Martin Moorhead
  • Patent number: 9523129
    Abstract: The invention is directed to methods of generating sequence profiles of populations of nucleic acids, whose member nucleic acids contain regions of high variability, such as populations of nucleic acids encoding T cell receptors or B cell receptors. In one aspect, the invention provides pluralities of sets of primers for generating nested sets of templates from nucleic acids in such populations, thereby insuring the production of at least one template from which sequence reads are generated, despite such variability, or despite limited lengths or quality of sequence reads. In another aspect, members of such populations are bidirectionally sequenced so that further sequence information is obtained by analyzing overlapping sequence reads in the zones of highest variability.
    Type: Grant
    Filed: February 5, 2014
    Date of Patent: December 20, 2016
    Assignee: Adaptive Biotechnologies Corp.
    Inventors: Malek Faham, Martin Moorhead, Thomas Willis
  • Publication number: 20160355893
    Abstract: The invention is directed to the use of sequence tags to improve sequence determination of amplicons of related sequences, particularly large and complex amplicons, such as those comprising recombined nucleic acids encoding immune receptor molecules. In one aspect, sequence reads having the same sequence tags are aligned after which final base calls are determined from a (possibly weighted) average base call from sequence read base calls at each position. Similarly, in another aspect, sequence reads comprising series of incorporation signals are aligned by common sequence tags and base calls in homopolymer regions are made as a function incorporation signal values at each “flow” position.
    Type: Application
    Filed: March 15, 2013
    Publication date: December 8, 2016
    Inventors: Malek Faham, Martin Moorhead, Thomas Willis, Jianbiao Zheng
  • Patent number: 9506119
    Abstract: The invention is directed to the use of sequence tags to improve sequence determination of amplicons of related sequences, particularly large and complex amplicons, such as those comprising recombined nucleic acids encoding immune receptor molecules. In one aspect, sequence reads having the same sequence tags are aligned after which final base calls are determined from a (possibly weighted) average base call from sequence read base calls at each position. Similarly, in another aspect, sequence reads comprising series of incorporation signals are aligned by common sequence tags and base calls in homopolymer regions are made as a function incorporation signal values at each “flow” position.
    Type: Grant
    Filed: March 15, 2013
    Date of Patent: November 29, 2016
    Assignee: Adaptive Biotechnologies Corp.
    Inventors: Malek Faham, Martin Moorhead, Thomas Willis, Jianbiao Zheng
  • Publication number: 20160258025
    Abstract: The invention is directed to a method of predicting clinical response of a patient to treatment of a cancer by an immune checkpoint pathway inhibitor, such as an anti-CTLA-4 or anti-PD-1 antibody binding compound. In one aspect the method comprises generating pre- and post-treatment clonotype profiles, determining a number of clonotypes that decrease in frequency between the first and second clonotype profiles, and predicting a lack of responsiveness in the patient to the treatment whenever the number of clonotypes that decrease in frequency is greater than a predetermined value.
    Type: Application
    Filed: October 17, 2014
    Publication date: September 8, 2016
    Inventors: Mark KLINGER, Malek FAHAM, Martin MOORHEAD, Lawrence FONG
  • Patent number: 9394567
    Abstract: The invention is directed to methods for detecting and quantifying nucleic acid contamination in a tissue sample of an individual containing T cells and/or B cells, which is used for generating a sequence-based clonotype profile. In one aspect, the invention is implemented by measuring the presence and/or level of an endogenous or exogenous nucleic acid tag by which nucleic acid from an intended individual can be distinguished from that of unintended individuals. Endogenous tags include genetic identity markers, such as short tandem repeats, rare clonotypes or the like, and exogenous tags include sequence tags employed to determine clonotype sequences from sequence reads.
    Type: Grant
    Filed: April 9, 2013
    Date of Patent: July 19, 2016
    Assignee: ADAPTIVE BIOTECHNOLOGIES CORPORATION
    Inventors: Thomas Asbury, Victoria Carlton, Malek Faham, Stephen C. Macevicz, Martin Moorhead, Thomas Willis, Jianbiao Zheng
  • Publication number: 20150259734
    Abstract: The invention is directed to sequence-based profiling of populations of nucleic acids by multiplex amplification and attachment of one or more sequence tags to target nucleic acids anchor copies thereof followed by high-throughput sequencing of the amplification product. In some embodiments, the invention includes successive steps of primer extension, removal of unextended primers and addition of new primers either for amplification (for example by PRC) or for additional primer extension. Some embodiments of the invention are directed to minimal residual disease (MRD) analysis of patients being treated for cancer. Sequence tags incorporated into sequence reads provide an efficient means for determining clonotypes and at the same time provide a convenient means for detecting carry-over contamination from other samples of the same patient or from samples of a different patient which were tested in the same laboratory.
    Type: Application
    Filed: June 27, 2014
    Publication date: September 17, 2015
    Inventors: Thomas Asbury, Kieran Hervold, Chitra Kotwaliwale, Malek Faham, Martin Moorhead, Li Weng, Tobias Wittkop, Jianbiao Zheng
  • Publication number: 20150252422
    Abstract: The invention includes a method for determining the disease status of an individual suffering from ankylosing spondylitis by monitoring the individual's T-cell repertoire for the presence and/or level of clonotypes encoding T-cell receptor chains with segments identical to and/or related to the peptide LCASSLEASGSSYNEQFFGPGTRLTV (SEQ ID NO: 1) or the peptide VYFCASSDSSGSTDTQYFGPGTRLTV (SEQ ID NO: 2). The invention also includes therapeutic antibodies specific for these peptides for ameliorating the effects of ankylosing spondylitis.
    Type: Application
    Filed: October 25, 2012
    Publication date: September 10, 2015
    Applicant: Sequenta LLC
    Inventors: Malek Faham, Victoria Carlton, Martin Moorhead, Jianbiao Zheng, Thomas Asbury
  • Publication number: 20150252419
    Abstract: The invention is directed so methods for determining clonotypes and clonotype profiles in assays for analyzing immune repertoires by high throughput nucleic acid sequencing of somatically recombined immune molecules. In one aspect the invention comprises generating a clonotype profile from an individual by generating sequence reads from a sample of recombined immune molecules; forming from the sequence reads a sequence free representing candidate clonotypes each having a frequency; coalescing with a highest frequency candidate clonotype any lesser frequency candidate clonotypes whenever such lesser frequency is below a predetermined value and whenever a sequence difference therebetween is below a predetermined value to form a clonotype. After such coalescence, the candidate clonotypes is removed from the sequence tree and the process is repeated.
    Type: Application
    Filed: February 2, 2015
    Publication date: September 10, 2015
    Inventors: Martin Moorhead, Malek Faham, Thomas Willis
  • Publication number: 20150247201
    Abstract: The invention is directed to a prognostic indicator for CLL patients who have undergone an allogeneic stem cell transplant (SCT). The indicator is based on a method of monitoring levels and changes in levels of correlating clonotypes of the CLLs at successive time points. The prognostic indicator applies to patients who have survived for at least one year from an allogeneic SCT and includes criteria based on the following two measurements: (a) frequency of CLL correlating clonotypes (e.g. in terms of number per 106 clonotypes) in an initial clonotype profile (from peripheral blood), and (b) fold change in such CLL correlating clonotype number between such initial measurement and a successively measured clonotype profile.
    Type: Application
    Filed: May 30, 2013
    Publication date: September 3, 2015
    Inventors: Malek Faham, Victoria Carlton, Martin Moorhead, Francois Pepin
  • Publication number: 20150167080
    Abstract: The invention is directed to methods for determining clonotypes and clonotype profiles in assays for analyzing immune repertoires by high throughput nucleic acid sequencing of somatically recombined immune molecules. In one aspect, the invention comprises generating a clonotype profile from an individual by generating sequence reads from a sample of recombined immune molecules; forming from the sequence reads a sequence tree representing candidate clonotypes each having a frequency; coalescing with a highest frequency candidate clonotype any lesser frequency candidate clonotypes whenever such lesser frequency is below a predetermined value and whenever a sequence difference therebetween is below a predetermined value to form a clonotype. After such coalescence, the candidate clonotypes is removed from the sequence tree and the process is repeated.
    Type: Application
    Filed: August 2, 2011
    Publication date: June 18, 2015
    Applicant: Sequenta, Inc.
    Inventors: Martin Moorhead, Malek Faham, Thomas Willis
  • Patent number: 9043160
    Abstract: The invention is directed to methods for determining clonotypes and clonotype profiles in assays for analyzing immune repertoires by high throughput nucleic acid sequencing of somatically recombined immune molecules. In one aspect, the invention comprises generating a clonotype profile from an individual by generating sequence reads from a sample of recombined immune molecules; forming from the sequence reads a sequence tree representing candidate clonotypes each having a frequency; coalescing with a highest frequency candidate clonotype any lesser frequency candidate clonotypes whenever such lesser frequency is below a predetermined value and whenever a sequence difference therebetween is below a predetermined value to form a clonotype. After such coalescence, the candidate clonotypes is removed from the sequence tree and the process is repeated.
    Type: Grant
    Filed: August 2, 2011
    Date of Patent: May 26, 2015
    Assignee: SEQUENTA, INC.
    Inventors: Martin Moorhead, Malek Faham, Thomas Willis
  • Publication number: 20140315725
    Abstract: The invention is directed to methods of generating sequence profiles of populations of nucleic acids, whose member nucleic acids contain regions of high variability, such as populations of nucleic acids encoding T cell receptors or B cell receptors. In one aspect, the invention provides pluralities of sets of primers for generating nested sets of templates from nucleic acids in such populations, thereby insuring the production of at least one template from which sequence reads are generated, despite such variability, or despite limited lengths or quality of sequence reads. In another aspect, members of such populations are bidirectionally sequenced so that further sequence information is obtained by analyzing overlapping sequence reads in the zones of highest variability.
    Type: Application
    Filed: February 5, 2014
    Publication date: October 23, 2014
    Applicant: Sequenta, Inc.
    Inventors: Malek Faham, Martin Moorhead, Thomas Willis