Patents Examined by Christian C Boesen
  • Patent number: 11905623
    Abstract: Some aspects of the present disclosure provide methods for evolving recombinases to recognize target sequences that differ from the canonical recognition sequences. Some aspects of this disclosure provide evolved recombinases, e.g., recombinases that bind and recombine naturally-occurring target sequences, such as, e.g., target sequences within the human Rosa26 locus. Methods for using such recombinases for genetically engineering nucleic acid molecules in vitro and in vivo are also provided. Some aspects of this disclosure also provide libraries and screening methods for assessing the target site preferences of recombinases, as well as methods for selecting recombinases that bind and recombine a non-canonical target sequence with high specificity.
    Type: Grant
    Filed: August 10, 2021
    Date of Patent: February 20, 2024
    Assignee: President and Fellows of Harvard College
    Inventors: David R. Liu, David B. Thompson, Jeffrey L. Bessen
  • Patent number: 11866484
    Abstract: The invention relates to the identification of a highly stable single domain antibody scaffold (hs2dAb) and its use in generating synthetic single domain antibody library (hs2dAb-L1). The invention also relates to antigen-binding proteins comprising said stable single domain antibody scaffold and their uses, in particular as therapeutics.
    Type: Grant
    Filed: March 3, 2021
    Date of Patent: January 9, 2024
    Inventors: Aurelien Olichon, Sandrine Moutel, Franck Perez
  • Patent number: 11834757
    Abstract: The present specification provides libraries of HLA homozygous induced pluripotent cell lines.
    Type: Grant
    Filed: December 5, 2018
    Date of Patent: December 5, 2023
    Assignee: New York Blood Center, Inc.
    Inventors: Pablo Rubinstein, Christopher D. Hillyer
  • Patent number: 11821111
    Abstract: Methods to create barcoded influenza viruses without disrupting the function of the viral proteins and the proper packaging of the viral genome segments are described. The barcoded influenza viruses can be used within deep mutational scanning libraries to map influenza resistance mutations to therapeutic treatments. The libraries can also be used to predict influenza strains that may become resistant to therapeutic treatments and/or more easily evolve to infect new species. The libraries include features that allow efficient collection and assessment of informative data, obviating bottlenecks of previous approaches.
    Type: Grant
    Filed: November 13, 2020
    Date of Patent: November 21, 2023
    Assignee: Fred Hutchinson Cancer Center
    Inventors: Jesse Bloom, Allison Greaney, Andrea Loes, Adam S. Dingens
  • Patent number: 11820810
    Abstract: The invention relates to the provision of antibody therapeutics and prophylactics that are tailored specifically for human use. The present invention provides libraries, vertebrates and cells, such as transgenic mice or rats or transgenic mouse or rat cells. Furthermore, the invention relates to methods of using the vertebrates to isolate antibodies or nucleotide sequences encoding antibodies. Antibodies, heavy chains, polypeptides, nucleotide sequences, pharmaceutical compositions and uses are also provided by the invention.
    Type: Grant
    Filed: May 28, 2020
    Date of Patent: November 21, 2023
    Assignee: Kymab Limited
    Inventors: Allan Bradley, Glenn Friedrich, E-Chiang Lee, Mark Strivens, Nicholas England
  • Patent number: 11821110
    Abstract: Provided herein are methods of detecting an antibody directed against a pathogen and uses thereof.
    Type: Grant
    Filed: July 8, 2020
    Date of Patent: November 21, 2023
    Assignees: The Brigham and Women's Hospital, Inc., President and Fellows of Harvard College
    Inventors: Stephen J. Elledge, Harry B. Larman, Tomasz Kula, George Xu
  • Patent number: 11814750
    Abstract: Provided herein are compositions, methods, and systems for sample processing and/or data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample from a human, non-human, and combinations thereof.
    Type: Grant
    Filed: November 20, 2020
    Date of Patent: November 14, 2023
    Assignee: Personalis, Inc.
    Inventors: John West, Richard Chen, Christian Haudenschild, Gabor Bartha, Shujun Luo
  • Patent number: 11807956
    Abstract: Disclosed herein are methods for the generation of highly accurate oligonucleic acid libraries encoding for predetermined variants of a nucleic acid sequence. The degree of variation may be complete, resulting in a saturated variant library, or less than complete, resulting in a selective library of variants. The variant oligonucleic acid libraries described herein may designed for further processing by transcription or translation. The variant oligonucleic acid libraries described herein may be designed to generate variant RNA, DNA and/or protein populations. Further provided herein are method for identifying variant species with increased or decreased activities, with applications in regulating biological functions and the design of therapeutics for treatment or reduction of disease.
    Type: Grant
    Filed: October 12, 2020
    Date of Patent: November 7, 2023
    Assignee: Twist Bioscience Corporation
    Inventors: Anthony Cox, Sebastian Treusch, Siyuan Chen
  • Patent number: 11795578
    Abstract: Presented herein are methods and compositions for analyzing rare nucleic acid species. Some methods presented herein use DNA reassociation kinetics following thermal denaturation to define populations of nucleic acid sequences, e.g., highly abundant (e.g., cDNA from rRNA), moderately abundant, and less abundant or rare sequences (e.g., cDNA from mRNA).
    Type: Grant
    Filed: April 25, 2022
    Date of Patent: October 24, 2023
    Assignee: Illumina, Inc.
    Inventors: Scott Kuersten, Agnes Radek, Ramesh Vaidyanathan, Haiying Li Grunenwald
  • Patent number: 11795579
    Abstract: Compositions and methods for displaying antibodies in the periplasmic space of yeast cells are disclosed. In particular, antibodies are linked to a cell membrane-spanning transmembrane domain, a cell-membrane associated protein domain that is on the external face of the yeast cell membrane, a protein that binds to the inner face of the yeast cell wall, or a periplasmic protein in order to display the antibodies in the yeast periplasmic space. In addition, a target protein of interest can be coexpressed in yeast such that it is localized to the plasma membrane or periplasmic space and accessible to binding by displayed antibodies. The disclosure further relates to high-throughput screening of antibody libraries using yeast cell periplasmic display.
    Type: Grant
    Filed: December 10, 2018
    Date of Patent: October 24, 2023
    Assignee: Abalone Bio, Inc.
    Inventors: Richard Yu, Carlos Gustavo Pesce, Rodrigo Baltanas, Brett Robison
  • Patent number: 11788205
    Abstract: The present invention generally relates to specificity assays using cell cultures, in particular to chimeric antigen receptor (CAR) expressing reporter T (CAR-T cell) assays to test antigen binding moieties in different formats. Furthermore, the present invention relates to the use of CAR-T cells, transfected/transduced with an engineered chimeric antigen receptor (CAR) comprising a target antigen binding moiety capable of specific binding to a target antigen, e.g., tumor associated antigens.
    Type: Grant
    Filed: June 19, 2020
    Date of Patent: October 17, 2023
    Inventors: Christian Klein, Ekkehard Moessner, Lydia Jasmin Hanisch, Wei Xu, Camille Loise Sophie Delon, Diana Darowski, Christian Jost, Vesna Pulko
  • Patent number: 11781248
    Abstract: The present disclosure provides, among other things, antibodies for detecting TALENs and/or FokI nucleases in a sample and methods of using the same.
    Type: Grant
    Filed: June 12, 2020
    Date of Patent: October 10, 2023
    Inventors: Thomas Charles Pertel, Barbra Johnson Sasu
  • Patent number: 11782053
    Abstract: Disclosed is a method for correlating at least one amino acid sequence from an antibody isolated from human or animal blood with at least one DNA sequence corresponding to the antibody in the immunorepertoire of the human or animal. The method also provides a means for pairing heavy and light chains to produce synthesized monoclonal antibodies.
    Type: Grant
    Filed: September 28, 2012
    Date of Patent: October 10, 2023
    Assignee: iRepertoire, Inc.
    Inventors: Jian Han, Miranda Byrne-Steele
  • Patent number: 11781247
    Abstract: The present disclosure relates to compositions and methods for targeting antigenically variable pathogens and diseases. Embodiments of the present disclosure involve of the construction of variable epitope libraries (VELs) containing mutated versions of epitopes derived from antigens associated with various diseases for treating subjects in both therapeutic and prophylactic settings. The present disclosure also provides compositions and methods for the production of VELs based on CTL-derived epitopes of survivin, an oncogenic inhibitor-of-apoptosis. Given the large number of potential epitopes expressed in tumors, and the dynamic nature of the tumor epitope landscape, there is a need to develop compositions and methods for targeting various antigenic epitopes to counteract immune escape.
    Type: Grant
    Filed: August 19, 2019
    Date of Patent: October 10, 2023
    Assignee: Primex Clinical Laboratories, Inc.
    Inventors: Karen Manucharyan, Gohar Gevorgyan
  • Patent number: 11773509
    Abstract: A method of preparing a conditionally active polypeptide from a parent polypeptide, comprising steps of evolving a DNA encoding the parent polypeptide by increasing a net charge of the parent polypeptide using one or more techniques selected from increasing a total number of codons of charged amino acid residues in the DNA and decreasing a total number of codons of uncharged amino acid residues in the DNA to create mutant DNAs; expressing the mutant DNAs to obtain mutant polypeptides; and selecting the conditionally active polypeptide from the mutant polypeptides which exhibits a decrease in activity in a first assay at a first value of a condition compared to the same activity in a second assay at a second value of the same condition. The conditionally active polypeptide, pharmaceutical compositions containing same, nanoparticle and drug conjugates thereof and uses thereof are also provided.
    Type: Grant
    Filed: August 13, 2021
    Date of Patent: October 3, 2023
    Assignee: BioAtla, Inc.
    Inventors: Jay M. Short, Hwai Wen Chang, Gerhard Frey
  • Patent number: 11773511
    Abstract: Methods and compositions are described herein for primer extension target enrichment of immune receptor (BCR or TCR) sequences.
    Type: Grant
    Filed: August 18, 2020
    Date of Patent: October 3, 2023
    Assignee: Roche Sequencing Solutions, Inc.
    Inventors: Jan Berka, Carolina Dallett, Richard Dannebaum, Brian Godwin, Seoyoung Kim, Jainee Lewis, Khai Luong, Sedide Ozturk, Joseph Platzer, Florian Rubelt, Dilduz Telman
  • Patent number: 11773510
    Abstract: The invention relates to a method for discovering specific functional antibodies, in particular to a method for discovering specific functional antibodies based on sequence composition and frequency analysis of variable regions of immune host antibodies. Compared with conventional high-throughput antibody sequencing method, this method can quickly and accurately obtain the full-length sequence of the variable region of antibody containing candidate CDR3, the success rate of antibody gene pairing is high and it is suitable for the detection of few samples, and improves the efficiency of obtaining specific functional antibodies.
    Type: Grant
    Filed: May 24, 2017
    Date of Patent: October 3, 2023
    Inventors: Weizhi Chen, Xin Wu, Wang Wang, Zhongping Sun, Guojuan Liao
  • Patent number: 11753637
    Abstract: Methods and compositions are provided for performing an in vivo proximity-ligation in combination with DNA capture technology to cross-link physically adjacent DNA sequences within a mixed population of cells and isolate cross-linked DNA junctions where at least one DNA sequence of interest is present.
    Type: Grant
    Filed: June 26, 2018
    Date of Patent: September 12, 2023
    Assignee: Phase Genomics Inc.
    Inventors: Ivan Liachko, Shawn Thomas Sullivan, Kyle Langford, Stephen M. Eacker
  • Patent number: 11753744
    Abstract: Compositions and methods are provided for DNA barcoding of designer mononucleosome and polynucleosome (chromatin array) libraries for use, for example, for the profiling of chromatin readers, writers, erasers, and modulators thereof.
    Type: Grant
    Filed: August 24, 2018
    Date of Patent: September 12, 2023
    Assignee: The Trustees of Princeton University
    Inventors: Tom W. Muir, Uyen T. T. Nguyen, Manuel M. Mueller
  • Patent number: 11739441
    Abstract: The present invention relates to a library of particles, the library displaying a plurality of different T cell receptors (TCRs), wherein the plurality of TCRs consists essentially of TCRs comprising an alpha chain comprising an alpha chain variable domain and a beta chain comprising a beta chain variable domain and the library comprises more than one TRAV gene product and/or more than one TRBV gene product, wherein the beta chain variable domain does not comprise one or more of a TRBV5-1, 5-3, 5-4, 5-5, 5-6, 5-7 or 5-8 gene product and wherein the plurality of TCRs do not consist essentially of TCRs comprising a TRAV12-2 gene product from a natural repertoire and a TRBV6 gene product from a natural repertoire and TCRs comprising a TRAV21 gene product from a natural repertoire and a TRBV6 gene product from a natural repertoire.
    Type: Grant
    Filed: August 18, 2021
    Date of Patent: August 29, 2023
    Assignee: Immunocore Limited
    Inventors: Peter Eamon Molloy, Arsen Valeryevich Volkov, Dhaval Jaykant Sangani, Graham Anthony Hood, Chandramouli Reddy Chillakuri