Iogenetics, LLC

United States of America

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IPC Class
A61K 39/00 - Medicinal preparations containing antigens or antibodies 16
G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations 8
G16B 20/30 - Detection of binding sites or motifs 7
A61P 35/00 - Antineoplastic agents 6
G01N 33/68 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing involving proteins, peptides or amino acids 6
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Found results for  patents

1.

TUMOR-ASSOCIATED ANTIGENS IN BRAIN TUMORS

      
Application Number 18852707
Status Pending
Filing Date 2023-03-27
First Publication Date 2025-07-24
Owner IOGENETICS, LLC (USA)
Inventor
  • Homan, Jane
  • Bremel, Robert D.

Abstract

The present invention relates to the identification and use of tumor epitopes from subjects with brain cancer, and particularly to epitopes from brevican, neurocan, versican, and aggrecan and their use in formulating cancer vaccines for treatment of tumor patients. In some preferred embodiments the methods provide a means of identifying T cell epitopes in proteins upregulated in brain tumors and the selection of those peptides which can stimulate T cell responses in individual subjects with a particular combination of HLA alleles. It further identifies the T cell exposed motifs comprised in T cell epitopes and enables the design of peptides with alternative amino acids in positions other than the T cell exposed motifs. In preferred embodiments, the MHC I and MHC II alleles of the affected subject are determined, and peptides are selected which bind to their MHC molecules with a desired affinity to elicit stimulation.

IPC Classes  ?

  • A61K 39/00 - Medicinal preparations containing antigens or antibodies
  • A61K 40/11 - T-cells, e.g. tumour infiltrating lymphocytes [TIL] or regulatory T [Treg] cellsLymphokine-activated killer [LAK] cells
  • A61K 40/42 - Cancer antigens
  • A61P 35/00 - Antineoplastic agents
  • C12N 5/0783 - T cellsNK cellsProgenitors of T or NK cells
  • C12Q 1/6881 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
  • G01N 33/574 - ImmunoassayBiospecific binding assayMaterials therefor for cancer

2.

IMMUNE REPERTOIRE PATTERNS

      
Application Number 18781270
Status Pending
Filing Date 2024-07-23
First Publication Date 2025-01-16
Owner IOGENETICS, LLC (USA)
Inventor
  • Bremel, Robert D.
  • Homan, Jane

Abstract

The present invention provides methods and systems for identifying and classifying patterns comprising the T cell exposed motifs and the frequencies of such motifs in collections of proteins that make up the human proteome, immunoglobulinome, T cell receptor repertoire or microbiome, and other proteomes of environmental of microbial origin, or subsets thereof. It further provides graphical representations that facilitate comparisons of T cell exposed motif patterns between samples or between time points. The present invention also provides methods and systems for identifying and classifying patterns in repertoires of cells including receptor bearing cells and cells of tissue samples and detecting patterns of utility in diagnosis and monitoring of health and disease.

IPC Classes  ?

  • G16B 20/30 - Detection of binding sites or motifs
  • G01N 33/68 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing involving proteins, peptides or amino acids
  • G16B 50/00 - ICT programming tools or database systems specially adapted for bioinformatics

3.

CLEAVED NEOEPITOPES

      
Application Number US2024014986
Publication Number 2024/168137
Status In Force
Filing Date 2024-02-08
Publication Date 2024-08-15
Owner IOGENETICS, LLC (USA)
Inventor
  • Homan, Jane
  • Bremel, Robert D.

Abstract

The present invention relates to methods for treating, by administration of a cathepsin inhibitor, a subject who is affected by a tumor comprising a specific tumor mutation in a peptide that is cleaved with high frequency by a cathepsin and in which such cleavage prevents the presentation of a neoantigen thereby enabling immune evasion and tumor progression.

IPC Classes  ?

  • C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
  • A61K 39/395 - AntibodiesImmunoglobulinsImmune serum, e.g. antilymphocytic serum
  • C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
  • C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
  • G16B 20/50 - Mutagenesis

4.

EXPEDITED NEOANTIGEN VACCINES

      
Application Number US2024014987
Publication Number 2024/168138
Status In Force
Filing Date 2024-02-08
Publication Date 2024-08-15
Owner IOGENETICS, LLC (USA)
Inventor
  • Homan, Jane
  • Bremel, Robert D.

Abstract

The present invention provides methods for evaluation of potential tumor neoepitopes to assess the probability that they constitute immunogenic neoantigens in a cancer affected subject. The present invention provides vaccines comprising immunogenic neoepitopes for treatment of cancer in subjects in need thereof, optionally with the coadministration of cathepsin inhibitor.

IPC Classes  ?

  • G01N 33/68 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing involving proteins, peptides or amino acids
  • A61K 39/00 - Medicinal preparations containing antigens or antibodies
  • C12Q 1/6869 - Methods for sequencing
  • C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
  • G01N 33/574 - ImmunoassayBiospecific binding assayMaterials therefor for cancer
  • G16B 20/30 - Detection of binding sites or motifs
  • G16B 20/50 - Mutagenesis
  • A61P 35/00 - Antineoplastic agents
  • C40B 40/10 - Libraries containing peptides or polypeptides, or derivatives thereof

5.

FORMULATION OF PEPTIDE IMMUNOTHERAPIES

      
Application Number 18256243
Status Pending
Filing Date 2021-12-07
First Publication Date 2024-07-11
Owner IOGENETICS, LLC (USA)
Inventor
  • Homan, Jane
  • Bremel, Robert D.
  • Benameur, Hassan

Abstract

This invention provides a method for maximizing the immune response to mutated tumor specific proteins, either by means of stimulation of dendritic cells or T cells in vitro followed by administration of these cells to a patient, or by means of administration of a neoantigen vaccine in which de novo peptides, or their encoding nucleic acids, have been designed to ensure an appropriate level of binding affinity to a particular cancer patient's MHC alleles. This invention further provides for modulating the immune response in an immunopathology

IPC Classes  ?

  • C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
  • A61K 38/03 - Peptides having up to 20 amino acids in an undefined or only partially defined sequenceDerivatives thereof
  • A61K 39/00 - Medicinal preparations containing antigens or antibodies

6.

PERSONALIZED ALLOGENEIC IMMUNOTHERAPY

      
Application Number 18287715
Status Pending
Filing Date 2022-04-20
First Publication Date 2024-06-20
Owner IOGENETICS, LLC (USA)
Inventor
  • Homan, Jane
  • Bremel, Robert D.

Abstract

The present invention provides methods for treating cancer by T cell therapy comprising the steps of obtaining a biopsy from a subject affected by cancer, identifying mutated amino acids in the tumor and the T cell exposed amino acid motifs which contain the mutated amino acids, identifying a donor with matching alleles, generating an array of alternate peptides in which the T cell exposed motifs are maintained constant, but the other amino acids are substituted, selecting one or more peptides from the array of alternative peptides, each having a desired binding affinity to the MHC allele while maintaining the tumor specific T cell exposed motif, contacting antigen presenting cells with the selected alternative peptides so that the peptide is presented by the MHC of the antigen presenting cells, contacting the antigen presenting cells carrying the selected peptide with T cells harvested from the donor, and infusing the subject with stimulated T cells responding to the peptide of interest presented by the dendritic cell MHC.

IPC Classes  ?

  • A61K 39/00 - Medicinal preparations containing antigens or antibodies
  • A61P 35/00 - Antineoplastic agents
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • G16B 15/30 - Drug targeting using structural dataDocking or binding prediction
  • G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection

7.

ADMINISTRATION OF ANTI-TUMOR VACCINES

      
Application Number 18256242
Status Pending
Filing Date 2021-12-07
First Publication Date 2024-01-25
Owner
  • IOGENETICS, LLC (USA)
  • ASTHRA, LLC (USA)
Inventor
  • Homan, Jane
  • Bremel, Robert D.
  • Kesari, Santosh

Abstract

The present invention relates to methods for stimulating the immune response to a tumor by implementing a two-phase vaccination strategy in which a first vaccination comprises epitopes from tumor associated antigens or epitopes which embody amino acid mutations commonly associated with the cancer that is administered before tissue diagnosis, and a second vaccination which comprises personal neoepitopes, the design of which is unique to that subject and is identified based on comparative sequencing of normal tissue and tumor tissue obtained by biopsy.

IPC Classes  ?

  • A61K 39/00 - Medicinal preparations containing antigens or antibodies
  • A61P 35/00 - Antineoplastic agents
  • G01N 33/574 - ImmunoassayBiospecific binding assayMaterials therefor for cancer
  • C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer

8.

BYSTANDER PROTEIN VACCINES

      
Application Number 18256241
Status Pending
Filing Date 2021-12-07
First Publication Date 2024-01-18
Owner IOGENETICS, LLC (USA)
Inventor
  • Homan, Jane
  • Bremel, Robert D.

Abstract

The present invention is related to T cell epitopes and methods of their use, in particular bystander proteins, and identification of peptides which may be used to stimulate a CD8+ cytotoxic T cell response, as well as peptides which stimulate a CD4+ helper T cell response to the cells carrying the proteins.

IPC Classes  ?

  • A61K 38/17 - Peptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from animalsPeptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from humans
  • C12Q 1/6872 - Methods for sequencing involving mass spectrometry
  • C07K 14/00 - Peptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof

9.

EPITOPE MIMICS

      
Application Number 18170396
Status Pending
Filing Date 2023-02-16
First Publication Date 2023-10-12
Owner IOGENETICS, LLC (USA)
Inventor
  • Bremel, Robert D.
  • Homan, Jane

Abstract

This invention pertains to the identification of antibody mediated epitope mimics and applications of the identification of said mimic peptides in the design of biotherapeutics and vaccines.

IPC Classes  ?

10.

TUMOR-ASSOCIATED ANTIGENS IN BRAIN TUMORS

      
Application Number US2023064988
Publication Number 2023/192820
Status In Force
Filing Date 2023-03-27
Publication Date 2023-10-05
Owner IOGENETICS, LLC (USA)
Inventor
  • Homan, Jane
  • Bremel, Robert D.

Abstract

The present invention relates to the identification and use of tumor epitopes from subjects with brain cancer, and particularly to epitopes from brevican, neurocan, versican, and aggrecan and their use in formulating cancer vaccines for treatment of tumor patients. In some preferred embodiments the methods provide a means of identifying T cell epitopes in proteins upregulated in brain tumors and the selection of those peptides which can stimulate T cell responses in individual subjects with a particular combination of HLA alleles. It further identifies the T cell exposed motifs comprised in T cell epitopes and enables the design of peptides with alternative amino acids in positions other than the T cell exposed motifs. In preferred embodiments, the MHC I and MHC II alleles of the affected subject are determined, and peptides are selected which bind to their MHC molecules with a desired affinity to elicit stimulation.

IPC Classes  ?

  • A61K 38/17 - Peptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from animalsPeptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from humans
  • A61K 39/385 - Haptens or antigens, bound to carriers
  • A61P 35/00 - Antineoplastic agents
  • G01N 33/50 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing
  • G01N 33/53 - ImmunoassayBiospecific binding assayMaterials therefor

11.

BIOINFORMATIC PROCESSES FOR DETERMINATION OF PEPTIDE BINDING

      
Application Number 17524123
Status Pending
Filing Date 2021-11-11
First Publication Date 2023-01-19
Owner IOGENETICS, LLC (USA)
Inventor
  • Bremel, Robert D.
  • Homan, Jane

Abstract

This invention relates to the identification of peptide binding to ligands, and in particular to identification of epitopes expressed by microorganisms and by mammalian cells. The present invention provides polypeptides comprising the epitopes, and vaccines, antibodies and diagnostic products that utilize or are developed using the epitopes.

IPC Classes  ?

  • G16B 15/20 - Protein or domain folding
  • A61K 39/085 - Staphylococcus
  • A61K 39/00 - Medicinal preparations containing antigens or antibodies
  • A61K 39/145 - Orthomyxoviridae, e.g. influenza virus
  • A61K 39/02 - Bacterial antigens
  • A61K 39/095 - Neisseria
  • A61K 39/09 - Streptococcus
  • A61K 39/04 - Mycobacterium, e.g. Mycobacterium tuberculosis
  • A61K 39/21 - Retroviridae, e.g. equine infectious anemia virus
  • A61K 39/285 - Vaccinia virus or variola virus
  • G16B 15/00 - ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
  • G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
  • G16B 15/30 - Drug targeting using structural dataDocking or binding prediction
  • G16B 40/20 - Supervised data analysis
  • G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
  • G16B 20/30 - Detection of binding sites or motifs
  • G16B 20/50 - Mutagenesis

12.

PERSONALIZED ALLOGENEIC IMMUNOTHERAPY

      
Application Number US2022025527
Publication Number 2022/226055
Status In Force
Filing Date 2022-04-20
Publication Date 2022-10-27
Owner IOGENETICS, LLC (USA)
Inventor
  • Homan, Jane
  • Bremel, Robert D.

Abstract

The present invention provides methods for treating cancer by T cell therapy comprising the steps of obtaining a biopsy from a subject affected by cancer, identifying mutated amino acids in the tumor and the T cell exposed amino acid motifs which contain the mutated amino acids, identifying a donor with matching alleles, generating an array of alternate peptides in which the T cell exposed motifs are maintained constant, but the other amino acids are substituted, selecting one or more peptides from the array of alternative peptides, each having a desired binding affinity to the MHC allele while maintaining the tumor specific T cell exposed motif, contacting antigen presenting cells with the selected alternative peptides so that the peptide is presented by the MHC of the antigen presenting cells, contacting the antigen presenting cells carrying the selected peptide with T cells harvested from the donor, and infusing the subject with stimulated T cells responding to the peptide of interest presented by the dendritic cell MHC.

IPC Classes  ?

  • A61K 39/35 - Allergens
  • A61K 39/00 - Medicinal preparations containing antigens or antibodies
  • G01N 33/50 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing
  • C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer

13.

BYSTANDER PROTEIN VACCINES

      
Application Number US2021062137
Publication Number 2022/125504
Status In Force
Filing Date 2021-12-07
Publication Date 2022-06-16
Owner IOGENETICS, LLC (USA)
Inventor
  • Homan, Jane
  • Bremel, Robert D.

Abstract

The present invention is related to T cell epitopes and methods of their use, in particular bystander proteins, and identification of peptides which may be used to stimulate a CD8+ cytotoxic T cell response, as well as peptides which stimulate a CD4+ helper T cell response to the cells carrying the proteins.

IPC Classes  ?

  • A61K 38/17 - Peptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from animalsPeptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from humans
  • A61K 39/00 - Medicinal preparations containing antigens or antibodies
  • A61K 39/385 - Haptens or antigens, bound to carriers
  • A61P 35/00 - Antineoplastic agents

14.

PERSONALIZED IMMUNOTHERAPIES

      
Application Number US2021062140
Publication Number 2022/125507
Status In Force
Filing Date 2021-12-07
Publication Date 2022-06-16
Owner IOGENETICS, LLC (USA)
Inventor
  • Homan, Jane
  • Bremel, Robert D.
  • Benameur, Hassan

Abstract

in vitro de novode novo peptides, or their encoding nucleic acids, have been designed to ensure an appropriate level of binding affinity to a particular cancer patient's MHC alleles. This invention further provides for modulating the immune response in an immunopathology

IPC Classes  ?

  • A61K 39/00 - Medicinal preparations containing antigens or antibodies
  • A61K 39/39 - Medicinal preparations containing antigens or antibodies characterised by the immunostimulating additives, e.g. chemical adjuvants
  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
  • G01N 33/50 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing

15.

ADMINISTRATION OF ANTI-TUMOR VACCINES

      
Application Number US2021062147
Publication Number 2022/125511
Status In Force
Filing Date 2021-12-07
Publication Date 2022-06-16
Owner
  • IOGENETICS, LLC (USA)
  • ASTHRA, LLC (USA)
Inventor
  • Homan, Jane
  • Bremel, Robert D.
  • Kesari, Santosh

Abstract

The present invention relates to methods for stimulating the immune response to a tumor by implementing a two-phase vaccination strategy in which a first vaccination comprises epitopes from tumor associated antigens or epitopes which embody amino acid mutations commonly associated with the cancer that is administered before tissue diagnosis, and a second vaccination which comprises personal neoepitopes, the design of which is unique to that subject and is identified based on comparative sequencing of normal tissue and tumor tissue obtained by biopsy.

IPC Classes  ?

  • G01N 21/65 - Raman scattering
  • G01N 33/50 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing
  • G01N 33/53 - ImmunoassayBiospecific binding assayMaterials therefor

16.

Bioinformatic processes for determination of peptide binding

      
Application Number 16921460
Grant Number 11640847
Status In Force
Filing Date 2020-07-06
First Publication Date 2021-12-02
Grant Date 2023-05-02
Owner IOGENETICS, LLC (USA)
Inventor
  • Bremel, Robert D.
  • Homan, Jane

Abstract

This invention relates to the identification of peptide binding to ligands, and in particular to identification of epitopes expressed by microorganisms and by mammalian cells. The present invention provides polypeptides comprising the epitopes, and vaccines, antibodies and diagnostic products that utilize or are developed using the epitopes.

IPC Classes  ?

  • G16B 20/30 - Detection of binding sites or motifs
  • G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
  • G16B 40/20 - Supervised data analysis
  • G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
  • G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
  • G16B 20/40 - Population geneticsLinkage disequilibrium

17.

MATHEMATICAL PROCESSES FOR DETERMINATION OF PEPTIDASE CLEAVAGE

      
Application Number 17376739
Status Pending
Filing Date 2021-07-15
First Publication Date 2021-11-04
Owner IOGENETICS, LLC (USA)
Inventor Bremel, Robert D.

Abstract

This invention relates to the identification of peptidase cleavage sites in proteins and in particular to identification protease cleavage by the endopeptidases. The present invention utilizes a bioinformatic methodology for prediction of peptidase cleavage sites based on principal component analysis and based on training sets obtained by experimental protein cleavage. This invention is not limited to training sets derived from CSL approaches, nor to any other experimental determination of cleavage site.

IPC Classes  ?

  • G16B 20/30 - Detection of binding sites or motifs
  • G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
  • G16B 5/00 - ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
  • G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
  • G06N 3/04 - Architecture, e.g. interconnection topology
  • G06N 3/08 - Learning methods

18.

IMMUNE REPERTOIRE PATTERNS

      
Application Number 17053955
Status Pending
Filing Date 2019-05-09
First Publication Date 2021-08-26
Owner Iogenetics, LLC (USA)
Inventor
  • Bremel, Robert D.
  • Homan, Jane

Abstract

The present invention provides methods and systems for identifying and classifying patterns comprising the T cell exposed motifs and the frequencies of such motifs in collections of proteins that make up the human proteome, immunoglobulinome, T cell receptor repertoire or microbiome, and other proteomes of environmental of microbial origin, or subsets thereof. It further provides graphical representations that facilitate comparisons of T cell exposed motif patterns between samples or between time points. The present invention also provides methods and systems for identifying and classifying patterns in repertoires of cells including receptor bearing cells and cells of tissue samples and detecting patterns of utility in diagnosis and monitoring of health and disease.

IPC Classes  ?

  • G16B 20/30 - Detection of binding sites or motifs
  • G01N 33/68 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing involving proteins, peptides or amino acids
  • G16B 50/00 - ICT programming tools or database systems specially adapted for bioinformatics

19.

IMMUNE MOTIFS IN PRODUCTS FROM DOMESTIC ANIMALS

      
Application Number 17066959
Status Pending
Filing Date 2020-10-09
First Publication Date 2021-01-28
Owner IOGENETICS, LLC (USA)
Inventor
  • Bremel, Robert D.
  • Homan, Jane

Abstract

The present invention provides a means to prepare a product from domestic animal milk, blood or eggs which comprises an array of T-cell exposed motifs similar in identity, distribution and concentration to those found in human immunoglobulin variable regions and to prepare and apply the product as an immune modulating agent for administration either as a nutritional supplement or as a pharmaceutical product.

IPC Classes  ?

  • A61K 39/395 - AntibodiesImmunoglobulinsImmune serum, e.g. antilymphocytic serum
  • C07K 16/00 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies
  • A61K 9/00 - Medicinal preparations characterised by special physical form
  • C07K 16/04 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies from milk

20.

IMMUNE RECOGNITION MOTIFS

      
Application Number 16986831
Status Pending
Filing Date 2020-08-06
First Publication Date 2020-12-24
Owner IOGENETICS, LLC (USA)
Inventor
  • Bremel, Robert D.
  • Homan, Jane
  • Imboden, Michael

Abstract

The present invention provides methods and systems for identifying and classifying epitopes and use of that information to analyze proteins and peptides within proteins, especially potential epitopes, and to use the information to design synthetic peptides and proteins, analyze biopharmaceutical proteins, and diagnose autoimmune conditions. Peptides which are bound in MHC grooves comprise two sets of amino acids: those that face inwards into the groove and determine the binding affinity to the MHC molecule (the groove exposed motifs or GEM) and those which do not interact with the groove but rather are on the obverse side exposed outwardly to the T-cells (the T-cell exposed Motifs or TCEM). The present invention utilizes information related to the identity and physiochemical characteristics of the GEM and TCEM.

IPC Classes  ?

  • G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
  • G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
  • G16B 50/00 - ICT programming tools or database systems specially adapted for bioinformatics
  • G01N 33/68 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing involving proteins, peptides or amino acids

21.

NEOANTIGEN IMMUNOTHERAPIES

      
Application Number 16898924
Status Pending
Filing Date 2020-06-11
First Publication Date 2020-12-17
Owner IOGENETICS, LLC (USA)
Inventor
  • Homan, Jane
  • Bremel, Robert D.

Abstract

This invention provides a method for maximizing the immune response to mutated tumor specific proteins, either by means of stimulation of dendritic cells or T cells in vitro followed by administration of these cells to a patient, or by means of administration of a neoantigen vaccine in which de novo peptides, or their encoding nucleic acids, have been designed to ensure an appropriate level of binding affinity to a particular cancer patient's WIC alleles. This invention further provides for modulating the immune response in an immunopathology other than cancer.

IPC Classes  ?

  • A61K 39/00 - Medicinal preparations containing antigens or antibodies

22.

NEOANTIGEN IMMUNOTHERAPIES

      
Application Number US2020037206
Publication Number 2020/252145
Status In Force
Filing Date 2020-06-11
Publication Date 2020-12-17
Owner IOGENETICS, LLC (USA)
Inventor
  • Homan, Jane
  • Bremel, Robert, D.

Abstract

in vitro de novode novo peptides, or their encoding nucleic acids, have been designed to ensure an appropriate level of binding affinity to a particular cancer patient's MHC alleles. This invention further provides for modulating the immune response in an immunopathology other than cancer.

IPC Classes  ?

  • A61K 39/00 - Medicinal preparations containing antigens or antibodies

23.

IMMUNE REPERTOIRE PATTERNS

      
Application Number US2019031484
Publication Number 2019/217655
Status In Force
Filing Date 2019-05-09
Publication Date 2019-11-14
Owner IOGENETICS,LLC (USA)
Inventor
  • Bremel, Robert D.
  • Homan, Jane

Abstract

The present invention provides methods and systems for identifying and classifying patterns comprising the T cell exposed motifs and the frequencies of such motifs in collections of proteins that make up the human proteome, immunoglobulinome, T cell receptor repertoire or microbiome, and other proteomes of environmental of microbial origin, or subsets thereof. It further provides graphical representations that facilitate comparisons of T cell exposed motif patterns between samples or between time points. The present invention also provides methods and systems for identifying and classifying patterns in repertoires of cells including receptor bearing cells and cells of tissue samples and detecting patterns of utility in diagnosis and monitoring of health and disease.

IPC Classes  ?

  • G01N 33/68 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing involving proteins, peptides or amino acids
  • G06F 19/18 - for functional genomics or proteomics, e.g. genotype-phenotype associations, linkage disequilibrium, population genetics, binding site identification, mutagenesis, genotyping or genome annotation, protein-protein interactions or protein-nucleic acid interactions
  • G06F 19/20 - for hybridisation or gene expression, e.g. microarrays, sequencing by hybridisation, normalisation, profiling, noise correction models, expression ratio estimation, probe design or probe optimisation

24.

Modified Zika virus NS1 protein with reduced cross-reactive immunogenicity

      
Application Number 16072357
Grant Number 11434259
Status In Force
Filing Date 2017-01-25
First Publication Date 2019-01-31
Grant Date 2022-09-06
Owner IOGENETICS, LLC (USA)
Inventor
  • Bremel, Robert D.
  • Homan, Jane
  • Imboden, Michael

Abstract

The present invention relates to vaccine compositions and therapeutic interventions for treating and preventing infections and diseases caused by flaviviruses, including Zika, dengue, and Usutu virus. It also relates to compositions and methods for diagnosis and differential diagnosis of flaviviruses and co-endemic pathogens.

IPC Classes  ?

  • C07K 14/005 - Peptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from viruses
  • A61K 39/12 - Viral antigens
  • A61K 39/00 - Medicinal preparations containing antigens or antibodies
  • C07K 14/18 - Togaviridae, e.g. flavivirus, pestivirus, yellow fever virus, hepatitis C virus, japanese encephalitis virus
  • C07K 16/10 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies against material from viruses from RNA viruses

25.

Immunoglobulin polypeptide fractions from products of domestic animals

      
Application Number 15325654
Grant Number 10799582
Status In Force
Filing Date 2015-07-10
First Publication Date 2018-08-09
Grant Date 2020-10-13
Owner IOGENETICS, LLC (USA)
Inventor
  • Bremel, Robert D.
  • Homan, Jane

Abstract

The present invention provides a means to prepare a product from domestic animal milk, blood or eggs which comprises an array of T-cell exposed motifs similar in identity, distribution and concentration to those found in human immunoglobulin variable regions and to prepare and apply the product as an immune modulating agent for administration either as a nutritional supplement or as a pharmaceutical product.

IPC Classes  ?

  • A61K 39/395 - AntibodiesImmunoglobulinsImmune serum, e.g. antilymphocytic serum
  • C07K 16/00 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies
  • A61K 9/00 - Medicinal preparations characterised by special physical form
  • C07K 16/04 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies from milk

26.

EPITOPE MIMICS

      
Application Number US2017021781
Publication Number 2017/156395
Status In Force
Filing Date 2017-03-10
Publication Date 2017-09-14
Owner IOGENETICS, LLC (USA)
Inventor
  • Bremel, Robert D.
  • Homan, Jane

Abstract

This invention pertains to the identification of antibody mediated epitope mimics and applications of the identification of said mimic peptides in the design of biotherapeutics and vaccines.

IPC Classes  ?

  • A61K 38/17 - Peptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from animalsPeptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from humans
  • A61K 39/00 - Medicinal preparations containing antigens or antibodies
  • A61P 25/16 - Anti-Parkinson drugs
  • G06F 19/18 - for functional genomics or proteomics, e.g. genotype-phenotype associations, linkage disequilibrium, population genetics, binding site identification, mutagenesis, genotyping or genome annotation, protein-protein interactions or protein-nucleic acid interactions
  • G06F 19/24 - for machine learning, data mining or biostatistics, e.g. pattern finding, knowledge discovery, rule extraction, correlation, clustering or classification
  • G06N 3/08 - Learning methods

27.

INTERVENTIONS FOR FLAVIVIRUS INFECTIONS

      
Application Number US2017014852
Publication Number 2017/132210
Status In Force
Filing Date 2017-01-25
Publication Date 2017-08-03
Owner IOGENETICS, LLC (USA)
Inventor
  • Bremel, Robert, D.
  • Homan, Jane
  • Imboden, Michael

Abstract

The present invention relates to vaccine compositions and therapeutic interventions for treating and preventing infections and diseases caused by flaviviruses, including Zika, dengue, and Usutu virus. It also relates to compositions and methods for diagnosis and differential diagnosis of flaviviruses and co-endemic pathogens.

IPC Classes  ?

28.

Identifying peptides having T-cell-exposed motifs with known frequency of occurrence in a reference database

      
Application Number 15325655
Grant Number 10755801
Status In Force
Filing Date 2015-07-10
First Publication Date 2017-06-08
Grant Date 2020-08-25
Owner IOGENETICS, LLC (USA)
Inventor
  • Bremel, Robert D.
  • Homan, Jane
  • Imboden, Michael

Abstract

The present invention provides methods and systems for identifying and classifying epitopes and use of that information to analyze proteins and peptides within proteins, especially potential epitopes, and to use the information to design synthetic peptides and proteins, analyze biopharmaceutical proteins, and diagnose autoimmune conditions. Peptides which are bound in MHC grooves comprise two sets of amino acids: those that face inwards into the groove and determine the binding affinity to the MHC molecule (the groove exposed motifs or GEM) and those which do not interact with the groove but rather are on the obverse side exposed outwardly to the T-cells (the T-cell exposed Motifs or TCEM). The present invention utilizes information related to the identity and physiochemical characteristics of the GEM and TCEM.

IPC Classes  ?

  • G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
  • G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
  • G16B 50/00 - ICT programming tools or database systems specially adapted for bioinformatics
  • G01N 33/68 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing involving proteins, peptides or amino acids

29.

Bioinformatic processes for determination of peptide binding

      
Application Number 14895746
Grant Number 12374421
Status In Force
Filing Date 2014-06-09
First Publication Date 2016-05-12
Grant Date 2025-07-29
Owner IOGENETICS, LLC (USA)
Inventor
  • Bremel, Robert D.
  • Homan, Jane

Abstract

This invention relates to the identification of peptide binding to ligands, and in particular to identification of epitopes expressed by microorganisms and by mammalian cells. The present invention provides polypeptides comprising the epitopes, and vaccines, antibodies and diagnostic products that utilize or are developed using the epitopes.

IPC Classes  ?

  • G16B 5/00 - ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
  • A61K 39/00 - Medicinal preparations containing antigens or antibodies
  • A61K 39/02 - Bacterial antigens
  • C07K 7/06 - Linear peptides containing only normal peptide links having 5 to 11 amino acids
  • C07K 7/08 - Linear peptides containing only normal peptide links having 12 to 20 amino acids
  • C12N 9/02 - Oxidoreductases (1.), e.g. luciferase
  • G06F 17/16 - Matrix or vector computation
  • G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
  • G16B 20/30 - Detection of binding sites or motifs
  • G16B 20/50 - Mutagenesis
  • G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
  • G16B 40/20 - Supervised data analysis

30.

Mathematical processes for determination of peptidase cleavage

      
Application Number 14895748
Grant Number 11069427
Status In Force
Filing Date 2014-06-09
First Publication Date 2016-04-28
Grant Date 2021-07-20
Owner IOGENETICS, LLC (USA)
Inventor Bremel, Robert D.

Abstract

This invention relates to the identification of peptidase cleavage sites in proteins and in particular to identification protease cleavage by the endopeptidases. The present invention utilizes a bioinformatic methodology for prediction of peptidase cleavage sites based on principal component analysis and based on training sets obtained by experimental protein cleavage. This invention is not limited to training sets derived from CSL approaches, nor to any other experimental determination of cleavage site.

IPC Classes  ?

  • G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
  • G16B 5/00 - ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
  • G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
  • G06N 3/04 - Architecture, e.g. interconnection topology
  • G06N 3/08 - Learning methods

31.

IMMUNE RECOGNITION MOTIFS

      
Application Number US2015039969
Publication Number 2016/007870
Status In Force
Filing Date 2015-07-10
Publication Date 2016-01-14
Owner IOGENETICS, LLC (USA)
Inventor
  • Bremel, Robert D.
  • Homan, Jane
  • Imboden, Michael

Abstract

The present invention provides methods and systems for identifying and classifying epitopes and use of that information to analyze proteins and peptides within proteins, especially potential epitopes, and to use the information to design synthetic peptides and proteins, analyze biopharmaceutical proteins, and diagnose autoimmune conditions. Peptides which are bound in MHC grooves comprise two sets of amino acids: those that face inwards into the groove and determine the binding affinity to the MHC molecule (the groove exposed motifs or GEM) and those which do not interact with the groove but rather are on the obverse side exposed outwardly to the T-cells (the T-cell exposed Motifs or TCEM). The present invention utilizes information related to the identity and physiochemical characteristics of the GEM and TCEM.

IPC Classes  ?

  • G06F 19/18 - for functional genomics or proteomics, e.g. genotype-phenotype associations, linkage disequilibrium, population genetics, binding site identification, mutagenesis, genotyping or genome annotation, protein-protein interactions or protein-nucleic acid interactions
  • G06F 19/24 - for machine learning, data mining or biostatistics, e.g. pattern finding, knowledge discovery, rule extraction, correlation, clustering or classification
  • G06N 3/08 - Learning methods

32.

IMMUNE MOTIFS IN PRODUCTS FROM DOMESTIC ANIMALS

      
Application Number US2015039970
Publication Number 2016/007871
Status In Force
Filing Date 2015-07-10
Publication Date 2016-01-14
Owner IOGENETICS, LLC (USA)
Inventor
  • Bremel, Robert D.
  • Homan, Jane

Abstract

The present invention provides a means to prepare a product from domestic animal milk, blood or eggs which comprises an array of T-cell exposed motifs similar in identity, distribution and concentration to those found in human immunoglobulin variable regions and to prepare and apply the product as an immune modulating agent for administration either as a nutritional supplement or as a pharmaceutical product.

IPC Classes  ?

  • A61K 39/00 - Medicinal preparations containing antigens or antibodies
  • A61K 39/38 - Antigens from snakes
  • A61K 38/08 - Peptides having 5 to 11 amino acids
  • A61K 38/00 - Medicinal preparations containing peptides
  • C40B 30/04 - Methods of screening libraries by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
  • C40B 30/10 - Methods of screening libraries by measuring physical properties, e.g. mass
  • C40B 50/02 - In silico or mathematical conception of libraries

33.

MATHEMATICAL PROCESSES FOR DETERMINATION OF PEPTIDASE CLEAVAGE

      
Application Number US2014041525
Publication Number 2014/200912
Status In Force
Filing Date 2014-06-09
Publication Date 2014-12-18
Owner IOGENETICS, LLC (USA)
Inventor Bremel, Robert D.

Abstract

The present invention provides a bioinformatic methodology for prediction of peptidase cleavage sites based on principal component analysis and based on training sets obtained by experimental protein cleavage. This invention is not limited to training sets derived from CSL approaches, nor to any other experimental determination of cleavage site. Undoubtedly there will be new approaches to developed for experimental measurement of cleavage sites and these too may be the source of training sources for the present invention.

IPC Classes  ?

  • C12Q 1/37 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving hydrolase involving peptidase or proteinase
  • G01N 33/48 - Biological material, e.g. blood, urineHaemocytometers
  • C40B 50/02 - In silico or mathematical conception of libraries

34.

BIOINFORMATIC PROCESSES FOR DETERMINATION OF PEPTIDE BINDING

      
Application Number US2014041523
Publication Number 2014/200910
Status In Force
Filing Date 2014-06-09
Publication Date 2014-12-18
Owner IOGENETICS, LLC (USA)
Inventor
  • Bremel, Robert D.
  • Homan, Jane

Abstract

This invention relates to the identification of peptide binding to ligands, and in particular to identification of epitopes expressed by microorganisms and by mammalian cells. The present invention provides polypeptides comprising the epitopes, and vaccines, antibodies and diagnostic products that utilize or are developed using the epitopes.

IPC Classes  ?

  • A61K 38/00 - Medicinal preparations containing peptides
  • A61K 38/04 - Peptides having up to 20 amino acids in a fully defined sequenceDerivatives thereof
  • A61K 39/00 - Medicinal preparations containing antigens or antibodies
  • G06F 7/60 - Methods or arrangements for performing computations using a digital non-denominational number representation, i.e. number representation without radixComputing devices using combinations of denominational and non-denominational quantity representations
  • G06E 1/00 - Devices for processing exclusively digital data
  • G01N 33/53 - ImmunoassayBiospecific binding assayMaterials therefor

35.

ANTIMICROBIAL COMPOSITIONS

      
Application Number US2013069828
Publication Number 2014/078373
Status In Force
Filing Date 2013-11-13
Publication Date 2014-05-22
Owner IOGENETICS, LLC (USA)
Inventor
  • Bremel, Robert Duane
  • Homan, Jane
  • Imboden, Michael
  • Keough, Brendan

Abstract

The present invention relates antimicrobial compositions, and in particular to antigen binding proteins comprising one or more domains that provide antimicrobial activity.

IPC Classes  ?

36.

Bioinformatic processes for determination of peptide binding

      
Application Number 13052733
Grant Number 10706955
Status In Force
Filing Date 2011-03-21
First Publication Date 2013-12-12
Grant Date 2020-07-07
Owner IOGENETICS, LLC (USA)
Inventor
  • Bremel, Robert D.
  • Homan, Jane

Abstract

This invention relates to processes for identifying peptide and polypeptide ligands for a binding partner by using principal component analysis of amino acids to derive vectors describing amino acid subsets corresponding to peptides with known binding affinities and then using this information in a neural network modeling process to derive binding prediction equations. These binding prediction equations are then used in the analysis of subsets of amino acids from a target source to identify peptides or polypeptides ligands in the target source that have affinity for a binding partner.

IPC Classes  ?

  • G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
  • G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding

37.

BIOINFORMATIC PROCESSES FOR DETERMINATION OF PEPTIDE BINDING

      
Application Number US2012055038
Publication Number 2013/040142
Status In Force
Filing Date 2012-09-13
Publication Date 2013-03-21
Owner IOGENETICS, LLC (USA)
Inventor
  • Bremel, Robert D.
  • Homan, Jane

Abstract

This invention relates to the identification of peptide binding to ligands, and in particular to identification of epitopes expressed by microorganisms and by mammalian cells. The present invention provides polypeptides comprising the epitopes, and vaccines, antibodies and diagnostic products that utilize or are developed using the epitopes.

IPC Classes  ?

  • C07K 1/00 - General processes for the preparation of peptides
  • C07K 5/00 - Peptides having up to four amino acids in a fully defined sequenceDerivatives thereof
  • C07K 14/00 - Peptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof
  • G01N 33/53 - ImmunoassayBiospecific binding assayMaterials therefor

38.

BIOINFORMATIC PROCESSES FOR DETERMINATION OF PEPTIDE BINDING

      
Application Number US2011029192
Publication Number 2011/119484
Status In Force
Filing Date 2011-03-21
Publication Date 2011-09-29
Owner IOGENETICS, LLC (USA)
Inventor
  • Bremel, Robert, D.
  • Homan, Jane

Abstract

Methods of identification of peptide binding to ligands, such as epitopes expressed by microorganisms and by mammalian cells. A method for identification in silico of peptides and sets of peptides internal to or on the surface of microorganisms and cells which have a high probability of being effective in stimulating humoral and cell mediated immune responses. The method combines multiple predictive tools to provide a composite of both topology and multiple sets of binding or affinity characteristics of specific peptides within an entire proteome. With a composite having topological distribution and spatial relationship, the method identifies regions which have a high probability of being B-cell or MHC binding sites comprising T-cell epitopes on the surface of microorganisms or cells, or MHC binding sites comprising T cell epitopes internal to microorganisms or cells. Polypeptides comprising the epitopes, and vaccines, antibodies and diagnostic products are developed using the epitopes.

IPC Classes  ?

  • G01N 33/48 - Biological material, e.g. blood, urineHaemocytometers
  • C40B 50/02 - In silico or mathematical conception of libraries

39.

TARGETED CRYPTOSPORIDIUM BIOCIDES

      
Application Number US2010020910
Publication Number 2010/083225
Status In Force
Filing Date 2010-01-13
Publication Date 2010-07-22
Owner
  • IOGENETICS, LLC. (USA)
  • ARIZONA BOARD OF REGENTS on behalf of THE UNIVERSITY OF ARIZONA (USA)
Inventor
  • Imboden, Michael
  • Riggs, Michael
  • Schaefer, Deborah, A.
  • Homan, Jane

Abstract

The present invention relates to fusion proteins comprising a microorganism targeting molecule (e.g., immunoglobulin) and a biocide. The present invention also relates to therapeutic and prophylactic methods of using a fusion protein comprising a microorganism targeting molecule and a biocide in diverse fields.

IPC Classes  ?

  • A01N 63/02 - Substances produced by, or obtained from, microorganisms or animals
  • A01N 63/00 - Biocides, pest repellants or attractants, or plant growth regulators containing microorganisms, viruses, microbial fungi, animals or substances produced by, or obtained from, microorganisms, viruses, microbial fungi or animals, e.g. enzymes or fermentates
  • A01P 1/00 - DisinfectantsAntimicrobial compounds or mixtures thereof
  • A01P 3/00 - Fungicides
  • A61K 38/16 - Peptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof
  • C07K 19/00 - Hybrid peptides
  • C12N 15/62 - DNA sequences coding for fusion proteins
  • C12N 15/867 - Retroviral vectors
  • A61K 39/44 - Antibodies bound to carriers
  • C07K 16/00 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies

40.

TARGETED BIOCIDES

      
Application Number US2006039361
Publication Number 2007/047189
Status In Force
Filing Date 2006-10-10
Publication Date 2007-04-26
Owner
  • IOGENETICS, LLC (USA)
  • ARIZONA BOARD OF REGENTS ON BEHALF OF THE UNIVERSITY OF ARIZONA (USA)
Inventor
  • Imboden, Michael
  • Riggs, Michael, W.
  • Schaefer, Deborah

Abstract

The present invention relates to retroviral constructs that encode novel monoclonal antibodies, novel fusion proteins, and chimeric monoclonal antibodies and to methods of using and producing the same. In particular, the present invention relates to methods of producing a fusion protein comprising a microorganism targeting molecule (e.g., immunoglobulin or innate immune system receptor molecule) and a biocide (e.g., bactericidal enzyme) in transgenic animals (e.g., bovines) and in cell cultures. The present invention also relates to therapeutic and prophylactic methods of using a fusion protein comprising a microorganism targeting molecule and a biocide in health care (e.g., human and veterinary), agriculture (e.g., animal and plant production), and food processing (e.g., beef carcass processing). The present invention also relates to methods of using a fusion protein comprising a microorganism targeting molecule and a biocide in various diagnostic applications in number of diverse fields such as agriculture, medicine, and national defense.

IPC Classes  ?

  • A61K 39/40 - AntibodiesImmunoglobulinsImmune serum, e.g. antilymphocytic serum bacterial
  • C07K 16/12 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies against material from bacteria