System and method related to improving an immune system

• US 20060047434A1
• Filed: 08/24/2004
• Published: 03/02/2006
• Est. Priority Date: 08/24/2004
• Status: Abandoned Application

• Current Assignee: Searete LLC (Intellectual Ventures LLC)
• Original Assignee: Searete LLC (Intellectual Ventures LLC)
• Inventors: Ishikawa, Muriel Y., Myhrvold, Nathan P., Wood, Lowell L. Jr., Jung, Edward K.Y., Wilson, Richa
• Application Number:
  US10/925,904
• Publication Number:
  US 20060047434A1
• Time in Patent Office: Days
• US Class Current: 702/19
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: G16B 20/30 Detection of binding sites or motifs
• CPC Class Codes: G16B 20/50 Mutagenesis
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/30 Data warehousing; Computing architectures

Abstract

The present application relates, in general, to a system and/or method for detection and/or treatment.

Claims

1. A system, comprising:

at least one computer program for use with at least one computer system and wherein the computer program includes a plurality of instructions including but not limited to

a first set of instructions for designating one or more epitopes of at least one agent,

a second set of instructions for predicting one or more changes in the one or more epitopes of the at least one agent, and

a third set of instructions for aiding the identification of one or more immune response components associated with the one or more epitopes of the at least one agent.

2. The system of claim 1, wherein the first set of instructions for designating one or more epitopes of at least one agent further comprises:

one or more instructions for associating the one or more epitopes with an evocation of at least a part of an immune response in a host.

3. The system of claim 1, wherein the first set of instructions for designating one or more epitopes of at least one agent further comprises:

one or more instructions for aiding the identification of the one or more epitopes displayed by the at least one agent.

4. The system of claim 1, wherein the first set of instructions for designating one or more epitopes of at least one agent further comprises:

one or more instructions for aiding the identification of the one or more epitopes present in at least two or more agents having a copy number of at least two.

5. The system of claim 1, wherein the first set of instructions for designating one or more epitopes of at least one agent comprises:

one or more instructions for aiding the identification of the one or more epitopes displayed by the at least one agent.

6. The system of claim 1, wherein the first set of instructions for designating one or more epitopes of at least one agent further comprises:

one or more instructions for aiding the identification of at least one substantially immunogenic epitope of the at least one agent.

7. The system of claim 1, wherein the one or more epitopes further comprises:

one or more epitopes of at least three amino acids.

8. The system of claim 1, wherein the one or more epitopes further comprises:

one or more epitopes of at least nine nucleotides.

9. The system of claim 1, wherein the one or more epitopes includes:

at least a portion of at least one of an amino acid residue, a nucleotide, a carbohydrate, a protein, a lipid, a capsid protein, a polysaccharide, a lipopolysaccharide, a glycolipid, or a glycoprotein.

10. The system of claim 1, wherein the one or more epitopes includes:

at least a part of at least one epitope of a virus, a bacterium, a yeast, a mold, a fungus, a mycoplasma, a ureaplasma, a Chlamydia, a rickettsia, a nanobacterium, a prion, an agent responsible for TSE, a multicellular parasite, a protein, an infectious protein, a nucleic acid, a metabolic by-product, a cellular by-product, or a toxin.

11. The system of claim 1, wherein the one or more epitopes includes:

one or more epitopes of a substantially linear form or a substantially non-linear form.

12. The system of claim 1, wherein the computer program further comprises:

a fourth set of instructions for assigning a confidence level to the one or more epitopes.

13. The system of claim 1, wherein the computer program further comprises:

a fourth set of instructions for ranking the one or more epitopes.

14. The system of claim 1, wherein the computer program further comprises:

a fourth set of instructions for designating at least one epitope associated with at least a part of a progression of an immune response in a host.

15. The system of claim 1, wherein the computer program further comprises:

a fourth set of instructions for designating a grouping of the one or more epitopes including at least one user chosen parameter.

16. The system of claim 15, wherein the at least one user chosen parameter includes:

one or more parameters of a species specificity, a family history, a medical history, a race, a geographical location, a severity of an immune response, or a genetic factor.

17. The system of claim 1, wherein the computer program comprises:

a fourth set of instructions for designating a grouping of the one or more epitopes associated with a predicted course of at least a part of an immune response including at least one user chosen parameter.

18. The system of claim 17, wherein the at least one user chosen parameter includes:

one or more parameters of a species specificity, a family history, a race, a geographical location, a severity of an immune response, or a genetic factor.

19. The system of claim 1, wherein the second set of instructions for predicting one or more changes in the one or more epitopes of the at least one agent further comprises:

one or more instructions for designating the one or more epitopes having up to about 80% amino acid sequence match to a host.

20. The system of claim 1, wherein the second set of instructions for predicting one or more changes in the one or more epitopes of the at least one agent further comprises:

one or more instructions for designating the one or more epitopes having up to about 80% nucleotide sequence match to a host.

21. The system of claim 1, wherein the second set of instructions for predicting one or more changes in the one or more epitopes of the at least one agent further comprises:

one or more instructions for designating the one or more epitopes having between 0 to 100% sequence match with an entity.

22. The system of claim 1, wherein the second set of instructions for predicting one or more changes in the one or more epitopes of the at least one agent further comprises:

one or more instructions for designating the one or more epitopes having at least 88% sequence match with an entity.

23. The system of claim 1, wherein the second set of instructions for predicting one or more changes in the one or more epitopes of the at least one agent further comprises:

one or more instructions for designating the one or more epitopes having a substantially similar functional sequence match with an entity.

24. The system of claim 1, wherein the second set of instructions for predicting one or more changes in the one or more epitopes of the at least one agent further comprises:

one or more instructions for designating the one or more epitopes having a substantially similar structural match with an entity.

25. The system of claim 1, wherein the second set of instructions for predicting one or more changes in the one or more epitopes of the at least one agent further comprises:

one or more instructions for designating the one or more epitopes having a substantially similar effect on the immune response.

26. The system of claim 1, wherein the second set of instructions for predicting one or more changes in the one or more epitopes of the at least one agent further comprises:

one or more instructions for designating the one or more epitopes having a substantially similar functionally effect.

27. The system of claim 1, wherein the second set of instructions for predicting one or more changes in the one or more epitopes of the at least one agent further comprises:

one or more instructions for designating the one or more epitopes having a substantially similar result in an assay.

28. The system of claim 1, wherein the second set of instructions for predicting one or more changes in the one or more epitopes of the at least one agent further comprises:

one or more instructions for aiding the identification of the one or more epitopes with a probable sequence match to a host sequence and wherein the host sequence includes single nucleotide polymorphisms.

29. The system of claim 1, wherein the third set of instructions for aiding the identification of one or more immune response components associated with the one or more epitopes of the at least one agent further comprises:

one or more instructions for providing one or more predicted courses of an immune response in a host and wherein the one or more predicted courses is responsive to one or more interventions.

30. The system of claim 29, wherein the one or more interventions includes:

at least one of a therapy, a treatment, a drug, a hormone, or an antibody.

31. The system of claim 1, wherein the computer program further comprises:

one or more instructions for changing an order of execution of the instructions.

32. The system of claim 1, wherein the third set of instructions for aiding the identification of one or more immune response components associated with the one or more epitopes of the at least one agent further comprises:

one or more instructions for providing a peptide sequence corresponding to the one or more epitopes associated with an evocation of an immune response.

33. The system of claim 32, wherein the one or more instructions for providing a peptide sequence corresponding to the one or more epitopes associated with the evocation of the immune response further comprise:

one or more instructions for providing a peptide sequence corresponding to the one or more epitopes associated with the evocation of the immune response and wherein the at least one peptide is operative for making corresponding antibodies.

34. The system of claim 1, wherein the computer program further comprises:

a fourth set of instructions for providing a plan for modulating at least a portion of an immune response in a host.

35. The system of claim 34, wherein the plan further includes:

at least one parameter of a dosage, a type of treatment, a type of immune response component, a length of treatment, a dosing pattern, or an effective route.

36. The system of claim 1, further comprising:

a storage medium for storing the computer program coupled to the computer system.

37. The system of claim 1, wherein the computer program further comprises:

a fourth set of instructions for obtaining information from one or more databases.

38. The system of claim 37, wherein the one or more databases includes:

databases including information associated with at least one of biological data, genetic data, genomic data, structural data, SNP data, immunological data, restriction fragment length polymorphism data, microsatellite marker data, short tandem repeat data, random amplified polymorphic DNA data, amplified fragment length polymorphism data, sequence repeat data, commercially available antibody data, or cross reactivity amongst antibody data.

39. The system of claim 37, wherein the one or more databases includes:

databases including information from a human database.

40. The system of claim 37, wherein the one or more databases includes:

databases including information from a pathogenic database.

41. The system of claim 1, wherein the one or more immune response components include:

at least a part of one or more of a macrophage, lymphocyte, T-lymphocyte, killer T-lymphocyte, immune response modulator, helper T-lymphocyte, antigen receptor, antigen presenting cell, cytotoxic T-lymphocyte, T-8 lymphocyte, a cluster differentiation (CD) molecule, a CD3 molecule, or CD1 molecule.

42. The system of claim 1, wherein the one or more immune response components include:

at least a part of at least one of a B-lymphocyte.

43. The system of claim 1, wherein the one or more immune response components include:

at least one of a modulator of at least a part of a B-lymphocyte.

44. The system of claim 1, wherein the one or more immune response components include:

one or more of a modulator of at least a part of at least one of a macrophage, lymphocyte, T-lymphocyte, killer T-lymphocyte, immune response modulator, helper T-lymphocyte, antigen receptor, antigen presenting cell, cytotoxic T-lymphocyte, T-8 lymphocyte, a cluster differentiation (CD) molecule, a CD3 molecule, or CD1 molecule.

45. The system of claim 1, wherein the one or more immune response components include:

at least a part of one or more of an antibody, a recombinant antibody, a genetically engineered antibody, a chimeric antibody, a monospecific antibody, a bispecific antibody, a multispecific antibody, a diabody, a chimeric antibody, a humanized antibody, a human antibody, a heteroantibody, a monoclonal antibody, a polyclonal antibody, or an antibody fragment.

46. The system of claim 1, wherein the one or more immune response components include:

one or more of a modulator of at least a part of at least one of an antibody, recombinant antibody, genetically engineered antibody, chimeric antibody, monospecific antibody, bispecific antibody, multispecific antibody, diabody, chimeric antibody, humanized antibody, human antibody, heteroantibody, monoclonal antibody, polyclonal antibody, or antibody fragment.

47. A method, comprising:

designating one or more epitopes of at least one agent;

predicting one or more changes in the one or more epitopes of the at least one agent; and

aiding the identification of one or more immune response components associated with the one or more epitopes of the at least one agent.

48. The method of claim 47, wherein the designating one or more epitopes of at least one agent further comprises:

associating the one or more epitopes with an evocation of at least a part of an immune response in a host.

49. The method of claim 47, wherein the designating one or more epitopes of at least one agent further comprises:

aiding the identification of the one or more epitopes displayed by the at least one agent.

50. The method of claim 47, wherein the designating one or more epitopes of at least one agent further comprises:

aiding the identification of the one or more epitopes present in at least two or more agents having a copy number of at least two.

51. The method of claim 47, wherein the designating one or more epitopes of at least one agent comprises:

aiding the identification of the one or more epitopes displayed by the at least one agent.

52. The method of claim 47, wherein the designating one or more epitopes of at least one agent further comprises:

aiding the identification of at least one substantially immunogenic epitope of the at least one agent.

53. The method of claim 47, wherein the one or more epitopes further comprises:

one or more epitopes of at least three amino acids.

54. The method of claim 47, wherein the one or more epitopes further comprises:

one or more epitopes of at least nine nucleotides.

55. The method of claim 47, wherein the one or more epitopes includes:

at least a portion of at least one of an amino acid residue, a nucleotide, a carbohydrate, a protein, a lipid, a capsid protein, a polysaccharide, a lipopolysaccharide, a glycolipid, or a glycoprotein.

56. The method of claim 47, wherein the one or more epitopes includes:

at least a part of at least one epitope of a virus, a bacterium, a yeast, a mold, a fungus, a mycoplasma, a ureaplasma, a Chlamydia, a rickettsia, a nanobacterium, a prion, an agent responsible for TSE, a multicellular parasite, a protein, an infectious protein, a nucleic acid, a metabolic by-product, a cellular by-product, or a toxin.

57. The method of claim 47, wherein the one or more epitopes includes:

one or more epitopes of a substantially linear form or a substantially non-linear form.

58. The method of claim 47, further comprising:

assigning a confidence level to the one or more epitopes.

59. The method of claim 47, further comprising:

ranking the one or more epitopes.

60. The method of claim 47, further comprising:

designating at least one epitope associated with at least a part of a progression of an immune response in a host.

61. The method of claim 47, further comprising:

designating a grouping of the one or more epitopes including at least one user chosen parameter.

62. The method of claim 61, wherein the at least one user chosen parameter includes:

one or more parameters of a species specificity, a family history, a medical history, a race, a geographical location, a severity of an immune response, or a genetic factor.

63. The method of claim 47, further comprising:

designating a grouping of the one or more epitopes associated with a predicted course of at least a part of an immune response including at least one user chosen parameter.

64. The method of claim 47, wherein the at least one user chosen parameter includes:

one or more parameters of a species specificity, a family history, a race, a geographical location, a severity of an immune response, or a genetic factor.

65. The method of claim 47, wherein the predicting one or more changes in the one or more epitopes of the at least one agent further comprises:

designating the one or more epitopes having up to about 80% amino acid sequence match to a host.

66. The method of claim 47, wherein the predicting one or more changes in the one or more epitopes of the at least one agent further comprises:

designating the one or more epitopes having up to about 80% nucleotide sequence match to a host.

67. The method of claim 47, wherein predicting one or more changes in the one or more epitopes of the at least one agent further comprises:

designating the one or more epitopes having between 0 to 100% sequence match with an entity.

68. The method of claim 47, wherein the predicting one or more changes in the one or more epitopes of the at least one agent further comprises:

designating the one or more epitopes having at least 88% sequence match with an entity.

69. The method of claim 47, wherein the predicting one or more changes in the one or more epitopes of the at least one agent further comprises:

designating the one or more epitopes having a substantially similar functional sequence match with an entity.

70. The method of claim 47, wherein predicting one or more changes in the one or more epitopes of the at least one agent further comprises:

designating the one or more epitopes having a substantially similar structural match with an entity.

71. The method of claim 47, wherein the predicting one or more changes in the one or more epitopes of the at least one agent further comprises:

designating the one or more epitopes having a substantially similar effect on the immune response.

72. The method of claim 47, wherein the predicting one or more changes in the one or more epitopes of the at least one agent further comprises:

designating the one or more epitopes having a substantially similar functionally effect.

73. The method of claim 47, wherein the predicting one or more changes in the one or more epitopes of the at least one agent further comprises:

designating the one or more epitopes having a substantially similar result in an assay.

74. The method of claim 47, wherein the predicting one or more changes in the one or more epitopes of the at least one agent further comprises:

aiding the identification of the one or more epitopes with a probable sequence match to a host sequence and wherein the host sequence includes single nucleotide polymorphisms.

75. The method of claim 47, wherein the aiding the identification of one or more immune response components associated with the one or more epitopes of the at least one agent further comprises:

providing one or more predicted courses of an immune response in a host and wherein the one or more predicted courses is responsive to one or more interventions.

76. The method of claim 75, wherein the one or more interventions includes:

at least one of a therapy, a treatment, a drug, a hormone, or an antibody.

77. The method of claim 47, further comprising:

changing an order of execution of the instructions.

78. The method of claim 47, wherein the aiding the identification of one or more immune response components associated with the one or more epitopes of the at least one agent further comprises:

providing a peptide sequence corresponding to the one or more epitopes associated with an evocation of an immune response.

79. The method of claim 78, wherein the providing a peptide sequence corresponding to the one or more epitopes associated with the evocation of the immune response further comprise:

providing a peptide sequence corresponding to the one or more epitopes associated with the evocation of the immune response and wherein the at least one peptide is operative for making corresponding antibodies.

80. The method of claim 47, wherein the computer program further comprises:

providing a plan for modulating at least a portion of an immune response in a host.

81. The method of claim 80, wherein the plan further includes:

at least one parameter of a dosage, a type of treatment, a type of immune response component, a length of treatment, a dosing pattern, or an effective route.

82. The method of claim 47, further comprising:

a storage medium for storing the computer program coupled to the computer system.

83. The method of claim 47, wherein the computer program further comprises:

obtaining information from one or more databases.

84. The method of claim 83, wherein the one or more databases includes:

databases including information associated with at least one of biological data, genetic data, genomic data, structural data, SNP data, immunological data, restriction fragment length polymorphism data, microsatellite marker data, short tandem repeat data, random amplified polymorphic DNA data, amplified fragment length polymorphism data, sequence repeat data, commercially available antibody data, or cross reactivity amongst antibody data.

85. The method of claim 83, wherein the one or more databases includes:

databases including information from a human database.

86. The method of claim 83, wherein the one or more databases includes:

databases including information from a pathogenic database.

87. The method of claim 47, wherein the one or more immune response components include:

at least a part of one or more of a macrophage, lymphocyte, T-lymphocyte, killer T-lymphocyte, immune response modulator, helper T-lymphocyte, antigen receptor, antigen presenting cell, cytotoxic T-lymphocyte, T-8 lymphocyte, a cluster differentiation (CD) molecule, a CD3 molecule, or CD1 molecule.

88. The method of claim 47, wherein the one or more immune response components include:

at least a part of at least one of a B-lymphocyte.

89. The method of claim 47, wherein the one or more immune response components include:

at least one of a modulator of at least a part of a B-lymphocyte.

90. The method of claim 47, wherein the one or more immune response components include:

one or more of a modulator of at least a part of at least one of a macrophage, lymphocyte, T-lymphocyte, killer T-lymphocyte, immune response modulator, helper T-lymphocyte, antigen receptor, antigen presenting cell, cytotoxic T-lymphocyte, T-8 lymphocyte, a cluster differentiation (CD) molecule, a CD3 molecule, or CD1 molecule.

91. The method of claim 47, wherein the one or more immune response components include:

at least a part of one or more of an antibody, a recombinant antibody, a genetically engineered antibody, a chimeric antibody, a monospecific antibody, a bispecific antibody, a multispecific antibody, a diabody, a chimeric antibody, a humanized antibody, a human antibody, a heteroantibody, a monoclonal antibody, a polyclonal antibody, or an antibody fragment.

92. The method of claim 47, wherein the one or more immune response components include:

one or more of a modulator of at least a part of at least one of an antibody, recombinant antibody, genetically engineered antibody, chimeric antibody, monospecific antibody, bispecific antibody, multispecific antibody, diabody, chimeric antibody, humanized antibody, human antibody, heteroantibody, monoclonal antibody, polyclonal antibody, or antibody fragment.

93. A method, comprising:

designating one or more epitopes of at least one agent associated with a progression of the at least one agent in a host; and

designating an immune response component related to treating the host in response to one or more aspects related to the progression of the at least one agent in the host.

94. A system, comprising:

circuitry for designating one or more epitopes of at least one agent associated with a progression of the at least one agent in a host; and

circuitry for designating an immune response component related to treating the host in response to one or more aspects related to the progression of the at least one agent in the host.

95. A method, comprising:

predicting one or more changes in one or more epitopes of at least one agent, and

aiding the identification of one or more immune response components associated with the one or more epitopes of the at least one agent.

96. A system, comprising:

circuitry for predicting one or more changes in one or more epitopes of at least one agent, and

circuitry for aiding the identification of one or more immune response components associated with the one or more epitopes of the at least one agent.

97. A system, comprising:

circuitry for designating one or more epitopes of at least one agent;

circuitry for predicting one or more changes in the one or more epitopes of the at least one agent, and

circuitry for aiding the identification of one or more immune response components associated with the one or more epitopes of the at least one agent.