System and method for improving a humoral immune response

• US 20060047439A1
• Filed: 01/26/2005
• 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:
  US11/044,656
• Publication Number:
  US 20060047439A1
• 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: G16C 20/50 Molecular design, e.g. of drugs

Abstract

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

Claims

1. A system, comprising:

means for designating one or more computable epitopes of at least one agent;

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

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

2. (canceled)

3. (canceled)

4. (canceled)

5. (canceled)

6. (canceled)

7. (canceled)

8. (canceled)

9. (canceled)

10. (canceled)

11. (canceled)

12. (canceled)

13. (canceled)

14. (canceled)

15. (canceled)

16. (canceled)

17. (canceled)

18. (canceled)

19. (canceled)

20. (canceled)

21. (canceled)

22. (canceled)

23. (canceled)

24. (canceled)

25. (canceled)

26. (canceled)

27. (canceled)

28. (canceled)

29. (canceled)

30. (canceled)

31. (canceled)

32. (canceled)

33. (canceled)

34. (canceled)

35. (canceled)

36. (canceled)

37. (canceled)

38. (canceled)

39. (canceled)

40. (canceled)

41. (canceled)

42. (canceled)

43. (canceled)

44. (canceled)

45. (canceled)

46. (canceled)

47. (canceled)

48. (canceled)

49. (canceled)

50. (canceled)

51. (canceled)

52. (canceled)

53. (canceled)

54. (canceled)

55. (canceled)

56. (canceled)

57. (canceled)

58. (canceled)

59. (canceled)

60. (canceled)

61. (canceled)

62. (canceled)

63. (canceled)

64. (canceled)

65. A method, comprising:

designating one or more computable epitopes of at least one agent;

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

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

66. The method of claim 65, wherein the designating one or more computable epitopes of at least one agent further comprises:

designating at least one meta-signature.

67. The method of claim 65, wherein the designating one or more computable epitopes of at least one agent further comprises:

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

68. The method of claim 65, wherein the designating one or more computable epitopes of at least one agent further comprises:

designating the one or more computable epitopes displayed by the at least one agent.

69. The method of claim 65, wherein the designating one or more computable epitopes of at least one agent further comprises:

designating the one or more computable epitopes present in at least two or more agents and having a copy number of at least two.

70. The method of claim 65, wherein the designating one or more computable epitopes of at least one agent comprises:

designating the one or more computable epitopes displayed by the at least one agent and having a copy number of at least two.

72. The method of claim 65, wherein the designating one or more computable epitopes of at least one agent further comprises:

designating one or more computable epitopes of at least three amino acids.

73. The method of claim 65, wherein the designating one or more computable epitopes of at least one agent further comprises:

designating one or more computable epitopes of at least nine nucleotides.

75. The method of claim 65, wherein the designating one or more computable epitopes of at least one agent further comprises:

designating at least a portion of at least one of an amino acid a nucleotide, a carbohydrate, a protein, a lipid, a capsid protein, a coat protein, a polysaccharide, a lipopolysaccharide, a glycolipid, a glycoprotein, a polyglycopeptide, and/or at least a part of a cell.

77. The method of claim 65, wherein the designating one or more computable epitopes of at least one agent further comprises:

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

78. The method of claim 65, further comprising:

assigning a confidence level to the one or more computable epitopes.

79. The method of claim 65, further comprising:

ranking the one or more computable epitopes.

80. The method of claim 65, further comprising:

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

81. The method of claim 65, further comprising:

designating one or more computable epitopes including at least one user-chosen parameter.

82. The method of claim 81, 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 characteristic of an immune response, or a genetic factor.

83. The method of claim 65, further comprising:

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

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

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

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

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

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

designating the one or more computable epitopes having 0 to 100% sequence match with the at least one agent or a host.

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

designating the one or more computable epitopes having at least 88% sequence match with the at least one agent or a host.

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

designating the one or more computable epitopes having a substantially similar functional sequence match with the at least one agent or a host.

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

designating the one or more computable epitopes having a substantially similar structural match with the at least one agent or a host.

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

designating the one or more computable epitopes having a substantially similar effect on the immune response as the at least one agent.

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

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

95. The method of claim 65, wherein the aiding the identification of one or more immune response components associated with the one or more computable 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 are responsive to one or more interventions.

98. The method of claim 65, wherein the aiding the identification of one or more immune response components associated with the one or more computable epitopes of the at least one agent further comprises:

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

100. The method of claim 65, further comprising:

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

103. The method of claim 65, further comprising:

obtaining information from one or more databases.

108. The method of claim 65, wherein the aiding the identification of one or more immune response components associated with the one or more computable epitopes of the at least one agent includes:

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

109. The method of claim 65, wherein the aiding the identification of one or more immune response components associated with the one or more computable epitopes of the at least one agent includes:

aiding the identification of at least a part of at least one B-lymphocyte.

110. The method of claim 65, wherein the aiding the identification of one or more immune response components associated with the one or more computable epitopes of the at least one agent includes:

aiding the identification of at least one modulator of at least a part of a B-lymphocyte.

111. The method of claim 65, wherein the aiding the identification of one or more immune response components associated with the one or more computable epitopes of the at least one agent includes:

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

112. The method of claim 65, wherein the aiding the identification of one or more immune response components associated with the one or more computable epitopes of the at least one agent includes:

aiding the identification of 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, a camelized antibody, a deimmunized antibody, an anti-idiotypic antibody, or an antibody fragment.

113. The method of claim 65, wherein the aiding the identification of one or more immune response components associated with the one or more computable epitopes of the at least one agent includes:

aiding the identification of one or more of a modulator of at least a part of at least one 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, a camelized antibody, a deimmunized antibody, an anti-idiotypic antibody, or an antibody fragment.

114. The method of claim 65, wherein the aiding the identification of one or more immune response components associated with the one or more computable epitopes of the at least one agent includes:

aiding the identification of at least a portion of a Fab region.

115. The method of claim 65, wherein the aiding the identification of one or more immune response components associated with the one or more computable epitopes of the at least one agent includes:

aiding the identification of at least a portion of a Fab′

region.

116. The method of claim 65, wherein the aiding the identification of one or more immune response components associated with the one or more computable epitopes of the at least one agent includes:

aiding the identification of at least a portion of a Fv region.

117. The method of claim 65, wherein the aiding the identification of one or more immune response components associated with the one or more computable epitopes of the at least one agent includes:

aiding the identification of at least a portion of a F(ab′

).sub.2 fragment.

118. The method of claim 65, wherein the aiding the identification of one or more immune response components associated with the one or more computable epitopes of the at least one agent includes:

aiding the identification of at least one paratope.

119. The method of claim 65, wherein the aiding the identification of one or more immune response components associated with the one or more computable epitopes of the at least one agent includes:

aiding the identification of at least a portion of an antibody operable for activating at least a part of a complement.

121. The method of claim 65, wherein the aiding the identification of one or more immune response components associated with the one or more computable epitopes of the at least one agent includes:

aiding the identification of at least a portion of a species-dependent antibody or a species-specific antibody.

123. The method of claim 65, wherein the aiding the identification of one or more immune response components associated with the one or more computable epitopes of the at least one agent includes:

aiding the identification of one or more immune response components directed to at least one of a cell-surface molecule or a cell-associated molecule.

124. The method of claim 65, wherein the aiding the identification of one or more immune response components associated with the one or more computable epitopes of the at least one agent includes:

aiding the identification of one or more immune response components directed to at least one of a secreted protein, a polypeptide, a glycoprotein, a receptor, and/or a receptor-ligand.

125. The method of claim 65, wherein the aiding the identification of one or more immune response components associated with the one or more computable epitopes of the at least one agent includes:

aiding the identification of one or more immune response components for binding at least a part of at least one antibody.

126. The method of claim 65, wherein the aiding the identification of one or more immune response components associated with the one or more computable epitopes of the at least one agent includes:

aiding the identification of at least one modulator of (a) an epitopic shift or (b) an epitopic drift predicted in the at least one agent.

127. The method of claim 126, wherein the at least one modulator of (a) an epitopic shift or (b) an epitopic drift predicted in the at least one agent, further comprises:

aiding the identification of at least one suppressor of mutational alteration of the at least one agent.

128. The method of claim 126, wherein the at least one modulator of (a) an epitopic shift or (b) an epitopic drift predicted in the at least one agent, further comprises:

aiding the identification of at least one interfering nucleic acid or nucleic acid sequence.

71. (canceled)

74. (canceled)

76. (canceled)

84. (canceled)

92. (canceled)

93. (canceled)

96. (canceled)

97. (canceled)

99. (canceled)

101. (canceled)

102. (canceled)

104. (canceled)

105. (canceled)

106. (canceled)

107. (canceled)

120. (canceled)

122. (canceled)

129. (canceled)

130. (canceled)

131. A method, comprising:

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

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

132. A system, comprising:

circuitry for predicting one or more changes in one or more computable 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 computable epitopes of the at least one agent.

133. A system, comprising:

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

circuitry for predicting one or more changes in the one or more computable 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 computable epitopes of the at least one agent.

134. A system, comprising:

means for predicting one or more changes in one or more computable epitopes of at least one agent; and

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