Computational systems for biomedical data

• US 20080082503A1
• Filed: 05/31/2007
• Published: 04/03/2008
• Est. Priority Date: 09/29/2006
• Status: Active Grant

• Current Assignee: Travera, LLC
• Original Assignee: Searete LLC (Intellectual Ventures LLC)
• Inventors: Lord, Robert W., Jung, Edward K.Y., Levien, Royce A., Wood, Lowell L.
• Granted Patent: US 8,122,073 B2
• Time in Patent Office: Days
• US Class Current: 707/3
• CPC Class Codes: G06Q 10/10 Office automation; Time management
• 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 20/40 Population genetics; Linkage disequilibrium
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/10 Gene or protein expression profiling; Expression-ratio estimation or normalisation
• CPC Class Codes: G16B 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• CPC Class Codes: G16B 40/30 Unsupervised data analysis
• CPC Class Codes: G16H 10/20 for electronic clinical trials or questionnaires
• CPC Class Codes: G16H 40/20 for the management or administration of healthcare resources or facilities, e.g. managing hospital staff or surgery rooms
• CPC Class Codes: G16H 50/70 for mining of medical data, e.g. analysing previous cases of other patients
• CPC Class Codes: Y10S 707/954 Relational
• CPC Class Codes: Y10S 707/99933 Query processing, i.e. searching
• CPC Class Codes: Y10S 707/99945 Object-oriented database structure processing

Abstract

Methods, apparatuses, computer program products, devices and systems are described that accepting an input identifying a treatment target in search of an agent, the input associated with at least one query parameter; determining, based on the input, at least one subset of study data for which at least one adverse event profile associated with administration of at least one agent is acceptable within a defined limit relative to a population for which the at least one adverse event profile is unacceptable with respect to the defined limit; and presenting the agent, based on the at least one subset and the at least one query parameter.

Claims

1-15. -15. (canceled)

16. A method comprising:

accepting an input identifying a treatment target in search of an agent, the input associated with at least one query parameter;

searching at least one dataset and extracting from the at least one dataset at least one subset of study data in response to said treatment target in search of an agent and said query parameter,

the at least one subset of study data including at least one subpopulation for which at least one adverse event profile associated with administration of at least one agent is acceptable within a defined limit relative to a population for which the at least one adverse event profile is unacceptable with respect to the defined limit; and

presenting the agent, based on the at least one subset and the at least one query parameter.

17. The method of claim 16 wherein searching at least one dataset comprises:

searching at least a Physicians'"'"' Desk Reference dataset as the at least one dataset.

18. The method of claim 16 wherein searching at least one dataset comprises:

searching at least the Adverse Event Reporting System dataset maintained by the United States Food and Drug Administration as the at least one dataset.

19. The method of claim 16 wherein extracting from the at least one dataset at least one subset of study data in response to said treatment target in search of an agent and said query parameter comprises:

extracting from the at least one dataset a subset characterized by one or more genetic parameters as the at least one subset of study data.

20. The method of claim 16 wherein extracting from the at least one dataset at least one subset of study data in response to said treatment target in search of an agent and said query parameter comprises:

extracting from the at least one dataset a subset characterized by one or more epigenetic parameters as the at least one subset of study data.

21. The method of claim 16 wherein extracting from the at least one dataset at least one subset of study data in response to said treatment target in search of an agent and said query parameter comprises:

extracting from the at least one dataset a subset characterized by one or more biochemical parameters as the at least one subset of study data.

22. The method of claim 16 wherein extracting from the at least one dataset at least one subset of study data in response to said treatment target in search of an agent and said query parameter comprises:

extracting from the at least one dataset a subset characterized by one or more gene expression parameters as the at least one subset of study data.

23. The method of claim 16 wherein extracting from the at least one dataset at least one subset of study data in response to said treatment target in search of an agent and said query parameter comprises:

extracting from the at least one dataset a subset of study data characterized by one or more protein expression parameters as the at least one subset of study data.

24. The method of claim 16 wherein extracting from the at least one dataset at least one subset of study data in response to said treatment target in search of an agent and said query parameter comprises:

extracting from the at least one dataset a subset of study data characterized by one or more behavioral parameters as the at least one subset of study data.

25. The method of claim 16 wherein extracting from the at least one dataset at least one subset of study data in response to said treatment target in search of an agent and said query parameter comprises:

extracting from the at least one dataset a subset of study data characterized by one or more physiologic parameters as the at least one subset of study data.

26. The method of claim 16 wherein extracting from the at least one dataset at least one subset of study data in response to said treatment target in search of an agent and said query parameter comprises:

extracting from the at least one dataset a subset of study data characterized by one or more demographic parameters as the at least one subset of study data.

27. The method of claim 16 wherein extracting from the at least one dataset at least one subset of study data in response to said treatment target in search of an agent and said query parameter comprises:

extracting from the at least one dataset a subset of study data characterized by one or more of age, gender, ethnicity, race, liver enzyme genotype, or medical history as the at least one subset of study data.

28. The method of claim 16 wherein extracting from the at least one dataset at least one subset of study data in response to said treatment target in search of an agent and said query parameter comprises:

extracting from the at least one dataset a subset of study data characterized by one or more of lifestyle, exercise regimen, diet, nutritional regimen, dietary supplementation, concomitant medical therapy, or concomitant alternative medical therapy as the at least one subset of study data.

29. The method of claim 16 wherein extracting from the at least one dataset at least one subset of study data in response to said treatment target in search of an agent and said query parameter comprises:

extracting from the at least one dataset a subset of study data characterized by one or more of linkage disequilibrium analysis profile, haplotype profile, single nucleotide polymorphism profile, or individual genetic sequence profile as the at least one subset of study data.

30. The method of claim 16 wherein extracting from the at least one dataset at least one subset of study data in response to said treatment target in search of an agent and said query parameter comprises:

extracting from the at least one dataset a subset of study data having a significantly lower incidence of at least one adverse event than that of at least one reported clinical trial for the at least one agent as the at least one subset of study data.

31. The method of claim 16 wherein extracting from the at least one dataset at least one subset of study data in response to said treatment target in search of an agent and said query parameter comprises:

extracting from the at least one dataset a subset having at least a defined level of efficacy in treating the at least one treatment target as the at least one subset of study data.

32. The method of claim 16 further comprising:

correlating the at least one subset of study data with subpopulation identifier data.

33. The method of claim 32 wherein correlating the at least one subset of study data with subpopulation identifier data comprises:

correlating the at least one subset with at least one of genetic data, epigenetic data, biochemical data, gene expression data, protein expression data, behavioral data, physiologic data, or demographic data as the subpopulation identifier data.

34. The method of claim 32 wherein correlating the at least one subset of study data with subpopulation identifier data comprises:

correlating the at least one subset with at least one of age data, gender data, ethnicity data, race data, liver enzyme genotype data, or medical history data as the subpopulation identifier data.

35. The method of claim 32 wherein correlating the at least one subset of study data with subpopulation identifier data comprises:

correlating the at least one subset with at least one of lifestyle data, exercise regimen data, diet data, nutritional regimen data, dietary supplementation data, concomitant medical therapy data, or concomitant alternative medical therapy data as the subpopulation identifier data.

36. The method of claim 32 wherein correlating the at least one subset of study data with subpopulation identifier data comprises:

correlating the at least one subset with at least one of linkage disequilibrium analysis data, haplotype data, single nucleotide polymorphism data, or individual genetic sequence data as the subpopulation identifier data.

37-52. -52. (canceled)

53. A system comprising:

circuitry for accepting an input identifying a treatment target in search of an agent, the input associated with at least one query parameter;

circuitry for searching at least one dataset and circuitry for extracting from the at least one dataset at least one subset of study data in response to said treatment target in search of an agent and said query parameter,

the at least one subset including at least one subpopulation for which at least one adverse event profile associated with administration of at least one agent is acceptable within a defined limit relative to a population for which the at least one adverse event profile is unacceptable with respect to the defined limit; and

circuitry for presenting the agent, based on the at least one subset and the at least one query parameter.

54. The system of claim 53 wherein the circuitry for searching at least one dataset comprises:

circuitry for searching at least a Physicians'"'"' Desk Reference dataset.

55. The system of claim 53 wherein the circuitry for searching at least one dataset comprises:

circuitry for searching at least the Adverse Event Reporting System dataset maintained by the United States Food and Drug Administration.

56. The system of claim 53 wherein the circuitry for extracting from the at least one dataset at least one subset of study data in response to said treatment target in search of an agent and said query parameter comprises:

circuitry for extracting from the at least one dataset a subset characterized by one or more genetic parameters as the at least one subset.

57. The system of claim 53 wherein the circuitry for extracting from the at least one dataset at least one subset of study data in response to said treatment target in search of an agent and said query parameter comprises:

circuitry for extracting from the at least one dataset a subset characterized by one or more epigenetic parameters as the at least one subset.

58. The system of claim 53 wherein the circuitry for extracting from the at least one dataset at least one subset of study data in response to said treatment target in search of an agent and said query parameter comprises:

circuitry for extracting from the at least one dataset a subset characterized by one or more biochemical parameters as the at least one subset.

59. The system of claim 53 wherein the circuitry for extracting from the at least one dataset at least one subset of study data in response to said treatment target in search of an agent and said query parameter comprises:

circuitry for extracting from the at least one dataset a subset characterized by one or more gene expression parameters as the at least one subset.

60. The system of claim 53 wherein the circuitry for extracting from the at least one dataset at least one subset of study data in response to said treatment target in search of an agent and said query parameter comprises:

circuitry for extracting from the at least one dataset a subset characterized by one or more protein expression parameters as the at least one subset.

61. The system of claim 53 wherein the circuitry for extracting from the at least one dataset at least one subset of study data in response to said treatment target in search of an agent and said query parameter comprises:

circuitry for extracting from the at least one dataset a subset characterized by one or more behavioral parameters as the at least one subset.

62. The system of claim 53 wherein the circuitry for extracting from the at least one dataset at least one subset of study data in response to said treatment target in search of an agent and said query parameter comprises:

circuitry for extracting from the at least one dataset a subset characterized by one or more physiologic parameters as the at least one subset.

63. The system of claim 53 wherein the circuitry for extracting from the at least one dataset at least one subset of study data in response to said treatment target in search of an agent and said query parameter comprises:

circuitry for extracting from the at least one dataset a subset characterized by one or more demographic parameters as the at least one subset.

64. The system of claim 53 wherein the circuitry for extracting from the at least one dataset at least one subset of study data in response to said treatment target in search of an agent and said query parameter comprises:

circuitry for extracting from the at least one dataset a subset characterized by one or more of age, gender, ethnicity, race, liver enzyme genotype, or medical history as the at least one subset.

65. The system of claim 53 wherein the circuitry for extracting from the at least one dataset at least one subset of study data in response to said treatment target in search of an agent and said query parameter comprises:

circuitry for extracting from the at least one dataset a subset characterized by one or more of lifestyle, exercise regimen, diet, nutritional regimen, dietary supplementation, concomitant medical therapy, or concomitant alternative medical therapy as the at least one subset.

66. The system of claim 53 wherein the circuitry for extracting from the at least one dataset at least one subset of study data in response to said treatment target in search of an agent and said query parameter comprises:

circuitry for extracting from the at least one dataset a subset characterized by one or more of linkage disequilibrium analysis profile, haplotype profile, single nucleotide polymorphism profile, or individual genetic sequence profile as the at least one subset.

67. The system of claim 53 wherein the circuitry for extracting from the at least one dataset at least one subset of study data in response to said treatment target in search of an agent and said query parameter comprises:

circuitry for extracting from the at least one dataset a subset having a significantly lower incidence of at least one adverse event than that of at least one reported clinical trial for the at least one agent as the at least one subset.

68. The system of claim 53 wherein the circuitry for extracting from the at least one dataset at least one subset of study data in response to said treatment target in search of an agent and said query parameter comprises:

circuitry for extracting from the at least one dataset at least one subset having at least a defined level of efficacy in treating the at least one treatment target as the at least one subset.

69. The system of claim 53 further comprising:

circuitry for correlating the at least one subset with subpopulation identifier data.

70. The system of claim 69 wherein the circuitry for correlating the at least one subset of study data with subpopulation identifier data comprises:

circuitry for correlating the at least one subset with at least one of genetic data, epigenetic data, biochemical data, gene expression data, protein expression data, behavioral data, physiologic data, or demographic data as the subpopulation identifier data.

71. The system of claim 69 wherein the circuitry for correlating the at least one subset of study data with subpopulation identifier data comprises:

circuitry for correlating the at least one subset with at least one of age data, gender data, ethnicity data, race data, liver enzyme genotype data, or medical history data as the subpopulation identifier data.

72. The system of claim 69 wherein the circuitry for correlating the at least one subset of study data with subpopulation identifier data comprises:

circuitry for correlating the at least one subset with at least one of lifestyle data, exercise regimen data, diet data, nutritional regimen data, dietary supplementation data, concomitant medical therapy data, or concomitant alternative medical therapy data as the subpopulation identifier data.

73. The system of claim 69 wherein the circuitry for correlating the at least one subset of study data with subpopulation identifier data comprises:

circuitry for correlating the at least one subset with at least one of linkage disequilibrium analysis data, haplotype data, single nucleotide polymorphism data, or individual genetic sequence data as the subpopulation identifier data.

74-81. -81. (canceled)

82. A computer program product comprising:

a signal-bearing medium bearing

(a) one or more instructions for accepting an input identifying a treatment target in search of an agent, the input associated with at least one query parameter;

(b) one or more instructions for searching at least one dataset and extracting from the at least one dataset at least one subset of study data in response to said treatment target in search of an agent and said query parameter,

the at least one subset of study data including at least one subpopulation for which at least one adverse event profile associated with administration of at least one agent is acceptable within a defined limit relative to a population for which the at least one adverse event profile is unacceptable with respect to the defined limit; and

(c) one or more instructions for presenting the agent, based on the at least one subset and the at least one query parameter.

83. The computer program product of claim 82, wherein the signal-bearing medium includes a computer-readable medium.

84. The computer program product of claim 82, wherein the signal-bearing medium includes a recordable medium.

85. The computer program product of claim 82, wherein the signal-bearing medium includes a communications medium.

86. A system comprising:

a computing device; and

instructions that when executed on the computing device cause the computing device to

(a) accept an input identifying a treatment target in search of an agent, the input associated with at least one query parameter;

(b) search at least one dataset and extract from the at least one dataset at least one subset of study data in response to said treatment target in search of an agent and said query parameter,

the at least one subset of study data including at least one subpopulation for which at least one adverse event profile associated with administration of at least one agent is acceptable within a defined limit relative to a population for which the at least one adverse event profile is unacceptable with respect to the defined limit; and

(c) present the agent, based on the at least one subset and the at least one query parameter.

87. The system of claim 86 wherein the computing device comprises:

one or more of a personal digital assistant (PDA), a laptop computer, a tablet personal computer, a networked computer, a computing system comprised of a cluster of processors, a computing system comprised of a cluster of servers, a workstation computer, and/or a desktop computer.

88. The system of claim 86 wherein the computing device is operable to receive information regarding the at least one subset of study data and to present the agent from at least one memory.