Computational systems for biomedical data

• US 7,853,626 B2
• Filed: 06/19/2007
• Issued: 12/14/2010
• Est. Priority Date: 09/29/2006
• Status: Active Grant

• Current Assignee: Travera, LLC
• Original Assignee: The Invention Science Fund I, L.L.C. (Intellectual Ventures LLC)
• Inventors: Wood, Lowell L. Jr., Lord, Robert W., Levien, Royce A., Jung, Edward K. Y.
• Primary Examiner(s): Fleurantin; Jean B
• Application Number:
  US11/821,105
• Publication Number:
  US 20080082522A1
• Time in Patent Office: 1,274 Days
• Field of Search: 700 1- 10, 700100-1041, 700200-206, 700600-831, 600/300, 435/6, 702/19
• US Class Current: 707/812
• CPC Class Codes: G16H 10/20 for electronic clinical trials or questionnaires
• CPC Class Codes: G16H 10/40 for data related to laboratory analysis, e.g. patient specimen analysis
• CPC Class Codes: G16H 20/10 relating to drugs or medications, e.g. for ensuring correct administration to patients
• CPC Class Codes: G16H 70/40 relating to drugs, e.g. their side effects or intended usage

Abstract

Methods, apparatuses, computer program products, devices and systems are described that accepting an input identifying at least one treatment target in search of an agent; accessing at least one dataset containing at least one agent for use in the context of the at least one treatment target; applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset, the subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent; and presenting the at least one agent in response to the subset of the at least one dataset.

Claims

1. A computer-implemented method comprising:

accepting an input identifying at least one treatment target in search of an agent;

accessing at least one dataset containing at least one agent for use in the context of the at least one treatment target;

applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset, the subset of the at least one dataset exhibiting an acceptable incidence level of at least one adverse event associated with administration of the at least one agent;

extracting from the at least one dataset the at least one agent in response to the accessing at least one dataset containing at least one agent for use in the context of the at least one treatment target and the applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset exhibiting an acceptable incidence level of at least one adverse event associated with administration of the at least one agent; and

presenting the at least one agent in response to the subset of the at least one dataset.

2. The method of claim 1 wherein extracting from the at least one dataset the at least one agent in response to the accessing at least one dataset containing at least one agent for use in the context of the at least one treatment target and the applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset comprises:

extracting from the at least one dataset at least one of an anti-cancer agent, an anti-obesity agent, an anti-arthritis agent, an anti-viral agent, an anti-diabetes agent, an anti-heart disease agent, an anti-Alzheimer'"'"'s disease agent, or an anti-aging agent.

3. The method of claim 1 further comprising:

correlating the at least one subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent with subpopulation identifier data.

4. The method of claim 3 wherein correlating the at least one subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent with subpopulation identifier data comprises:

correlating the at least one subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent 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.

5. The method of claim 3 wherein correlating the at least one subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent with subpopulation identifier data comprises:

correlating the at least one subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent 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.

6. The method of claim 3 wherein correlating the at least one subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent with subpopulation identifier data comprises:

correlating the at least one subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent 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.

7. The method of claim 3 wherein correlating the at least one subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent with subpopulation identifier data comprises:

correlating the at least one subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent 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.

8. The method of claim 1 wherein accepting an input identifying at least one treatment target in search of an agent comprises:

accepting at least one of a medical condition treatment target, a nutritional deficiency treatment target, an obesity condition treatment target, a chronic condition treatment target, or an acute condition treatment target as the at least one treatment target in search of an agent.

9. The method of claim 1 wherein accepting an input identifying at least one treatment target in search of an agent comprises:

accepting an input identifying at least one filter criterion as the at least one treatment target in search of an agent.

10. The method of claim 1 wherein accessing at least one dataset containing at least one agent for use in the context of the at least one treatment target comprises:

accessing data associated with at least one clinical trial as the at least one dataset containing at least one agent for use in the context of the at least one treatment target.

11. The method of claim 1 wherein accessing at least one dataset containing at least one agent for use in the context of the at least one treatment target comprises:

accessing at least one of a genomic dataset, a proteomic dataset, a biochemical dataset, or a population dataset as the at least one dataset containing at least one agent for use in the context of the at least one treatment target.

12. The method of claim 1 wherein accessing at least one dataset containing at least one agent for use in the context of the at least one treatment target comprises:

accessing at least one dataset containing at least an FDA-approved drug, an FDA-approved biologic, a drug metabolite, or a prodrug as the at least one agent for use in the context of the at least one treatment target.

13. The method of claim 1 wherein accessing at least one dataset containing at least one agent for use in the context of the at least one treatment target comprises:

accessing at least one dataset containing at least an experimental small molecule or an experimental biologic as the at least one agent for use in the context of the at least one treatment target.

14. The method of claim 1 wherein applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset, the subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent comprises:

applying at least a quantitative limit on one or more adverse events as the at least one filter criterion.

15. The method of claim 1 wherein applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset, the subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent comprises:

applying at least a qualitative limit on one or more adverse events as the at least one filter criterion.

16. The method of claim 1 wherein applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset, the subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent comprises:

applying at least a statistical adverse event limit as the at least one filter criterion.

17. The method of claim 1 wherein applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset, the subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent comprises:

applying at least a maximum mean incidence of one or more adverse events as the at least one filter criterion.

18. The method of claim 1 wherein applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset, the subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent comprises:

applying at least a maximum adverse event limit and a minimum efficacy limit as the at least one filter criterion.

19. The method of claim 1 wherein applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset, the subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent comprises:

applying one or more statistical filters as the at least one filter criterion.

20. The method of claim 19 wherein applying one or more statistical filters as the at least one filter criterion comprises:

applying at least a standard deviation statistical filter, a mean value statistical filter, a confidence interval statistical filter, an ANOVA statistical filter, or a p-value statistical filter as the one or more statistical filters.

21. The method of claim 1 wherein applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset, the subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent comprises:

applying at least a coincidence of data between two or more datasets as the at least one filter criterion.

22. The method of claim 1 wherein applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset, the subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent comprises:

applying at least one of an exclusion of data from two or more datasets or an inverse correlation of data between two or more datasets as the at least one filter criterion.

23. The method of claim 1 wherein applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset, the subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent comprises:

applying at least a correlation between an adverse event and an individual or group characteristic as the at least one filter criterion.

24. The method of claim 1 wherein applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset, the subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent comprises:

applying at least one filter criterion to the at least one dataset to identify a genomic data subset, proteomic data subset, hepatic enzyme profile data subset, RNA expression data subset, biochemical data subset, nutritional supplementation data subset, lifestyle data subset, medical history data subset, ethnicity data subset, age data subset, or gender data subset as the subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent.

25. The method of claim 1 wherein applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset, the subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent comprises:

applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset, the subset of the at least one dataset associated with a defined level of at least one allergy as the at least one adverse event associated with administration of the at least one agent.

26. The method of claim 1 wherein applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset, the subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent comprises:

applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset, the subset of the at least one dataset associated with a defined level of at least one physiologic effect as the at least one adverse event associated with administration of the at least one agent.

27. The method of claim 1 wherein applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset, the subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent comprises:

applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset, the subset of the at least one dataset associated with a defined level of at least one cardiovascular effect as the at least one adverse event associated with administration of the at least one agent.

28. The method of claim 1 wherein applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset, the subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent comprises:

applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset, the subset of the at least one dataset associated with a defined level of at least one neutral or beneficial event that is not the intended effect of administration of the at least one agent as the at least one adverse event associated with administration of the at least one agent.

29. The method of claim 1 wherein applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset, the subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent comprises:

applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset, the subset of the at least one dataset characterized by one or more epigenetic parameters.

30. The method of claim 1 wherein applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset, the subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent comprises:

applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset characterized by one or more behavioral parameters.

31. The method of claim 1 wherein applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset, the subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent comprises:

applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset characterized by one or more of lifestyle, exercise regimen, diet, nutritional regimen, dietary supplementation, concomitant medical therapy, or concomitant alternative medical therapy.

32. The method of claim 1 wherein applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset, the subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent comprises:

applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset characterized by one or more of linkage disequilibrium analysis profile, haplotype profile, single nucleotide polymorphism profile, or individual genetic sequence profile.

33. The method of claim 1 wherein applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset, the subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent comprises:

applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset 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.

34. The method of claim 1 wherein applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset, the subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent comprises:

applying at least one filter criterion to the at least one dataset to identify at least one subset of the at least one dataset exhibiting at least a defined level of efficacy in treating the at least one treatment target and a defined level of at least one adverse event associated with administration of the at least one agent.

35. A system comprising:

means for accepting an input identifying at least one treatment target in search of an agent;

means for accessing at least one dataset containing at least one agent for use in the context of the at least one treatment target;

means for applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset, the subset of the at least one dataset exhibiting an acceptable incidence level of at least one adverse event associated with administration of the at least one agent;

means for extracting from the at least one dataset the at least one agent in response to the accessing at least one dataset containing at least one agent for use in the context of the at least one treatment target and the applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset exhibiting an acceptable incidence level of at least one adverse event associated with administration of the at least one agent; and

means for presenting the at least one agent in response to the subset of the at least one dataset.

36. The system of claim 35 wherein the means for extracting from the at least one dataset the at least one agent in response to the accessing at least one dataset containing at least one agent for use in the context of the at least one treatment target and the applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset comprises:

means for extracting from the at least one dataset at least one of an anti-cancer agent, an anti-obesity agent, an anti-arthritis agent, an anti-viral agent, an anti-diabetes agent, an anti-heart disease agent, an anti-Alzheimer'"'"'s disease agent, or an anti-aging agent.

37. The system of claim 35 further comprising:

means for correlating the at least one subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent with subpopulation identifier data.

38. The system of claim 37 wherein the means for correlating the at least one subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent with subpopulation identifier data comprises:

means for correlating the at least one subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent 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.

39. The system of claim 37 wherein the means for correlating the at least one subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent with subpopulation identifier data comprises:

means for correlating the at least one subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent 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.

40. The system of claim 37 wherein the means for correlating the at least one subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent with subpopulation identifier data comprises:

means for correlating the at least one subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent 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.

41. The system of claim 37 wherein the means for correlating the at least one subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent with subpopulation identifier data comprises:

means for correlating the at least one subset of the at least one dataset associated with a defined level of at least one adverse event associated with administration of the at least one agent 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.

42. An article of manufacture including a non-transitory signal bearing storage medium configured by one or more instructions related to:

(a) accepting an input identifying at least one treatment target in search of an agent;

(b) accessing at least one dataset containing at least one agent for use in the context of the at least one treatment target;

(c) applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset, the subset of the at least one dataset exhibiting an acceptable incidence level of at least one adverse event associated with administration of the at least one agent;

(d) extracting from the at least one dataset the at least one agent in response to the accessing at least one dataset containing at least one agent for use in the context of the at least one treatment target and the applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset exhibiting an acceptable incidence level of at least one adverse event associated with administration of the at least one agent; and

(e) presenting the at least one agent in response to the subset of the at least one dataset.

43. The article of manufacture of claim 42, wherein the non-transitory signal-bearing storage medium includes a computer-readable medium.

44. The article of manufacture of claim 42, wherein the non-transitory signal-bearing storage medium includes a recordable medium.

45. The article of manufacture of claim 42, wherein the non-transitory signal-bearing storage medium includes a communications medium.

46. 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 at least one treatment target in search of an agent;

(b) access at least one dataset containing at least one agent for use in the context of the at least one treatment target;

(c) apply at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset, the subset of the at least one dataset exhibiting an acceptable incidence level of at least one adverse event associated with administration of the at least one agent; and

(d) extract from the at least one dataset the at least one agent in response to accessing at least one dataset containing at least one agent for use in the context of the at least one treatment target and applying at least one filter criterion to the at least one dataset to identify a subset of the at least one dataset exhibiting an acceptable incidence level of at least one adverse event associated with administration of the at least one agent; and

(e) present the at least one agent in response to the subset of the at least one dataset.

47. The system of claim 46 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.

48. The system of claim 46 wherein the computing device is operable to receive information regarding the subset of the at least one dataset and to present the at least one agent from at least one memory.