Systems and methods for biomarker analysis

• US 8,318,105 B2
• Filed: 10/18/2010
• Issued: 11/27/2012
• Est. Priority Date: 02/10/2010
• Status: Expired due to Fees

• Current Assignee: Companion Diagnostics, Inc.
• Original Assignee: Companion Diagnostics, Inc.
• Inventors: Selinfreund, Richard H., Vig, Rakesh, Gill, Richard P.
• Primary Examiner(s): Warden, Jill
• Assistant Examiner(s): COLE, MONIQUE T
• Application Number:
  US12/906,204
• Publication Number:
  US 20110195874A1
• Time in Patent Office: 771 Days
• Field of Search: 436/176, 436/501, 435/7.1, 435/325, 435/6.16, 435/6, 422/400
• US Class Current: 422/400
• CPC Class Codes: A61B 10/0045 Devices for taking samples of body liquids devices for taking blood samples A61B5/15
• CPC Class Codes: C12Q 1/40 involving amylase
• CPC Class Codes: G01N 33/50 Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing measuring or testing processes involving enzymes or microorganisms, compositions or test papers therefor; processes for forming such compositions, condition responsive control in microbiological or enzymological processes C12Q
• CPC Class Codes: G01N 33/54393 Improving reaction conditions or stability, e.g. by coating or irradiation of surface, by reduction of non-specific binding, by promotion of specific binding
• CPC Class Codes: Y10T 436/10 Composition for standardization, calibration, simulation, stabilization, preparation or preservation; processes of use in preparation for chemical testing
• CPC Class Codes: Y10T 436/105831 Protein or peptide standard or control [e.g., hemoglobin, etc.]
• CPC Class Codes: Y10T 436/2525 Stabilizing or preserving

Abstract

Systems and methods of biomarker analysis. In at least one embodiment of a system for determining the therapeutic potential of a therapeutic compound the present disclosure, the system comprises a detection platform, a computer database capable of receiving a plurality of binding characteristics, a processor operably coupled to the computer database and the detection platform. In at least one embodiment, the processor has and executes a software program operational to determine a binding characteristic of the detection agent and a stabilized diagnostic agent in each of the plurality of detection sites, compare the binding characteristic among each of the plurality of detection sites, wherein the comparison of binding characteristics is capable of determining the stabilizing agent with the greatest effect on the binding characteristic between the detection agent and the diagnostic agent, generate a binding record using the compared binding characteristics, and deliver the binding record to a recipient.

Claims

1. A system for determining the therapeutic potential of a therapeutic compound, the system comprising:

a detection platform comprising a plurality of detection sites each capable of receiving a therapeutic potential diagnostic marker, a diagnostic marker stabilization agent, and an indicator labeled detection agent;

a computer writeable database capable of receiving a plurality of binding characteristics, the plurality of binding characteristics comprising at least one binding property of a therapeutic potential diagnostic marker to an indicator labeled detection agent;

wherein

a processor operably coupled to the computer database and the detection platform, is programmed to determine and record said at least one binding property which is characteristic of the therapeutic potential diagnostic marker to an indicator labeled detection agent in each of the plurality of detection sites;

wherein comparison of said plurality of binding characteristics is capable of determining the diagnostic marker stabilizing agent with the greatest effect on the binding characteristic of the therapeutic potential diagnostic marker to the indicator labeled detection agent.

2. The system of claim 1, wherein the stabilizing agent is a protease inhibitor.

3. The system of claim 1, wherein the stabilizing agent is useful to prevent degradation or inactivation of a therapeutic potential diagnostic marker selected from the group consisting of a protein, a glycoprotein, an enzyme, and an enzyme inhibitor.

4. The system of claim 1, wherein the diagnostic marker stabilizing agent is useful to prevent or reduce degradation or inactivation of a therapeutic potential diagnostic marker indicative of a disease state.

5. The system of claim 4, wherein the disease state is selected from the group consisting of a cancer, a metabolic disease, a cardiac disease, diabetes, a bacterial infection, a viral infection, a fungal infection, and a parasitic infection.

6. The system of claim 1, wherein the stabilizing agent is selected from the group consisting of a citric acid sodium hydroxide pH 6.0 buffer (Fixanal®

Buffer 6.0 (Sigma-Aldrich Co.)), acetic acid, aluminum hydroxide bentonite, aluminum sulfate hydrate, benzoic acid, aluminum potassium sulfate dodecahydrate, caffeine, and 3-tert-butyl-hydroxyanisole, or a combination thereof.

7. The system of claim 1, wherein the detection platform is comprised of a material selected for the group consisting of nylon, quartz, glass, metal, silica-based materials, resins, polymers, or combinations thereof.

8. The system of claim 1, wherein the stabilizing agent comprises a plurality of stabilizing agents each present in approximately the same concentration.

9. The system of claim 1, wherein the stabilizing agent is capable of inhibiting degradation of the diagnostic marker to an inhibitory degree, wherein the inhibitory degree is selected from the group consisting of at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, and at least about 99%.

10. The system of claim 1, wherein the stabilizing agent has a concentration selected from the group consisting of about 200 parts per million (ppm) to about 2000 ppm, about 400 ppm to about 1600 ppm, about 600 ppm to about 1400 ppm, about 800 ppm to about 1200 ppm, and about 400 ppm to about 600 ppm.

11. The system of claim 1, wherein the stabilizing agent is able to inhibit the degradation or inactivation of the diagnostic marker for an inhibitory period selected from the group consisting of at least one minute, at least about five minutes, at least about ten minutes, at least about fifteen minutes, at least about thirty minutes, at least about one hour, at least about two hours, at least about four hours, and at least about eight hours.

12. A system for determining the therapeutic potential of a therapeutic compound, the system comprising:

a detection platform comprising a plurality of detection sites each capable of receiving a therapeutic potential diagnostic marker protein, a diagnostic marker protein stabilization agent, and an indicator labeled diagnostic marker protein detection agent;

a computer writeable database capable of receiving a plurality of binding characteristics, the plurality of binding characteristics comprising at least one binding property of a therapeutical potential diagnostic marker protein to an indicator labeled detection agent;

wherein

a processor operably coupled to the computer database and the detection platform, is programmed to determine and record said at least one binding property which is characteristic of the indicator labeled detection agent to said stabilized diagnostic marker protein agent in each of the plurality of detection sites;

wherein comparison of said plurality of binding characteristics is capable of determining the diagnostic marker protein stabilizing agent with the greatest effect on the binding characteristic of the therapeutic potential diagnostic marker protein to the indicator labeled detection agent;

wherein the diagnostic marker protein stabilizing agent is selected from the group consisting of citric acid sodium hydroxide pH 6.0 buffer (Fixanal®

Buffer 6.0 (Sigma-Aldrich Co.)), acetic acid, aluminum hydroxide bentonite, aluminum sulfate hydrate, benzoic acid, aluminum potassium sulfate dodecahydrate, caffeine, and 3-tert-butyl-hydroxyanisole, or a combination thereof; and

wherein

the therapeutic potential of the marker protein is diagnosed on the basis of observed binding characteristics.

13. The system of claim 12, wherein the diagnostic marker protein is specific for a plurality of diseases including a cancer or pre-cancerous condition, cardiac disease, fungal infection, or a parasitic infection.

14. The system of claim 12, wherein the diagnostic marker protein is binding a plurality of different indicator labeled detection molecules as recognized, compared and memory recorded by said processor in the computer data base.

15. The system of claim 13, wherein the cancer marker proteins are capable of binding to cancer specific antigens selected from the group consisting of alpha-fetoprotein, CA15-3, CA-125, Carcinoembryonic antigen, and prostate specific antigen.

16. The system of claim 12, wherein the marker protein stabilizing agent is benzoic acid.