System and method for determining individualized medical intervention for a disease state

• US 9,372,193 B2
• Filed: 08/29/2014
• Issued: 06/21/2016
• Est. Priority Date: 05/18/2006
• Status: Active Grant

• Current Assignee: Caris Mpi, Inc.
• Original Assignee: Caris Mpi, Inc.
• Inventors: Von Hoff, Daniel D., Penny, Robert J.
• Primary Examiner(s): Lin, Jerry
• Application Number:
  US14/473,881
• Publication Number:
  US 20140371111A1
• Time in Patent Office: 662 Days
• Field of Search: 702/19
• US Class Current: 1/1
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/106 Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: G01N 2333/71 for growth factors; for growth regulators
• CPC Class Codes: G01N 2333/91205 Phosphotransferases in general
• CPC Class Codes: G01N 2333/914 Hydrolases (3)
• CPC Class Codes: G01N 33/574 for cancer
• CPC Class Codes: G01N 33/57488 involving compounds identifable in body fluids
• CPC Class Codes: G01N 33/6893 related to diseases not provided for elsewhere
• 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 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 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/10 Ontologies; Annotations
• CPC Class Codes: G16H 10/40 for data related to laboratory analysis, e.g. patient specimen analysis
• CPC Class Codes: G16H 15/00 ICT specially adapted for medical reports, e.g. generation or transmission thereof
• CPC Class Codes: G16H 20/10 relating to drugs or medications, e.g. for ensuring correct administration to patients
• CPC Class Codes: G16H 50/20 for computer-aided diagnosis, e.g. based on medical expert systems
• CPC Class Codes: G16H 70/20 : relating to practices or guidelines

Abstract

A system and method for determining individualized medical intervention for a particular disease state, and especially for cancers, that includes the molecular profiling of a biological sample from the patient, determining whether any molecular findings including one or more genes, one or more gene expressed proteins, one or more molecular mechanisms, and/or combinations of such exhibit a change in expression compared to a reference, and identifying a non-specific disease therapy or agent capable of interacting with the genes, gene expressed proteins, molecular mechanisms, or combinations of such molecular findings that exhibited a change in expression.

Claims

1. A system for generating a report identifying at least one therapeutic agent for an individual with a cancer comprising:

a. at least one device configured to assay a plurality of molecular targets in a biological sample to determine molecular profile test values for the plurality of molecular targets, wherein the plurality of molecular targets comprises AR, EGFR, HER2, KIT, MLH1, PTEN, and PDGFRA; and

b. at least one computer database comprising;

i. a reference value for each of the plurality of molecular targets; and

ii. a listing of available therapeutic agents for each of the plurality of molecular targets;

c. a computer-readable program code comprising instructions to input the molecular profile test values and to compare each of the molecular profile test values with a corresponding reference value from the at least one computer database in (b)(i);

d. a computer-readable program code comprising instructions to access the at least one computer database and to identify at least one therapeutic agent from the listing of available therapeutic agents for the plurality of molecular targets wherein the comparison to the reference values in (c) indicates a likely benefit of the at least one therapeutic agent; and

e. a computer-readable program code comprising instructions to generate a report that comprises a listing of the molecular targets for which the comparison to the reference value indicated a likely benefit of the at least one therapeutic agent in (d) and the at least one therapeutic agent identified in (d).

2. The system of claim 1, wherein the molecular profile test values are input into the system from a location that is remote from the at least one computer database.

3. The system of claim 1, wherein the molecular profile test values are input into the system over an internet connection.

4. The system of claim 1, wherein the report is in electronic or paper format.

5. The system of claim 1, wherein the at least one computer database further comprises data corresponding to at least one clinical trial of a member of the plurality of molecular targets.

6. The system of claim 1, wherein the reference value for each of the plurality of molecular targets comprises at least one of a nucleic acid and a protein.

7. The system of claim 1, wherein the molecular profile test values for the plurality of molecular targets are determined after the individual has received drug therapy for the cancer.

8. The system of claim 1, wherein the molecular profile test values are determined by assessing a cell, a tissue sample, a blood sample or a combination thereof.

9. The system of claim 1, wherein the molecular profile test values are determined by performing a test for a gene and/or a protein.

10. The system of claim 1, wherein the reference value for each of the plurality of molecular targets is obtained from at least one individual without the cancer.

11. The system of claim 1, wherein the individual has been treated by and failed to respond to at least one cancer therapeutic.

12. The system of claim 1, wherein the at least one device configured to assay the plurality of molecular targets is configured to perform at least one of immunohistochemistry (IHC), an expression microarray, a comparative genomic hybridization (CGH) microarray, a single nucleotide polymorphism (SNP) microarray, a fluorescent in-situ hybridization (FISH), in-situ hybridization (ISH), and a proteomic array.

13. The system of claim 1, wherein the at least one device configured to assay the plurality of molecular targets is configured to perform at least one of a microarray, genotyping and proteomic analysis.

14. The system of claim 1, wherein the molecular targets assayed in (a) are assayed at the genetic and/or protein level.