MOLECULAR PROFILING OF TUMORS
Provided herein are methods and systems of molecular profiling of diseases, such as cancer. In some embodiments, the molecular profiling can be used to identify treatments for a disease, such as treatments that were not initially identified as a treatment for the disease or not expected to be a treatment for a particular disease.
1 . A system for generating a report identifying a therapeutic agent for an individual with uterine cancer comprising:
a. one or more computer database comprising:
i. a reference value for a plurality of molecular targets;
ii. a listing of available therapeutic agents for said plurality of molecular targets;
b. a computer-readable program code for inputting individualized molecular profile test values obtained for molecular targets comprising PTEN and RRM1 in a biological sample from the individual and comparing said test values with a corresponding reference value in (a)(i);
c. a computer-readable program code for accessing the database in (a) and identifying one or more therapeutic agent if present in (a)(ii) for the molecular targets wherein said comparison to said reference in (b) indicates a likely benefit of the one or more therapeutic agent; and
d. a computer-readable program for generating a report that comprises a listing of all the molecular targets exhibiting a change in (b) and the one or more therapeutic agent identified in (c).
2 . The system of claim 1 , wherein the inputting in (b) is performed from a location that is remote from said database in (a).
3 . The system of claim 1 , wherein the inputting is performed 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 one or more computer database further comprise data corresponding to one or more clinical trial of a molecular target.
6 . The system of claim 1 , wherein the reference value for each of the plurality of molecular targets comprises a nucleic acid and/or protein.
7 . The system of claim 1 , wherein the testing of the molecular target is performed after the individual has received drug therapy for the cancer.
8 . The system of claim 1 , wherein the molecular profile comprises assessing a cell, tissue sample, blood sample or combination thereof.
9 . The system of claim 1 , wherein the molecular profiling comprises performing a test for a gene and/or protein.
10 . The system of claim 1 , wherein the reference is obtained from one or more normal individual without the cancer.
11 . The system of claim 1 , wherein the molecular targets further comprise KRAS.
12 . The system of claim 1 , wherein said report further comprises a listing of one or more additional molecular target for which said comparison to said reference in (b) indicates a likely lack of benefit of one or more therapeutic agent in (a)(ii) for the one or more additional molecular target.
13 . The system of claim 1 , further comprising a computer-readable program configured to prioritize the list of one or more therapeutic agent.
14 . The system of claim 1 , wherein the report provides a prioritized list of the one or more therapeutic agent.
15 . The system of claim 1 , wherein the individual has been treated by and failed to respond to one cancer therapeutic.
16 . The system of claim 1 , wherein the individual has failed to respond to at least one treatment for the uterine cancer.
17 . The system of claim 16 , wherein the molecular targets further comprise APC, CTNNB1, cKIT, BRAF and PIK3CA.
18 . The system of claim 17 , wherein the molecular target PTEN is assessed by protein and nucleic acid testing.
19 . The system of claim 17 , wherein the molecular target RRM1 is assessed by immunohistochemistry testing.
20 . The system of claim 17 , wherein the molecular targets APC, CTNNB1, cKIT, BRAF and PI3K are assessed by sequencing.
21 . The system of claim 17 , wherein the testing comprises: (a) sequencing of the molecular targets APC, CTNNB1, cKIT, BRAF, PTEN and PI3K; and (b) immunohistochemistry of the molecular targets PTEN and RRM1.