# US 2014/0156199 A1 · Molecular profiling of tumors

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- Number: US 2014/0156199 A1
- Document ID: US20140156199A1
- Status: Published application
- Kind: A1
- Application number: 14/175,800
- Filed: 2014-02-07
- Published: 2014-06-05
- Earliest claimed: 2006-05-18
- Assignees: Caris MPI, Inc.
- Applicants: Caris MPI, Inc.
- Inventors: Daniel D. Von Hoff; David M. Loesch; Arlet Alarcon; Robert J. Penny; Alan Wright; Matthew J. McGinniss; Ryan P. Bender; Traci Pawlowski
- Web page: https://patentgrep.com/patent/US20140156199A1

## CPC

- G01N 35/00029: {provided with flat sample substrates, e.g. slides (G01N35/028 takes precedence)}
- B01L 7/52: {with provision for submitting samples to a predetermined sequence of different temperatures, e.g. for treating nucleic acid samples}
- C12Q 1/6841: In situ hybridisation
- C12Q 1/6874: involving nucleic acid arrays, e.g. sequencing by hybridisation
- C12Q 1/6886: for cancer (immunoassay for cancer G01N33/575)
- C40B 60/12: for screening libraries
- G01N 33/54366: {Apparatus specially adapted for solid-phase testing}
- G01N 33/575: for cancer
- G01N 33/5751: of the skin, e.g. melanoma
- G01N 33/57515: of the breast
- G01N 33/5752: of the lungs
- G01N 33/57525: of the liver or pancreas
- G01N 33/57535: of the large intestine, e.g. colon, rectum or anus
- G01N 33/57545: of the ovaries
- G01N 33/5755: of the uterine cervix, uterine corpus or endometrium
- G01N 33/57555: of the prostate
- G01N 33/57557: {of other specific parts of the body, e.g. brain}
- G01N 33/5758: {involving compounds serving as markers for tumours, cancers or neoplasias, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides or metabolites}
- G01N 35/00871: {Communications between instruments or with remote terminals}
- G16B 20/00: ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
- G16B 20/10: Ploidy or copy number detection
- G16B 20/20: Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
- G16B 20/40: Population genetics; Linkage disequilibrium
- G16B 25/00: ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
- G16B 25/10: Gene or protein expression profiling; Expression-ratio estimation or normalisation
- G16B 30/00: ICT specially adapted for sequence analysis involving nucleotides or amino acids
- G16B 30/10: Sequence alignment; Homology search
- G16B 35/00: ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
- 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
- G16B 40/10: Signal processing, e.g. from mass spectrometry [MS] or from PCR
- G16B 45/00: ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
- G16B 50/00: ICT programming tools or database systems specially adapted for bioinformatics
- G16B 50/30: Data warehousing; Computing architectures
- G16B 99/00: Subject matter not provided for in other groups of this subclass
- G16C 20/60: In silico combinatorial chemistry
- G16H 10/20: for electronic clinical trials or questionnaires
- G16H 15/00: ICT specially adapted for medical reports, e.g. generation or transmission thereof
- G16H 20/10: relating to drugs or medications, e.g. for ensuring correct administration to patients
- G16H 40/63: for local operation
- G16H 50/20: for computer-aided diagnosis, e.g. based on medical expert systems
- G16H 70/40: relating to drugs, e.g. their side effects or intended usage
- C12Q 2600/106: Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
- C12Q 2600/112: Disease subtyping, staging or classification
- C12Q 2600/156: Polymorphic or mutational markers
- C12Q 2600/158: Expression markers
- C12Q 2600/16: Primer sets for multiplex assays
- G01N 2035/00138: {Slides}
- G01N 2035/00158: {Elements containing microarrays, i.e. "biochip"}
- G01N 2035/00326: {Analysers with modular structure}
- G01N 2035/00346: {Heating or cooling arrangements}
- G01N 2035/00366: {Several different temperatures used}
- G01N 2035/00881: {network configurations}
- G01N 2035/0091: {GUI [graphical user interfaces]}
- G01N 2333/47: Assays involving proteins of known structure or function as defined in the subgroups
- G01N 2333/9029: acting on -CH2- groups (1.17)
- G01N 2333/91205: Phosphotransferases in general
- G01N 2333/99: Isomerases (5.)
- G01N 2500/04: Screening involving studying the effect of compounds C directly on molecule A (e.g. C are potential ligands for a receptor A, or potential substrates for an enzyme A)
- G01N 2800/52: Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis
- Y02A 90/10: Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation
- G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q)
- B01L: CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
- C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C40B: COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES (in silico combinatorial libraries of nucleic acids, proteins or peptides G16B35/00; in silico combinatorial chemistry G16C20/60)
- G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16C: COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
- G16H: HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
- Y02A: TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE

## Abstract

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.

## Claims

### Claim 1

A system for generating a report identifying a therapeutic agent for an individual with 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 EGFR and PDGFRA 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 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).

### Claim 2 (depends on 1)

The system of claim 1, wherein the inputting in (b) is performed from a location that is remote from said database in (a).

### Claim 3 (depends on 1)

The system of claim 1, wherein the inputting is performed over an internet connection.

### Claim 4 (depends on 1)

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

### Claim 5 (depends on 1)

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.

### Claim 6 (depends on 1)

The system of claim 1, wherein the reference value for each of the plurality of molecular targets comprises a nucleic acid and/or protein.

### Claim 7 (depends on 1)

The system of claim 1, wherein the testing of the molecular target is performed after the individual has received drug therapy for the cancer.

### Claim 8 (depends on 1)

The system of claim 1, wherein the molecular profile comprises assessing a cell, tissue sample, blood sample or combination thereof.

### Claim 9 (depends on 1)

The system of claim 1, wherein the molecular profile comprises performing a test for a gene and/or protein.

### Claim 10 (depends on 1)

The system of claim 1, wherein the reference is obtained from one or more normal individual without the cancer.

### Claim 11 (depends on 1)

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

### Claim 12 (depends on 1)

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.

### Claim 13 (depends on 1)

The system of claim 1, further comprising a computer-readable program configured to prioritize the list of one or more therapeutic agent.

### Claim 14 (depends on 1)

The system of claim 1, wherein the report provides a prioritized list of the one or more therapeutic agent.

### Claim 15 (depends on 1)

The system of claim 1, wherein the molecular target EGFR is assessed by protein and nucleic acid testing.

### Claim 16 (depends on 1)

The system of claim 1, wherein the cancer is mesothelioma.

### Claim 17 (depends on 16)

The system of claim 16, wherein the molecular targets further comprise MGMT, AR, BRAF and PI3K.

### Claim 18 (depends on 17)

The system of claim 17, wherein the molecular targets PDGFRA and EGFR are assessed by protein and nucleic acid testing.

### Claim 19 (depends on 17)

The system of claim 17, wherein the molecular targets MGMT, AR, BRAF and PI3K are assessed by sequencing.

### Claim 20 (depends on 17)

The system of claim 17, wherein the testing comprises: (a) sequencing of the molecular targets, MGMT, BRAF, EGFR, PDGFRA and PI3K; and (b) immunohistochemistry of the molecular targets PDGFRA, EGFR, MGMT and AR.