# US 2014/0193435 A1 · Method for integrating large scale biological data with imaging

> Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt

- Number: US 2014/0193435 A1
- Document ID: US20140193435A1
- Status: Published application
- Kind: A1
- Application number: 14/098,762
- Filed: 2013-12-06
- Published: 2014-07-10
- Earliest claimed: 2005-05-31
- Assignees: Algeomics, LLC
- Applicants: Algeomics, LLC
- Inventors: Michael D. Kuo
- Web page: https://patentgrep.com/patent/US20140193435A1

## CPC

- G16H 50/20: for computer-aided diagnosis, e.g. based on medical expert systems
- A61B 5/0059: {using light, e.g. diagnosis by transillumination, diascopy, fluorescence (photoacoustic A61B5/0093; optical measurement of heart rate A61B5/02416; optical measurement of blood flow A61B5/0261; optical measurement of analytes A61B5/1455)}
- A61B 5/7271: {Specific aspects of physiological measurement analysis (specific diagnostics methods using bioelectric or biomagnetic signals A61B5/316)}
- A61B 5/7275: {Determining trends in physiological measurement data; Predicting development of a medical condition based on physiological measurements, e.g. determining a risk factor}
- A61B 6/032: {Transmission computed tomography [CT]}
- A61B 6/037: {Emission tomography}
- A61B 6/481: {involving the use of contrast agents}
- A61B 8/13: Tomography (A61B8/10, A61B8/12 take precedence)
- A61K 49/0002: {General or multifunctional contrast agents, e.g. chelated agents}
- A61K 49/0004: {Screening or testing of compounds for diagnosis of disorders, assessment of conditions, e.g. renal clearance, gastric emptying, testing for diabetes, allergy, rheuma, pancreas functions}
- A61K 49/06: Nuclear magnetic resonance [NMR] contrast preparations; Magnetic resonance imaging [MRI] contrast preparations
- C12Q 1/6837: using probe arrays or probe chips (C12Q1/6874 takes precedence)
- G01R 33/5601: {involving use of a contrast agent for contrast manipulation, e.g. a paramagnetic, super-paramagnetic, ferromagnetic or hyperpolarised contrast agent}
- G06V 10/70: using pattern recognition or machine learning (optical pattern recognition or electronic computations therefor G06V10/88)
- G16H 50/50: for simulation or modelling of medical disorders
- G06V 2201/03: Recognition of patterns in medical or anatomical images
- G16H: HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
- A61B: DIAGNOSIS; SURGERY; IDENTIFICATION (usefulness limited to only animals A61D)
- A61K: PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES (devices or methods specially adapted for bringing pharmaceutical products into particular physical or administering forms A61J3/00; chemical aspects of, or use of materials for deodorisation of air, for disinfection or sterilisation, or for bandages, dressings, absorbent pads or surgical articles A61L; soap compositions C11D)
- 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
- G01R: MEASURING ELECTRIC VARIABLES; MEASURING MAGNETIC VARIABLES (indicating correct tuning of resonant circuits H03J3/12)
- G06V: IMAGE OR VIDEO RECOGNITION OR UNDERSTANDING

## Abstract

There is disclosed a method of extracting large scale biological, biochemical or molecular information about an index disease, biological state, or systems from imaging by correlating the imaging features associated with said disease, state or system with corresponding large scale biological data.

## Claims

### Claim 1

A method of predicting a possible prognosis, treatment outcome, or diagnosis of a patient comprising:
a) imaging said patient;
b) identifying radiophenotype(s) in said images of said patient; and
c) diagnosing or predicting a treatment outcome or prognosis of said patient based on the presence and/or absence of said radiophenotype(s).

### Claim 2 (depends on 1)

The method of claim 1 wherein said possible treatment outcome is said patient's possible response to a particular treatment perturbation or drug treatment.

### Claim 3 (depends on 2)

The method of claim 2 wherein said treatment outcome is whether said patient will respond to a particular therapy or drug treatment.

### Claim 4 (depends on 2)

The method of claim 2 wherein said drug treatment is an adverse response to said therapy or said drug treatment.

### Claim 5 (depends on 2)

The method of claim 2 wherein said particular treatment perturbation is a medical device.

### Claim 6 (depends on 2)

The method of claim 2 wherein said treatment is an administration of a drug.

### Claim 7 (depends on 6)

The method as recited in claim 6 wherein said patient prognosis to said administration of said drug is a desired response.

### Claim 8 (depends on 6)

The method as recited in claim 6 wherein said patient prognosis to said administration of said drug is an adverse response.

### Claim 9 (depends on 2)

The method of claim 2 wherein said particular treatment perturbation is a focused external energy source.

### Claim 10 (depends on 1)

The method of claim 1 wherein said patient prognosis is a clinical, functional, physiological, molecular or biochemical measure of said patient's disease.

### Claim 11 (depends on 10)

The method of claim 10 wherein said clinical measure is overall patient survival.

### Claim 12 (depends on 10)

The method of claim 10 wherein said measure is disease free survival.

### Claim 13 (depends on 10)

The method of claim 10 wherein said measure is likelihood of recurrence.

### Claim 14 (depends on 10)

The method of claim 10 wherein said measure is likelihood of metastasis.

### Claim 15 (depends on 1)

The method of claim 1 wherein said patient diagnosis is a clinical, functional, physiological, biological, molecular or biochemical description or basis of said patient's disease.

### Claim 16 (depends on 15)

The method of claim 15 wherein said diagnosis is a molecular subtype based on RNA expression, function, or modification.

### Claim 17 (depends on 15)

The method of claim 15 wherein said diagnosis is a molecular subtype based on microRNA expression, function, or modification.

### Claim 18 (depends on 15)

The method of claim 15 wherein said diagnosis is a molecular subtype based on RNAi expression, function, or modification.

### Claim 19 (depends on 15)

The method of claim 15 wherein said diagnosis is a molecular subtype based on protein expression, function, or modification.

### Claim 20 (depends on 15)

The method of claim 15 wherein said diagnosis is a molecular subtype based on alterations in DNA.

### Claim 21 (depends on 20)

The method of claim 20 wherein said alterations in DNA are changes in copy number.

### Claim 22 (depends on 20)

The method of claim 20 wherein said alterations in DNA are epigenetic changes

### Claim 23 (depends on 15)

The method of claim 15 wherein said diagnosis is a molecular subtype based on cellular pathways, networks or modules or biological systems.

### Claim 24 (depends on 1)

The method as recited in claim 1 wherein said biological state is characterized based on said correlation.

### Claim 25 (depends on 1)

The method as recited in claim 1 wherein said patient prognosis, treatment outcome, or diagnosis is based on radiophenotypes, radiogenotypes, radiogenomic associations, or an association map.

### Claim 26 (depends on 1)

The method as recited in claim 1 wherein said specimen is a tissue, system, organism or animal.

### Claim 27 (depends on 1)

The method according to claim 1 wherein said imaging is selected from the group consisting of MRI, MRS, nuclear scintigraphy, PET, CT, ultrasonography, optical imaging, infrared imaging, and x-ray radiography.

### Claim 28 (depends on 1)

The method as recited in claim 1 further comprising the use of an imaging agent or image-enhancing agent.

### Claim 29 (depends on 1)

The method as recited in claim 1 further comprising the use of an imaging agent having a binding moiety specific for a cell surface molecule that is expressed in said specimen and an image enhancing label.

### Claim 30 (depends on 29)

The method of claim 29 wherein said imaging agent is a small molecular weight, extracellular fluid space (ECF) contrast agent.

### Claim 31 (depends on 1)

The method according to claim 1 wherein said imaging is repeated throughout the course of a disease of said patient.

### Claim 32 (depends on 1)

The method according to claim 1 wherein said patient has a tumor.

### Claim 33 (depends on 29)

The method according to claim 29 wherein two or more binding moieties are selected for imaging.

### Claim 34 (depends on 29)

The method according to claim 29 further comprising the step of treating said patient with a therapeutic moiety conjugated to said binding moiety.

### Claim 35 (depends on 29)

The method according to claim 29 wherein said imaging agent is activated by an enzyme that is expressed in said target tissue and which can induce image enhancement by catalysis.

### Claim 36

A method of identifying radiophenotype(s) of a biological state of a specimen comprising;
a) Providing large scale biological, biochemical or molecular data of said biological state;
b) Imaging said specimen; and
c) Correlating the information contained in said images with said large scale biological, biochemical or molecular information.

### Claim 37 (depends on 36)

The method as recited in claim 36 wherein said large scale biological, biochemical or molecular data of said biological state is created by providing a specimen having said biological state and generating large scale biological, biochemical or molecular data of said biological state of said specimen.

### Claim 38 (depends on 36)

The method as recited in claim 36 wherein said specimen is a tissue, system, organism or animal.

### Claim 39 (depends on 36)

The method as recited in claim 36 wherein the underlying biological state of said tissue, specimen, system, organism, or patient's is inferred from the structure, function, composition, physiology, morphology or organization of said image of said tissue, specimen, system, organism, or patient.

### Claim 40 (depends on 39)

The method as recited in claim 39 wherein said large scale biological data information is at least one of the following; DNA, genes, gene expression, RNA, RNA modifications, epigenetic alterations, proteins, protein modification, protein function, drug sensitivity profiles, drug/chemical toxicity profiles, systemic response profiles, single nuclear polymorphisms (SNPs), Haplotype maps, RNAi screens, microRNA, genome, transcriptome, metabolome, proteome, physiome, phenome, morpheme, interactome, glycome, secretome, ribonome, orfeome, regulome, cellome, operome, unknome, functome, imagome, modulome and motifome and chromosomal, gene mutations, alterations, losses, gains, amplifications, deletions and metabolites thereof of the above.

### Claim 41

A method of determining the likelihood of an adverse reaction to a drug candidate in a patient comprising:
a) Determining the pharmacogenomic or pharmacogenetic profile of the drug candidate on a population;
b) Determining adverse responder population to said drug candidate;
c) Image said adverse responder population;
d) Imaging said patient;
e) Correlate the image of said adverse responder population to imaging said patient; and
f) Determining whether said patient is a candidate for said drug therapy based on said correlation.

### Claim 42

A method of determining whether a patient having a disease state is a candidate for a drug therapy comprising:
a) Determining the pharmacogenomic or pharmacogenetic profile of the drug candidate on a population;
b) Determining responder population to said drug candidate;
c) Image said responder population;
d) Imaging said patient;
e) Correlate the image of said responder population to imaging said patient; and
f) Determining whether said patient is a candidate for said drug therapy based on said correlation.

### Claim 43

A tangible medium of expression comprising data related to radiophenotype, radiogenotype, radiogenomic association, or association map.

### Claim 44 (depends on 43)

The tangible medium of expression of claim 43 which is a database.

### Claim 45 (depends on 43)

The tangible medium of expression of claim 43 wherein data are images and/or descriptions of the radiophenotype(s), or radiogenomic association(s).

### Claim 46 (depends on 45)

The tangible medium of expression of claim 45 wherein said images and/or descriptions are a reference that is graphical in nature, text, or both.