Identification, monitoring and treatment of disease and characterization of biological condition using gene expression profiles

• US 20050250148A1
• Filed: 06/22/2005
• Published: 11/10/2005
• Est. Priority Date: 06/28/1999
• Status: Active Grant

• Current Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Original Assignee: Source Precision Medicine Inc.
• Inventors: Bankaitis-Davis, Danute M., Cheronis, John C., Tryon, Victor, Bevilacqua, Michael P.
• Granted Patent: US 7,957,909 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: G01N 2800/042 Disorders of carbohydrate metabolism, e.g. diabetes, glucose metabolism
• CPC Class Codes: G01N 33/5088 of vertebrates
• CPC Class Codes: G01N 33/57415 of breast
• CPC Class Codes: G01N 33/6803 General methods of protein analysis not limited to specific proteins or families of proteins
• CPC Class Codes: G01N 33/6863 Cytokines, i.e. immune system proteins modifying a biological response such as cell growth proliferation or differentiation, e.g. TNF, CNF, GM-CSF, lymphotoxin, MIF or their receptors
• CPC Class Codes: G01N 33/6869 Interleukin
• CPC Class Codes: G01N 33/6893 related to diseases not provided for elsewhere
• 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: Y02A 90/10 Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

Abstract

Gene expression data, in particular gene expression profiles, are created and used in the identification, monitoring and treatment of disease and characterization of biological conditions. Profile data sets are derived from subject samples and include quantitative substantially repeatable measures of a distinct amount of RNA or protein constituent in a panel selected to enable evaluation of a biological condition. Such profile data sets may be used to provide an index indicative of the biological state of a subject, which may be compared to a normative value of the index determined with respect to a relevant population of subjects.

Claims

1. A method, for evaluating a biological condition of a target population of cells affected by an agent based on a sample from the population of cells, the sample providing a source of RNAs, the method comprising:

using amplification for measuring the amount of RNA of at least two constituents from any one of Tables 1 through 12 from the sample of the target population of cells, where a panel of constituents is selected so that measurement of the constituents enables measurement of the biological condition and wherein the measures of all constituents in the panel form a first profile data set;

using amplification for measuring the amount of RNA of all constituents in said panel wherein measures of all constituents in the panel are from a relevant population of target cells and form a normative baseline profile data set; and

producing a calibrated profile data set for said panel, wherein each member of the calibrated profile data set is a function of a corresponding member of the first profile data set and the corresponding member of a baseline profile data set, and

wherein the calibrated profile data set providing a measure of the biological condition of the target population of cells as affected by the agent.

2. A method according to claim 1, wherein the relevant population of target cells is a population of cells from healthy subjects.

3. A method according to claim 1, wherein the relevant population of target cells has in common a property that is at least one of age group, gender, ethnicity, geographic location, diet, medical disorder, clinical indicator, medication, physical activity, body mass, and environmental exposure.

4. A method according to claim 1, the panel including at least two of the constituents of the Inflammation Gene Expression Panel of Table 1 and wherein the measures for each constituent are performed under measurement conditions that are substantially repeatable and the efficiencies of amplification for all constituents are substantially similar.

5. A method, for evaluating the effect on a biological condition by a first agent in relation to the effect by a second agent, based on first and second target populations of cells to which the first and second agents have been respectively administered, the first and second samples respectively, providing a source of RNAs, the method comprising:

using amplification for measuring the amount of RNA of at least two constituents from any one of Tables 1 through 12 from the first sample of the target population of cells and from the second sample of target population of cells, where

a panel of constituents is selected so that measurement of the constituents for both first and second samples enables measurement of the biological condition and wherein the measures of all constituents in the panel form a first profile data set and a second profile data set;

using amplification for measuring the amount of RNA of all constituents in said first and second panels wherein measures of all constituents in the panels are from a relevant population of target cells and form first and second normative baseline profile data sets; and

producing a first calibrated profile data set and a second profile data set for said panel, wherein each member of the first calibrated profile data set is a function of a member of the first profile data set and the corresponding member of the first normative baseline profile data, and each member of the second calibrated data set is a function of a member of the second profile data set and the corresponding member of the second normative baseline profile data set,

wherein the first and second calibrated profile data sets provide a measure of the effect by the first agent on the biological condition of the target population of cells in relation to the effect by the second agent.

6. A method according to claim 5, wherein the measures for each constituent in the first and second profile data sets and the normative baseline profile data sets are performed under measurement conditions that are substantially repeatable and the efficiencies of amplification for all constituents are substantially similar.

7. A method according to claim 5, wherein the first agent is a first drug and the second agent is a second drug.

8. A method according to claim 5, wherein the first agent is a drug and the second agent is a complex mixture.

9. A method according to claim 5, wherein the first agent is a drug and the second agent is a nutraceutical.