Systems and methods for characterizing a biological condition or agent using selected gene expression profiles

• US 20040225447A1
• Filed: 02/16/2004
• Published: 11/11/2004
• Est. Priority Date: 06/28/1999
• Status: Abandoned Application

• Current Assignee: Source Precision Medicine Inc.
• Original Assignee: Source Precision Medicine Inc.
• Inventors: Bankaitis-Davis, Danute M., Cheronis, John C., Tryon, Victor, Bevilacqua, Michael P.
• Application Number:
  US10/778,679
• Publication Number:
  US 20040225447A1
• Time in Patent Office: Days
• US Class Current: 702/19
• CPC Class Codes: G01N 33/5088 of vertebrates
• CPC Class Codes: G01N 33/6803 General methods of protein analysis not limited to specific proteins or families of proteins

Abstract

Methods are provided for evaluating a biological condition of a subject using a calibrated profile data set derived from a data set having a plurality of members, each member being a quantitative measure of the amount of a subject'"'"'s RNA or protein as distinct constituents in a panel of constituents. The biological condition may be a naturally occurring physiological state or may be responsive to treatment of the subject with one or more agents. Calibrated profile data sets may be used as a descriptive record for an agent.

Claims

1. A kit of primer-probe combinations for measuring expression products of at least four constituents selected from any one of Tables 1 through 7.

2. A kit according to claim 1, wherein each primer probe combination is constructed so as to hybridize only to at least one of cDNA and mRNA at a biologically relevant locus.

3. A kit according to claim 1, wherein in each combination a reverse primer is complementary to a coding DNA strand located across an intron-exon junction, with not more than three bases of a three-prime end of the reverse primer being complementary to a proximal exon.

4. A method of using a kit according to any of claims 1-3 for analyzing a patient for a biological condition at a remote site, comprising:

a. providing a kit for measuring a profile data base for evaluating a biological condition, the kit including reagents for quantitative analysis of RNA for a panel of gene loci;

b. accessing a centralized database containing baseline profile data sets corresponding to the panel;

c. determining a calibrated profile data set for the patient; and

d. analyzing the biological condition of the patient with respect to a library of calibrated profile data sets.

5. A method of using a kit according to claim 4, wherein quantitative analysis of RNA comprises:

quantitatively measuring the amount of a distinct RNA constituent in a panel of constituents selected so that measurement enables evaluation of a biological condition of patient, based on a sample from the patient, the sample providing a source of RNAs, wherein such measure for each constituent is obtained under measurement conditions that are substantially reproducible.

6. A method of using a kit according to claim 5, wherein the measurement conditions that are substantially repeatable are within a degree of repeatability of better than five percent.

7. A method of using a kit according to claim 5, wherein the measurement conditions that are substantially repeatable are within a degree of repeatability of better than three percent.

8. A method of using a kit according to claim 5, wherein the measurement conditions that are reproducible include intra-assay variability and inter-assay variability.

9. A method of using a kit according to claim 8, wherein intra-assay variability is reproducible such that the average coefficient of variation for measurements for each assay is less than 1 percent.

10. A method of using a kit according to claim 8, wherein inter-assay variability is reproducible such that the average coefficient of variation for measurements for each value is less than 2 percent.