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

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.

We claim:  
     
         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.