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 digital storage medium on which is stored a computer readable calibrated profile data set, wherein: 
 a. the calibrated profile data set relates to a sample providing a source of RNAs derived from a target cell population to which an agent has been administered; and    b. the calibrated profile data set includes a first plurality of members, each member being a quantitative measure of a change in an amount of a distinct RNA constituent in a panel of constituents selected so that measurement of the constituents enables evaluation of a biological condition as affected by administration of the agent, wherein such measure for each constituent is obtained under measurement conditions that are reproducible such that the coefficient of variation for each value is less than approximately 3 percent, the calibrated profile data set being a comparison between a first profile data set and a baseline profile data set, thereby providing an evaluation of the biological condition of the target cell population to which the agent has been administered.    
     
     
         2 . A digital storage medium according to  claim 1 , wherein: (i) each member of the calibrated profile data set is a function of a corresponding member of a post-administration data set and a corresponding member of a baseline data set; (ii) each member of the baseline data set is a quantitative measure of the amount of a distinct RNA constituent in the panel under a normative condition; and (iii) each member of the post-administration data set is a quantitative measure of the amount of a distinct RNA constituent in the panel under a condition following administration of the agent to the target cell population.  
     
     
         3 . A medium according to  claim 2 , wherein the function is a second function of the ratio of the corresponding member of baseline data set to the corresponding member of the post-administration data set.  
     
     
         4 . A medium according to  claim 3 , wherein the second function is a logarithmic function.  
     
     
         5 . A digital storage medium according to any of claims  1 - 4 , wherein the agent is a pharmaceutical.  
     
     
         6 . A digital storage medium according to any of claims  1 - 4 , wherein the agent includes a second plurality of components.  
     
     
         7 . A digital storage medium according to any of claims  1 - 4 , wherein the agent is a nutraceutical.  
     
     
         8 . A digital storage medium according to any of claims  1 - 4 , wherein the first plurality is at least three but less than 1000.  
     
     
         9 . A digital storage medium according to any of claims  1 - 4 , wherein the first plurality is at least four but less than 1000.  
     
     
         10 . A digital storage medium according to any of claims  1 - 4 , wherein the first plurality is at least five but less than 1000.  
     
     
         11 . A digital storage medium according to any of claims  1 - 4 , wherein the first plurality is at least six.  
     
     
         12 . A digital storage medium according to  claim 1 , wherein the measurement conditions that are reproducible include intra-assay variability and inter-assay variability.  
     
     
         13 . A digital storage medium according to  claim 12 , wherein intra-assay variability is reproducible such that the average coefficient of variation for measurements for each assay is less than 1 percent.  
     
     
         14 . A digital storage medium according to  claim 12 , wherein inter-assay variability is reproducible such that the average coefficient of variation for measurements for each value is less than 2 percent.  
     
     
         15 . A digital storage medium on which is stored a plurality of records R i  relating to a population of subjects, each record R i  corresponding to a distinct instance Pi of a computer readable profile data set P wherein: 
 a. each instance P i  of the profile data set P relates to a distinct sample derived from a subject, the sample providing a source of RNAs;    b. the profile data P set includes a plurality of members M j , each member M j  being a quantitative measure of the amount of a distinct RNA constituent in a panel of constituents selected so that measurement of the constituents enables evaluation of a biological condition, wherein such measure for each constituent is obtained under measurement conditions that are reproducible such that the coefficient of variation for each value is less than approximately 3 percent;    c. each record R i  includes, for each member M ij  of a corresponding distinct instance P i  of the profile data set P, a value corresponding to the value of the member M ij ; and    d. each record R i  also includes a reference to a characteristic of the subject relative to the record, the characteristic being at least one of age group;    gender, ethnicity, geographic location, diet, medical disorder, clinical indicator, medication, physical activity, body mass, and environmental exposure.    
     
     
         16 . A digital storage medium according to  claim 15 , wherein each sample is derived from a target cell population to which has been administered an agent, such target cell population being derived from a subject.  
     
     
         17 . A digital storage medium on which is stored a large number of computer readable profile data sets, wherein: 
 a. each profile data set relates to a sample derived from a target cell population to which has been administered an agent, the sample having RNAs;    b. each profile data set includes a plurality of members, each member being a quantitative measure of the amount of a distinct RNA constituent in a panel of constituents selected so that measurement of the constituents enables evaluation of a biological condition, wherein such measure for each constituent is obtained under measurement conditions that are reproducible such that the coefficient of variation for each value is less than approximately 3 percent; and    c. the panel is the same for all profile data sets.    
     
     
         18 . A method for accessing biological information on a digital storage medium according to  claim 15 , comprising making the information available to a user.  
     
     
         19 . A method according to  claim 18 , wherein the method further comprises making the information available to the user on any of a network, World Wide Web, email, internet access site or hard copy.  
     
     
         20 . A method according to  claim 18 , wherein the method further comprises accessing the information for loading to a second access site.  
     
     
         21 . A method according to claim  30 , wherein the process for loading includes downloading the information.  
     
     
         22 . A method according to  claim 18 , wherein access to the information is controlled.  
     
     
         23 . A method according to  claim 22 , wherein the process of control includes the use of a password.  
     
     
         24 . A method according to  claim 18 , wherein the user can annotate the available information, the annotation becoming part of the biological information.  
     
     
         25 . A method according to  claim 18 , wherein the user can add one or more records to the data set, the one or more records becoming part of the biological information.