Expression miniarrays and uses thereof

Abstract

The present invention provides methods and devices for making new and inexpensive miniarrays suitable for gene expression analysis. Also provided herein are methods of diagnosis for specific tissue or condition using specialized diagnostic miniarrays that exhibit specific visual pattern as diagnostic readout.

1 . A method of diagnosis for specific tissue or condition using specialized: diagnostic miniarrays targeted to the analysis of said tissue or condition, comprising the steps of: 
 (a) preparing one or more set of gene specific elements that correspond to genes known to be significantly up-regulated or down-regulated in said tissue or condition relative to control sample;    (b) preparing one or more sets of gene specific elements that correspond to genes commonly expressed in both control sample and in said tissue or said condition;    (c) arranging the gene specific elements of (a) and (b) on a miniarray; and    (d) applying a target sample to said miniarray, wherein detection of a visually distinct image from said miniarray indicates the presence of said tissue or condition.    
     
     
         2 . The method of  claim 1 , wherein said condition is a disease, a cancer, responses to an infection, responses to a therapeutic or toxic agent, or stages of development or aging.  
     
     
         3 . The method of  claim 1 , wherein the total number of said gene specific elements in (a) and (b) is from about 10 to about 1000.  
     
     
         4 . The method of  claim 3 , wherein the total number of said gene specific elements in (a) and (b) is from about 50 to about 300.  
     
     
         5 . The method of  claim 1 , wherein said genes commonly expressed in both control sample and in said tissue or said condition are common housekeeping genes or tissue specific genes.  
     
     
         6 . The method of  claim 1 , wherein said target sample comprises expressed RNAs or nucleic acid copies thereof, and wherein said gene specific elements spotted on said miniarray are amplified cDNAs, cloned cDNAs, synthetic oligonucleotides or PNAs.  
     
     
         7 . The method of  claim 1 , wherein said target sample comprises expressed proteins, and wherein said gene specific elements spotted on said miniarray are a selected subset of specific antibodies.  
     
     
         8 . The method of  claim 1 , wherein said visually distinct image comprises a pattern that resembles a stoplight with clusters of red, yellow and green spots, of alphanumeric characters, of an abstract sign, of a shape or symbol, or of a simplified symbol or picture representing a tissue or condition.  
     
     
         9 . The method of  claim 8 , wherein said pattern is distinguished by a difference in color, a difference in intensity or a location within said miniarray.  
     
     
         10 . The method of  claim 8 , wherein said shape or symbol is a triangle, a rectangle, a square, a circle, an oval, a trapezoid, a star, a hexagon, a pentagon, an octagon, a bar, a stripe, a squiggle, a ring, a mathematical symbol or a language symbol.  
     
     
         11 . The method of  claim 8 , wherein said simplified symbol or picture representing a tissue or condition is a shape of a lung, a shape of a heart, a shape of a brain, a shape of a kidney, a shape of a stomach, a shape of a breast, a shape of a colon, a shape of a ragged rough-edged cell or a shape of a smooth round cells.  
     
     
         12 . The method of  claim 1 , wherein said gene specific elements corresponding to up-regulated genes and down-regulated genes are clustered in separated groups.  
     
     
         13 . The method of  claim 12 , wherein the clusters of gene specific elements corresponding to up-regulated and down-regulated genes are further subdivided into two or more subgroups based upon significant differences in modified expression levels in said tissue or said condition.  
     
     
         14 . The method of  claim 1 , wherein said gene specific elements are not clustered into specific groups on said miniarray and said visually distinct image is generated by computer means.  
     
     
         15 . A method of diagnosis for specific tissue or condition using specialized diagnostic miniarrays targeted to the analysis of said tissue or condition, comprising the steps of: 
 (a) providing one or more target samples comprising gene expression products;    (b) constructing an addressable miniarray spotted with different binding elements;    (c) providing a set of intermediate probes comprising a specific binding element that binds to a specific gene expression product in a target sample and a generic binding element that binds to a matching binding element spotted on said addressable miniarray;    (d) binding said set of intermediate probes to said target sample(s) in solution hybridization conditions, wherein different target samples are handled separately and intermediate probes capable of binding with different reporter elements are bound to different target samples;    (e) capturing and washing the complex of gene expression products and bound intermediate probes to remove unbound intermediate probes;    (f) denaturing or removing said gene expression products if necessary to produce a subset of intermediate probes reflecting said gene expression products and their relative frequency in the original sample;    (g) binding the resulting subset of intermediate probes to said addressable miniarray; and    (f) examining the binding pattern of said subset of intermediate probes, wherein detection of a visually distinct image from said miniarray indicates the presence of said tissue or condition.    
     
     
         16 . The method of  claim 15 , wherein said reporter elements are direct labeling agents, indirect label-binding molecules, haptens, or linker sequences that can bind a separate reporter that is a labeled DNA, GeneTAGs or ChipTAGs.  
     
     
         17 . The method of  claim 16 , wherein said reporter elements or reporters are bound to the intermediate probes before or after said intermediate probes are bound to said miniarray.  
     
     
         18 . The method of  claim 15 , wherein said intermediate probes comprises: 
 (1) a first half-probe comprising a first binding element that binds to a first sequence in a target sample and a binding element that binds to a matching binding element spotted on said miniarray; and    (2) a second half-probe comprising a reporter element and a second binding element that binds to a second sequence in said target sample, wherein said first sequence and said second sequence are adjacent sequences in said target sample and said first half-probe and said second half-probe are joined together to form a singular unit by a ligase enzyme after binding to said first sequence and said second sequence.    
     
     
         19 . The method of  claim 15 , wherein said intermediate probes are constructed as WRAP-Probes with universal linker/primer sequences at both ends, wherein increased signaling can be obtained by binding additional reporters to said universal linkers or exponentially amplifying said intermediate probes with a single primer set matching said primer sequences.  
     
     
         20 . The method of  claim 15 , wherein said binding elements printed on said miniarray are generic oligonucleotides that are not substantially complementary to sequences of the target sample and that constitute an arbitrary set of unique addresses and unique locations on said miniarray.  
     
     
         21 . The method of  claim 15 , wherein said binding elements printed on said miniarray are organized in pre-defined patterns to facilitate the creation of said visually distinct image.  
     
     
         22 . The method of  claim 15 , wherein said miniarray is printed with a small subset of binding elements that create different common capture areas on said miniarray to form said visually distinct image, wherein said intermediate probes are grouped into different groups that each has a common binding element which binds to a matching binding element spotted on said miniarray.  
     
     
         23 . The method of  claim 22 , wherein said groups of intermediate probes detect expression of genes selected from the group consisting of up-regulated genes in said tissue or condition, down-regulated genes in said tissue or condition, and genes with unchanged expression levels in said tissue or condition as compared to control sample.  
     
     
         24 . The method of  claim 15 , wherein said binding elements printed on said miniarray are avidin, streptavidin, anti-hapten antibodys, anti-fluorescent dye antibodys or anti-nonfluorescent dye antibody, wherein the matching binding elements on said intermediate probes are biotin, haptens, a fluorescent dye or a nonfluorescent dye.  
     
     
         25 . The method of  claim 24 , wherein said hapten is dinitrophenyl or nitrotyrosine.  
     
     
         26 . The method of  claim 24 , wherein said fluorescent dye or nonfluorescent dye is digoxygenin, fluorescein, tetramethylrhodamine, Texas Red, dansyl, Alexa Fluor 488, BODIPY FL, lucifer yellow, Cascade Blue or Marina Blue.  
     
     
         27 . The method of  claim 22 , wherein said binding elements printed on said miniarray are generic oligonucleotides, wherein said intermediate probes are grouped into different groups that each has a common binding element which binds to said oligonucleotides spotted on said miniarray.  
     
     
         28 . The method of  claim 15 , wherein said condition is a disease, a cancer, responses to an infection, responses to a therapeutic or toxic agent, or stages of development or aging.  
     
     
         29 . The method of  claim 15 , wherein said visually distinct image comprises a pattern that resembles a stoplight with clusters of red, yellow and green spots, of alphanumeric characters, of an abstract sign, of a shape or symbol, or of a simplified symbol or picture representing a tissue or condition.  
     
     
         30 . The method of  claim 29 , wherein said pattern is distinguished by a difference in color, a difference in intensity or a location within said miniarray.  
     
     
         31 . The method of  claim 29 , wherein said shape or symbol is a triangle, a rectangle, a square, a circle, an oval, a trapezoid, a star, a hexagon, a pentagon, an octagon, a bar, a stripe, a squiggle, a ring, a mathematical symbol or a language symbol.  
     
     
         32 . The method of  claim 29 , wherein said simplified symbol or picture representing a tissue or condition is a shape of a lung, a shape of a heart, a shape of a brain, a shape of a kidney, a shape of a stomach, a shape of a breast, a shape of a colon, a shape of a ragged rough-edged cell or a shape of a smooth round cells.