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 .- 32 . (canceled) 
     
     
         33 . A method of making a diagnostic miniarray, the method comprising:
 a. providing a miniarray substrate;   b. providing a plurality of analyte specific reagents for detecting analytes in a sample; and   c. dispensing the analyte specific reagents on the miniarray substrate, wherein the analyte specific reagents are dispensed in a selected pattern such that application of analytes in a sample allows for the diagnosis of a specific disease or condition by the observation of a common visual image.   
     
     
         34 . The method of  claim 33 , wherein the miniarray substrate is selected from the group consisting of a coated microscope slide, flexible membrane, rigid glass, plastic, semi-rigid film, paper-based printing substrate, semi-rigid printing material, photographic paper, and high quality computer printing paper. 
     
     
         35 . The method of  claim 33 , wherein the analyte specific reagents are gene specific elements. 
     
     
         36 . The method of  claim 35 , wherein the gene specific elements are selected from the list consisting of amplified cDNAs, cloned cDNAs, synthetic oligonucleotides, and proteins manufactured to mimic nucleic acid segments (PNAs). 
     
     
         37 . The method of  claim 35 , wherein a subset of the gene specific elements arranged on the miniarray represent genes that are up-regulated or down-regulated in the disease or condition relative to a control. 
     
     
         38 . The method of  claim 35 , wherein a subset of the gene specific elements arranged on the miniarray represent tissue-specific or housekeeping genes that are not up-regulated or down-regulated in the disease or condition relative to a control. 
     
     
         39 . The method of  claim 33 , wherein the analytes in the sample are selected from the list consisting of RNA, cDNA probes made from RNA transcripts, intracellular proteins, and secreted proteins. 
     
     
         40 . The method of  claim 33 , wherein the common visual image is selected from the group consisting of a stoplight, an abstract sign, a shape, a symbol, an alphanumeric character, a picture representing an organ or a condition, and combinations thereof. 
     
     
         41 . The method of  claim 40 , wherein the shape or symbol is selected from the group consisting of 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, a language symbol, and combinations thereof. 
     
     
         42 . The method of  claim 40 , wherein the picture representing an organ or a condition is selected from the group consisting of a lung, a heart, a brain, a kidney, a stomach, a breast, a colon, a ragged-rough edged cell, a smooth round cell, and combinations thereof. 
     
     
         43 . The method of  claim 33 , wherein the disease or condition is selected from the group consisting of a cancer, an infection, a toxicity, a stage of development or aging, and combinations thereof. 
     
     
         44 . A method of making an addressable diagnostic miniarray, the method comprising:
 a. providing a miniarray substrate;   b. providing a plurality of generic capture probes for detecting analytes in a sample; and   c. dispensing the generic capture probes on the miniarray substrate, wherein the generic capture probes are dispensed in a selected pattern such that application of analytes in a sample allows for the diagnosis of a specific disease or condition by the observation of a common visual image.   
     
     
         45 . The method of  claim 44 , wherein the miniarray substrate is selected from the group consisting of a coated microscope slide, flexible membrane, rigid glass, plastic, semi-rigid film, paper-based printing substrate, semi-rigid printing material, photographic paper, and high quality computer printing paper. 
     
     
         46 . The method of  claim 44 , wherein the generic capture probes are selected from the group consisting of synthetic oligonucleotides, hapten binding elements, and selected antibodies. 
     
     
         47 . The method of  claim 44 , wherein the analytes in the sample are selected from the group consisting of total RNA, mRNA, cDNA probes made from RNA transcripts, and intracellular proteins or secreted proteins. 
     
     
         48 . The method of  claim 44 , wherein the common visual image is selected from the group consisting of a stoplight, an abstract sign, a shape, a symbol, an alphanumeric character, a picture representing an organ or a condition, and combinations thereof. 
     
     
         49 . The method of  claim 48 , wherein the shape or symbol is selected from the group consisting of 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, a language symbol, and combinations thereof. 
     
     
         50 . The method of  claim 48 , wherein the picture representing an organ or a condition is selected from the group consisting of a lung, a heart, a brain, a kidney, a stomach, a breast, a colon, a ragged-rough edged cell, a smooth round cell, and combinations thereof. 
     
     
         51 . The method of  claim 44 , wherein the disease or condition is selected from the group consisting of a cancer, an infection, a toxicity, a stage of development or aging, and combinations thereof. 
     
     
         52 . A diagnostic miniarray comprising a miniarray substrate and analyte specific reagents, wherein the analyte specific reagents are arranged in a distinct pattern such that the application of analytes to the miniarray results in a common visual image consistent with the diagnosis of a specific disease or condition. 
     
     
         53 . The diagnostic miniarray of  claim 52 , wherein the miniarray substrate is selected from the group consisting of a coated microscope slide, flexible membrane, rigid glass, plastic, semi-rigid film, paper-based printing substrate, semi-rigid printing material, photographic paper, and high quality computer printing paper. 
     
     
         54 . The diagnostic miniarray of  claim 52 , wherein the analyte specific reagents are gene specific elements. 
     
     
         55 . The diagnostic miniarray of  claim 54 , wherein the gene specific elements are selected from the group consisting of amplified cDNAs, cloned cDNAs, synthetic oligonucleotides, and proteins manufactured to mimic nucleic acid segments (PNAs). 
     
     
         56 . The diagnostic miniarray of  claim 54 , wherein a subset of the gene specific elements arranged on the miniarray represent genes that are up-regulated or down-regulated in the disease or condition relative to a control. 
     
     
         57 . The diagnostic miniarray of  claim 54 , wherein a subset of the gene specific elements arranged on the miniarray represent tissue-specific or housekeeping genes that are not up-regulated or down-regulated in the disease or condition relative to a control. 
     
     
         58 . The diagnostic miniarray of  claim 52 , wherein the analytes in the sample are selected from the group consisting of RNA, cDNA probes made from RNA transcripts, intracellular proteins, and secreted proteins. 
     
     
         59 . The diagnostic miniarray of  claim 52 , wherein the common visual image is selected from the group consisting of a stoplight, an abstract sign, a shape, a symbol, an alphanumeric character, a picture representing an organ or a condition, and combinations thereof. 
     
     
         60 . The diagnostic miniarray of  claim 59 , wherein the shape or symbol is selected from the group consisting of 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, a language symbol, and combinations thereof. 
     
     
         61 . The diagnostic miniarray of  claim 59 , wherein the picture representing an organ or a condition is selected from the group consisting of a lung, a heart, a brain, a kidney, a stomach, a breast, a colon, a ragged-rough edged cell, a smooth round cell, and combinations thereof. 
     
     
         62 . The diagnostic miniarray of  claim 52 , wherein the disease or condition is selected from the group consisting of a cancer, an infection, a toxicity, a stage of development or aging, and combinations thereof. 
     
     
         63 . An addressable diagnostic miniarray comprising a miniarray substrate and generic capture probes, wherein the generic capture probes are arranged in a distinct pattern such that application of analytes results in a common visual image consistent with the diagnosis of a specific disease or condition. 
     
     
         64 . The addressable diagnostic miniarray of  claim 63 , wherein the miniarray substrate is selected from the group consisting of a coated microscope slide, flexible membrane, rigid glass, plastic, semi-rigid film, paper-based printing substrate, semi-rigid printing material, photographic paper, and high quality computer printing paper. 
     
     
         65 . The addressable diagnostic miniarray of  claim 63 , wherein the generic capture probes are selected from the group consisting of synthetic oligonucleotides, hapten binding elements, and selected antibodies. 
     
     
         66 . The addressable diagnostic miniarray of  claim 63 , wherein the analytes in the sample are selected from the group consisting of RNA, cDNA probes made from RNA transcripts, intracellular proteins, and secreted proteins. 
     
     
         67 . The addressable diagnostic miniarray of  claim 63 , wherein the common visual image is selected from the group consisting of a stoplight, an abstract sign, a shape, a symbol, an alphanumeric character, a picture representing an organ or a condition, and combinations thereof. 
     
     
         68 . The addressable diagnostic miniarray of  claim 67 , wherein the shape or symbol is selected from the group consisting of 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, a language symbol, and combinations thereof. 
     
     
         69 . The addressable diagnostic miniarray of  claim 67 , wherein the picture representing an organ or a condition is selected from the group consisting of a lung, a heart, a brain, a kidney, a stomach, a breast, a colon, a ragged-rough edged cell, a smooth round cell, and combinations thereof. 
     
     
         70 . The addressable diagnostic miniarray of  claim 63 , wherein the disease or condition is selected from the group consisting of a cancer, an infection, a toxicity, a stage of development or aging, and combinations thereof.