Gene-expression profiling with reduced numbers of transcript measurements

Abstract

The present invention provides compositions and methods for making and using a transcriptome-wide gene-expression profiling platform that measures the expression levels of only a select subset of the total number of transcripts. Because gene expression is believed to be highly correlated, direct measurement of a small number (for example, 1,000) of appropriately-selected transcripts allows the expression levels of the remainder to be inferred. The present invention, therefore, has the potential to reduce the cost and increase the throughput of full-transcriptome gene-expression profiling relative to the well-known conventional approaches that require all transcripts to be measured.

What is claimed is: 
     
         1 .- 15 . (canceled) 
     
     
         16 . A method of assaying gene expression, comprising:
 a) providing:
 i) a plurality of different barcode sequences; 
 ii) a plurality of a solid support, each solid support comprising a homogeneous set of nucleic acid probes, each set complementary to a different barcode sequence of said plurality of barcode sequences; 
 iii) a population of more than 1000 different transcripts, each transcript comprising a gene-specific sequence; 
 iv) an algorithm capable of predicting the level of expression of unmeasured transcripts; 
   b) processing said population of transcripts to create a plurality of different templates, each template comprising one of said plurality of barcode sequences operably associated with a different gene-specific sequence, wherein said plurality of different templates represents less than the total number of transcripts within said population;   c) measuring the amount of each of said plurality of different templates to create a plurality of measurements; and   d) applying said algorithm to said plurality of measurements, thereby predicting the level of expression of unmeasured transcripts within said population.   
     
     
         17 . The method according to  claim 16 , wherein said method further comprises a device capable of measuring the amount of each of said plurality of different templates. 
     
     
         18 . The method according to  claim 16 , wherein said solid support are optically addressed. 
     
     
         19 . The method according to  claim 16 , wherein said processing comprises ligation-mediated amplification. 
     
     
         20 . The method according to  claim 18 , wherein said measuring comprises detecting said optically addressed solid support. 
     
     
         21 . The method according to  claim 20 , wherein said measuring comprises hybridizing said plurality of different templates to said plurality of a solid support through said nucleic-acid probes complementary to said plurality of barcode sequences. 
     
     
         22 . The method according to  claim 16 , wherein said measuring comprises a flow cytometer. 
     
     
         23 . A method according to claim  1 , wherein expression levels of a set of substantially invariant transcripts are additionally measured. 
     
     
         24 . A method according to  claim 23 , wherein said expression levels of said unmeasured transcripts are normalized with respect to said expression levels of said invariant transcripts. 
     
     
         25 . A kit for use in the method of  claim 16 , the kit comprising:
 a) the population of different transcripts;   b) the plurality of different bar code sequences;   c) the plurality of solid support; and   d) a set of instructions for assaying the expression level of said transcripts.   
     
     
         26 . The method of  claim 16 , wherein the solid support is a bead, membrane, filter, or slide. 
     
     
         27 . The method of  claim 16 , wherein the solid support is made of a material selected from the group consisting of polystyrene, polycarbonate, polypropylene, nylon, glass, dextran, chitin, sand, pumice, agarose, polysaccharides, dendrimers, buckyballs, polyacrylamide, silicon, and rubber. 
     
     
         28 . The method of  claim 16 , wherein the plurality of different barcode sequences is approximately 500 to approximately 1000 different barcode sequences, the plurality of solid support is approximately 500 to approximately 1000 solid supports, the population of different transcripts is approximately 500 to approximately 1000 different transcripts, and/or the plurality of different templates is approximately 500 to approximately 1000 different templates. 
     
     
         29 . The method of  claim 16 , wherein the plurality of different barcode sequences is approximately 1000 different barcode sequences, the plurality of solid support is approximately 1000 solid supports, the population of different transcripts is approximately 1000 different transcripts, and/or the plurality of different templates is approximately 1000 different templates.