Use of pooled probes in genetic analysis

Abstract

The invention provides arrays of polynucleotide probes having at least one pooled position. A typical array comprises a support having at least three discrete regions. A first region bears a pool of polynucleotide probes comprising first and second probes. A second region bears the first probe without the second probe and a third region bears the second probe without the first probe. A target nucleic acid having segments complementary to both the first and second probes shows stronger normalized binding to the first region than to the aggregate of binding to the second and third regions due to cooperative binding of pooled probes in the first region. The invention provide methods of using such arrays for e.g., linkage analysis, sequence analysis, and expression monitoring.

1 - 18 . (canceled)  
     
     
         19 . An array, comprising: 
 (a) a support comprising a first and a second discrete region;    (b) a pool of probes bound to the first discrete region comprising a first and a second component probe respectively complementary to nonoverlapping segments of a mRNA molecule; and    (c) a mismatch probe or pool of mismatch probes bound to the second discrete region, wherein 
 the mismatch probe has the same sequence as one of the first and second component probes except for a single base mismatch; and  
 the pool of mismatch probes comprises a first and a second mismatch probe that respectively have the same sequence as the first and second component probe except for a single base mismatch.  
   
     
     
         20 . The array of  claim 19 , wherein 
 the first and second discrete region are one of a plurality of first and second discrete regions;    the pool of probes is one of a plurality of different pools of probes, the first and second component probes in different pools complementary to nonoverlapping segments from different mRNA molecules, with different pools bound to different first discrete regions; and    the array comprises a mismatch probe or pool of mismatch probes corresponding to each of the different pools of probes, mismatch probes or mismatch pool of probes corresponding to different pools bound at different second discrete regions.    
     
     
         21 . A method of analyzing gene expression, comprising: 
 (a) providing an array comprising 
 (i) a plurality of different pools of probes each comprising a first and a second component probe respectively complementary to nonoverlapping segments of a known mRNA molecule, different pools of probes complementary to different known mRNA molecules and bound to different discrete regions of a support; and  
 (ii) a mismatch probe or pool of mismatch probes corresponding to each of the plurality of different probe pools, wherein the mismatch probe has the same sequence as one of the first and second component probes in the corresponding pool except for a single base mismatch; and  
 the pool of mismatch probes comprises a first and a second mismatch probe that respectively have the same sequence as the first and second component probe in the corresponding pool except for a single base mismatch; and  
 the mismatch probe or pool of mismatch probes that correspond to different pools are bound to different regions of the support and at regions distinct from the corresponding probe pools;  
   (b) hybridizing a sample comprising a population of mRNA or nucleic acids copied therefrom to the array; and    (c) comparing binding of members of the population to at least one of the pool of probes and the corresponding mismatch probe or pool of mismatched probes to determine at least one mRNA that is present in the sample.