Composition for the detection of blood cell and immunological response gene expression

Abstract

The present invention relates to a composition comprising a plurality of polynucleotide probes. The composition can be used as hybridizable array elements in a microarray. The present invention also relates to a method for selecting polynucleotide probes for the composition.

What is claimed is:  
     
         1 . A composition comprising a plurality of polynucleotide probes, wherein said plurality of polynucleotide probes comprise: 
 I) first polynucleotide probes, wherein each of said first polynucleotide probes comprises at least a portion of a gene differentially expressed in an immunological response;    II) second polynucleotide probes, wherein each of said second polynucleotide probes comprises at least a portion of a gene abundantly expressed in an immunological response; and    III) third polynucleotide probes, wherein each of said third polynucleotide probes comprises at least a portion of a gene coding for a polypeptide known to regulate blood cell biology.    
     
     
         2 . The composition of  claim 1 , wherein each of said first polynucleotide probes is selected by a first method comprising: 
 a) preparing at least one first target transcript profile from a first biological sample selected from the group consisting of hematopoietic cells and inflamed tissue and at least one first subtraction transcript profile from a noninflamed, nonhematopoietic biological sample;    b) subtracting said first subtraction transcript profile from said first target profile to detect a plurality of genes that are differentially expressed in an immunological response; and    c) identifying one of said detected genes that are differentially expressed in an immunological response.    
     
     
         3 . The composition of  claim 1 , wherein each of said second polynucleotide probes is selected by a second method comprising: 
 a) preparing at least one second target transcript profile from a second biological sample selected from the group consisting of hematopoietic cells and inflamed tissue to detect genes that are abundantly expressed in said second biological sample; and    b) identifying one of said detected genes that are abundantly expressed.    
     
     
         4 . The composition of  claim 1 , wherein each of said third polynucleotide probes is selected by a third method comprising identifying a gene coding for a polypeptide with a known function in immunological responses.  
     
     
         5 . An isolated polynucleotide selected from the group consisting of SEQ ID NOs:1-1508, or the complete complement thereof.  
     
     
         6 . The polynucleotide of  claim 5 , wherein said polynucleotide is immobilized on a substrate.  
     
     
         7 . The polynucleotide of  claim 5 , wherein said polynucleotide is a hybridizable element on a microarray.  
     
     
         8 . A composition comprising the polynucleotide of  claim 5  and a labeling moiety.  
     
     
         9 . A method for using a polynucleotide to detect expression of a nucleic acid in a sample comprising: 
 a) hybridizing the composition of  claim 8  to nucleic acids of the sample under conditions to form at least one hybridization complex; and    b) detecting hybridization complex formation, wherein complex formation indicates expression of the nucleic acid in the sample.    
     
     
         10 . The method of  claim 9  further comprising amplifying the nucleic acids of the sample prior to hybridization.  
     
     
         11 . The method of  claim 10  wherein complex formation is compared to a standard and is diagnostic of an immunopathological condition.