Systemic lupus erythematosus diagnostic assay

Abstract

The present invention provides compositions and methods for aiding in the diagnosis, monitoring and prognosis of SLE in a subject and for identifying potential therapeutic agents to treat and/or ameliorate the symptoms associated with SLE. Accordingly, embodiments of the invention are directed to methods of identifying the gene expression profile of a suitable sample by screening for the presence of a differentially expressed SLE-associated gene isolated from a sample containing or suspected of containing a cell that can differentially express an SLE-associated gene.

1 - 32 . (canceled) 
   
   
       33 . A systemic lupus erythematosus diagnostic array comprising:
 at least 10 probes that hybridize under stringent conditions to one or more polynucleotides listed Table 1A and/or Table 1B;   at least 375 probes that hybridize under stringent conditions to one or more polynucleotides listed in Table 2A and/or Table 2B;   at least 10 probes that hybridize under stringent conditions to one or more polynucleotides listed Table 3A and/or Table 3B; and   at least 2 probes that hybridize under stringent conditions to one or more polynucleotides listed Table 4, mixtures and combinations thereof.   
   
   
       34 . The array of  claim 33 , wherein the polynucleotides are probes. 
   
   
       35 . The array of  claim 33 , wherein the polynucleotides are amplification primers. 
   
   
       36 . The array of  claim 33 , wherein the polynucleotides are attached to an array in a pre-determined location. 
   
   
       37 . A kit comprising:
 an array comprising:   at least 10 probes that hybridize under stringent conditions to a polynucleotide of Table 1A and/or Table 1B;   at least 375 probes that hybridize under stringent conditions to a polynucleotide of Table 2A and/or Table 2B;   at least 10 probes that hybridize under stringent conditions to a polynucleotide of Table 3A and/or Table 3B;   at least 2 probes that hybridize under stringent conditions to a polynucleotide of Table 4, mixtures and combinations thereof; and   instructions for determining the identity of each polynucleotide and its location in the array.   
   
   
       38 - 41 . (canceled) 
   
   
       42 . A computer implemented method for determining the genotype of a sample comprising:
 obtaining a plurality of sample probe intensities from a patient suspected of having SLE;   diagnosing systemic lupus erythematosus based upon the sample probe intensities; and   calculating linear correlation coefficient between the sample probe intensities and reference probe intensities; and accepting the tentative genotype as the genotype of the sample if the linear correlation coefficient is greater than a threshold value.   
   
   
       43 . The method of  claim 42 , wherein the probes comprise:
 at least 10 probes that hybridize under stringent conditions to a polynucleotide of Table 1A and/or Table 1B;   at least 375 probes that hybridize under stringent conditions to a polynucleotide of Table 2A and/or Table 2B;   at least 10 probes that hybridize under stringent conditions to a polynucleotide of Table 3A and/or Table 3B;   at least 2 probes that hybridize under stringent conditions to a polynucleotide of Table 4, mixtures and combinations thereof; and   mixtures and combinations thereof.   
   
   
       44 . The method of  claim 42 , wherein the probes comprise one or more genes selected from: 
     
       
         
               
               
               
               
             
                   
                   
               
                   
                 Accession No. 
                 Database 
                 Gene 
               
                   
                   
               
                   
                 NM_019096 
                 GenBank 
                 GTPBP2 
               
                   
                 AK002064.1 
                 GenBank 
                 DNAPTP6 
               
                   
                 AF237762 
                 GenBank 
                 GPR84 
               
                   
                 NM_004776.1 
                 GenBank 
                 B4GALT5 
               
                   
                 AB045118.1 
                 GenBank 
                 FRAT2 
               
                   
                 L13386.1 
                 GenBank 
                 PAFAH1B1. 
               
                   
                   
               
           
              
              
              
             
             
              
              
              
              
              
              
              
             
          
         
       
     
   
   
       45 . The method of  claim 42 , wherein at least one gene comprises C1 ORF 29 (Affymetrix ID 204439_at).