Methods and compositions for producing labeled probe nucleic acids for use in array based comparative genomic hybridization applications

Abstract

Methods and compositions for producing labeled probe nucleic acids from genomic nucleic acid template are provided. In the subject methods, a conserved coding consensus region primer is employed to enzymatically generate a select set of labeled probe nucleic acids corresponding to coding regions of genes from a genomic template via a primer extension protocol. The subject methods find use in a variety of different applications, and are particularly suited for use in the preparation of labeled probe nucleic acids for use in array based comparative genomic hybridization applications. Also provided are kits for use in practicing the subject methods.

1 - 17 . (canceled)  
     
     
         18 . An oligonucleotide primer comprising a conserved coding consensus region.  
     
     
         19 . The oligonucleotide primer according to  claim 18 , wherein said primer ranges in length from about 5 to about 20 nt.  
     
     
         20 . The oligonucleotide primer according to  claim 19 , wherein said primer further comprises at least one of a 5′ and a 3′ random sequence, each of which independently ranges in length from about 1 to about 10 nt.  
     
     
         21 . The oligonucleotide primer according to  claim 19 , wherein said primer is an ATG comprising primer.  
     
     
         22 . The oligonucleotide primer according to  claim 19 , wherein said primer comprises a consensus splice site.  
     
     
         23 . A kit for use for use in comparing the relative copy number of nucleic acid sequences in two or more collections of nucleic acid molecules, said kit comprising: 
 (a) an oligonucleotide primer comprising conserved coding consensus region; and    (b) instructions for practicing the method according to claim  1 .    
     
     
         24 . The kit according to  claim 23 , wherein said kit further comprises first and second nucleic acid labeling reagents having distinguishable labels.  
     
     
         25 . The kit according to  claim 24 , wherein said distinguishable labels are fluorescent distinguishable labels.  
     
     
         26 . The kit according to  claim 23 , wherein said further comprises a plurality of target elements bound to a solid surface.