Comparative Genomic Hybridization Assays Using Immobilized Oligonucleotide Features and Compositions for Practicing the Same

Abstract

Comparative genomic hybridization assays and compositions for use in practicing the same are provided. A characteristic of the subject comparative genomic hybridization assays is that solid support immobilized oligonucleotide feature elements, e.g., in the form of an array, are employed. Specifically, at least first and second nucleic acid populations prepared from genomic templates are contacted with a plurality of distinct oligonucleotide feature elements immobilized on a solid support surface and the binding of the at least first and second populations is then evaluated. Also provided are kits for use in practicing the subject methods.

1 - 49 . (canceled) 
     
     
         50 . A method for comparing the copy number of at least one nucleic acid sequence in at least two genomic sources, said method comprising:
 (a) preparing at least a first collection of nucleic acid molecules from a first genomic source and a second collection of nucleic acid molecules from a second genomic source, wherein said first and second genomic sources have a complexity of 1×10 9  base pairs or more and said first and second collections are of non-reduced complexity;   (b) contacting said first and second collections of nucleic acid molecules with one or more pluralities of distinct oligonucleotide features bound to a surface of a solid support, wherein said one or more pluralities of distinct oligonucleotide features comprise oligonucleotides that range in size from 20 nt to 200 nt in length and said contacting occurs under stringent assay conditions;   (c) measuring the binding of the first and second collections of nucleic acid molecules to said features to produce data; and   (d) identifying a quantitative difference in the copy number of at least one nucleic acid sequence in said at least two genomic sources using said data.   
     
     
         51 . The method according to  claim 50 , wherein said oligonucleotides range from 20 to 100 nt in length. 
     
     
         52 . The method according to  claim 51 , wherein said oligonucleotides range from 50 to 90 nt in length. 
     
     
         53 . The method according to  claim 50 , wherein the first and second genomic sources comprise mammalian genomic DNA. 
     
     
         54 . The method according to  claim 50 , wherein the first and second genomic sources comprise human genomic DNA, and said oligonucleotides range from 20 to 100 nt in length. 
     
     
         55 . The method according to  claim 50 , wherein said plurality of oligonucleotide features bound to a surface of a solid support include sequences of locations distributed across at least a portion of a chromosome. 
     
     
         56 . The method according to  claim 55 , wherein said locations have a non-uniform spacing across at least a portion of the chromosome. 
     
     
         57 . The method according to  claim 50 , wherein said nucleic acids of said first and second collections range from 100 to 10000 nt in length. 
     
     
         58 . The method according to  claim 50 , wherein said collections of nucleic acids are contacted with the same plurality of distinct oligonucleotide features. 
     
     
         59 . The method according to  claim 50 , wherein said collections of nucleic acids are distinguishably labeled. 
     
     
         60 . The method according to  claim 50 , wherein the solid support is a planar substrate. 
     
     
         61 . The method according to  claim 50 , wherein said non-reduced complexity collections have a complexity that is at least 25% of their respective genomic sources. 
     
     
         62 . The method according to  claim 50 , wherein said non-reduced complexity collections have a complexity that is at least 50% of their respective genomic sources. 
     
     
         63 . The method according to  claim 50 , wherein said plurality of distinct oligonucleotide features are bound to a solid surface in an array. 
     
     
         64 . The method according to  claim 50 , wherein each of said first and second collections is prepared by a primer extension reaction using a set of random primers and using said genomic sources as genomic templates. 
     
     
         65 . The method according to  claim 50 , wherein said preparing comprises amplifying said first genomic source and second genomic source in a manner such that said first and second collections are of non-reduced complexity. 
     
     
         66 . The method according to  claim 50 , wherein said first and second genomic sources are obtained from a plant. 
     
     
         67 . The method according to  claim 50 , wherein step (d) comprises identifying a single copy number heterozygous deletion in a genomic region of said first or second genomic sources. 
     
     
         68 . A method for comparing the copy number of at least one nucleic acid sequence in at least two genomic sources, said method comprising:
 (a) preparing at least a first collection of nucleic acid molecules from a first genomic source and a second collection of nucleic acid molecules from a second genomic source, wherein said first and second genomic collections have a complexity of 1×10 8  base pairs or more;   (b) contacting said first and second collections of nucleic acid molecules with one or more pluralities of distinct oligonucleotide features bound to a surface of a solid support, wherein said one or more pluralities of distinct oligonucleotide features comprise oligonucleotides that range in size from 20 nt to 200 nt in length and said contacting occurs under stringent assay conditions;   (c) measuring the binding of the first and second collections of nucleic acid molecules to said features to produce data; and   (d) identifying a quantitative difference in the copy number of at least one nucleic acid sequence in said at least two genomic sources using said data.   
     
     
         69 . The method of  claim 68 , wherein the first and second collections have a complexity that is at least 25% of their respective genomic sources.