Comparative fluorescence hybridization to nucleic acid arrays

Abstract

The present invention provides methods of determining relative copy number of target nucleic acids and precise mapping of chromosomal abnormalities associated with disease. The methods of the invention use target nucleic acids immobilized on a solid surface, to which a sample comprising two sets of differentially labeled nucleic acids are hybridized. The hybridization of the labeled nucleic acids to the solid surface is then detected using standard techniques.

What is claimed is:  
     
         1 . A method for comparing copy number of nucleic acid sequences in a two or more collections of nucleic acid molecules, the method comprising: 
 (a) providing a plurality of target elements bound to a solid surface, each target element comprising a target nucleic acid;    (b) contacting the target elements with: 
 (i) a first collection of labelled nucleic acid comprising a sequence substantially complementary to a target nucleotide sequence, and  
 (ii) at least a second labelled nucleic acid comprising a sequence complementary to the target nucleotide sequence; 
 wherein the first and second labels are distinguishable from each other; and  
 
   (c) detecting the amount of binding of the first and second labelled complementary nucleic acids to the target nucleic acids.    
     
     
         2 . The method of  claim 1 , wherein the target nucleic acids are DNA.  
     
     
         3 . The method of  claim 1 , wherein the target nucleic acids are cDNA.  
     
     
         4 . The method of  claim 1 , wherein the first and second labelled nucleic acids comprise human DNA.  
     
     
         5 . The method of  claim 1 , wherein the target nucleic acids are about 1000 to about 1,000,000 nucleotides in complexity.  
     
     
         6 . The method of  claim 1 , wherein the complexity of the sequence complementary to the target nucleic acid sequence is less than 1% of the total complexity of the collection.  
     
     
         7 . The method of  claim 1 , wherein the solid support is a plurality of beads.  
     
     
         8 . The method of  claim 1 , wherein the solid support is glass.  
     
     
         9 . The method of  claim 1 , wherein the first and second labels are fluorescent labels.  
     
     
         10 . The method of  claim 1 , wherein the first and second collections of nucleic acids are treated to inhibit the binding of repetitive sequences.  
     
     
         11 . The method of  claim 10 , wherein the first and second collections of nucleic acids are mixed with unlabeled blocking nucleic acids comprising repetitive sequences.  
     
     
         12 . The method of  claim 11 , wherein the unlabeled blocking nucleic acids are Cot-1 DNA.  
     
     
         13 . The method of  claim 1 , wherein the first labeled nucleic acids comprise mRNA or cDNA from a test cell and the second labeled nucleic acids comprise mRNA or cDNA from a reference cell.  
     
     
         14 . The method of  claim 1 , wherein the first labeled nucleic acids are from a test genome and the second labeled nucleic acids are from a normal reference genome.  
     
     
         15 . The method of  claim 14 , wherein the test genome comprises nucleic acids from fetal tissue.  
     
     
         16 . The method of  claim 14 , wherein the test genome comprises nucleic acids from a tumor.  
     
     
         17 . A kit for quantifying nucleic acid sequences in a nucleic acid sample, the kit comprising: 
 (a) a solid support having an array of preselected target nucleic acids bound thereto where the array has at least two members; and    (b) a container containing reference nucleic acids, where said reference nucleic acids comprise sequences that are complementary and non-complementary to at least one member of the array.    
     
     
         18 . The kit of  claim 17 , wherein the molar ratio of complementary and non-complementary nucleic acids is less than 1:100.  
     
     
         19 . The kit of  claim 17 , wherein the target nucleic acids are between about 1,000 and about 1,000,000 nucleotides in complexity.  
     
     
         20 . The kit of  claim 17 , wherein the kit further comprises two different fluorescent labels.  
     
     
         21 . The kit of  claim 17 , wherein the solid support is glass.  
     
     
         22 . The kit of  claim 17 , wherein the reference nucleic acids are mammalian are mammalian genomic nucleic acids.  
     
     
         23 . The kit of  claim 22 , wherein the mammalian genomic nucleic acid is of human origin.