Products and methods for analyzing nucleic acids including identification of substitutes, insertions and deletions

Abstract

Systems and methods for detecting monomer changes in a sample when an unknown quantity of expected monomers may also be present. Homogeneous and heterogeneous samples are exposed to polymer probes for hybridization. The hybridization affinities of the polymer probes to the samples are then compared to determine differences between the polymers in the samples. Accordingly, deletion, substitution and insertion mutations may be detected in a heterogeneous sample of nucleic acids.

What is claimed is:  
     
         1 . A method of analyzing a heterogeneous sample of nucleic acids, comprising: 
 receiving hybridization affinities of a homogeneous sample of nucleic acids to a plurality of nucleic acid probes;    receiving hybridization affinities of a heterogeneous sample of nucleic acids to the plurality of nucleic acid probes; and    comparing hybridization affinities of the homogeneous and heterogeneous samples to identify a mutation in the heterogeneous sample.    
     
     
         2 . The method of  claim 1 , wherein the plurality of nucleic acid probes includes at least one wild-type probe and non-wild-type probe.  
     
     
         3 . The method of  claim 2 , wherein the comparing hybridization affinities includes: 
 calculating a first ratio of a hybridization affinity of a non-wild-type probe to a hybridization affinity of a wild-type probe for the homogeneous sample of nucleic acids; and    calculating a second ratio of a hybridization affinity of a non-wild-type probe to a hybridization affinity of a wild-type probe for the heterogeneous sample of nucleic acids.    
     
     
         4 . The method of  claim 3 , wherein the mutation in the heterogeneous sample is identified if the first ratio is less than the second ratio.  
     
     
         5 . The method of  claim 1 , wherein the mutation is a substitution, deletion or insertion.  
     
     
         6 . The method of  claim 1 , wherein the comparing hybridization affinities includes testing a region of the nucleic acids for acceptable data.  
     
     
         7 . The method of  claim 1 , wherein the comparing hybridization affinities includes testing sites of the nucleic acids for acceptable data.  
     
     
         8 . The method of  claim 1 , wherein the comparing hybridization affinities includes testing sites of the nucleic acids for a deletion.  
     
     
         9 . The method of  claim 1 , wherein the comparing hybridization affinities includes testing sites of the nucleic acids for a substitution.  
     
     
         10 . The method of  claim 1 , wherein the comparing hybridization affinities includes testing sites of the nucleotides for an insertion.  
     
     
         11 . A computer program product for analyzing a heterogeneous sample of nucleic acids, comprising: 
 computer code that receives hybridization affinities of a homogeneous sample of nucleic acids to a plurality of nucleic acid probes;    computer code that receives hybridization affinities of a heterogeneous sample of nucleic acids to the plurality of nucleic acid probes;    computer code that compares hybridization affinities of the homogeneous and heterogeneous samples to identify a mutation in the heterogeneous sample; and    a computer readable medium that stores the computer codes.    
     
     
         12 . The computer program product of  claim 11 , wherein the computer readable medium is a floppy, tape, CD-ROM, hard drive, or flash memory.  
     
     
         13 . The computer program product of  claim 11 , wherein the plurality of nucleic acid probes includes at least one wild-type probe and non-wild-type probe.  
     
     
         14 . The computer program product of  claim 13 , wherein the comparing hybridization affinities includes: 
 calculating a first ratio of a hybridization affinity of a non-wild-type probe to a hybridization affinity of a wild-type probe for the homogeneous sample of nucleic acids; and    calculating a second ratio of a hybridization affinity of a non-wild-type probe to a hybridization affinity of a wild-type probe for the heterogeneous sample of nucleic acids.    
     
     
         15 . The computer program product of  claim 14 , wherein the mutation in the heterogeneous sample is identified if the first ratio is less than the second ratio.  
     
     
         16 . The computer program product of  claim 11 , wherein the mutation is a substitution, deletion or insertion.  
     
     
         17 . The computer program product of  claim 11 , wherein the comparing hybridization affinities includes testing a region of the nucleic acids for acceptable data.  
     
     
         18 . The computer program product of  claim 11 , wherein the comparing hybridization affinities includes testing sites of the nucleic acids for acceptable data.  
     
     
         19 . The computer program product of  claim 11 , wherein the comparing hybridization affinities includes testing sites of the nucleic acids for a deletion.  
     
     
         20 . The computer program product of  claim 11 , wherein the comparing hybridization affinities includes testing sites of the nucleic acids for a substitution.  
     
     
         21 . The computer program product of  claim 11 , wherein the comparing hybridization affinities includes testing sites of the nucleotides for an insertion.