Complexity management and anaylysis of genomic data

Abstract

The present invention provides for novel methods of sample preparation and analysis involving reproducibly reducing the complexity of a nucleic sample. The invention further provides for analysis of the above sample by hybridization to an array which may be specifically designed to interrogate the desired fragments for particular characteristics, such as, for example, the presence or absence of a polymorphism. The invention further provides for novel methods of using a computer system to model enzymatic reactions in order to determine experimental conditions before conducting actual experiments.

1 - 38 . (canceled)  
     
     
         39 . A method for detecting the presence or absence of a single nucleotide polymorphism (SNP) allele in a genomic DNA sample, the method comprising: 
 preparing a reduced complexity genome (RCG) from the genomic DNA sample, wherein the RCG is a randomly primed PCR-derived RCG, and    analyzing the RCG directly by hybridization for the presence or absence of a SNP allele.    
     
     
         40 . The method of  claim 39 , wherein the analysis comprises hybridizing a SNP-ASO and the RCG, wherein the SNP-ASO is complementary to one allele of a SNP whereby the allele of the SNP is present in the genomic DNA sample if the SNP-ASO hybridizes with the RCG, and wherein the presence or absence of the SNP allele is used to characterize the genomic DNA sample.  
     
     
         41 . The method of  claim 40 , wherein the RCG is immobilized on a surface.  
     
     
         42 . The method of  claim 40 , wherein the SNP-ASO is immobilized on a surface.  
     
     
         43 . The method of  claim 42 , wherein a plurality of different SNP-ASOs are attached to the surface.  
     
     
         44 . The method of  claim 40 , wherein the SNP-ASO is individually hybridized with a plurality of RCGs.  
     
     
         45 . The method of  claim 40 , wherein the SNP-ASO is a plurality of SNP ASOs, at least a fraction which are labeled.  
     
     
         46 . The method of  claim 45 , wherein the label is a radioactive isotope.  
     
     
         47 . The method of  claim 46 , further comprising the step of exposing the RCG to a film to produce a signal on the film which corresponds to the radioactively labeled hybridization products if the SNP is present in the RCG.  
     
     
         48 . The method of  claim 45 , wherein the label is a fluorescent molecule.  
     
     
         49 . The method of  claim 48 , further comprising the step of exposing the RCG to an automated fluorescence reader to generate an output signal which corresponds to the fluorescently labeled hybridization products if the SNP is present in the RCG.  
     
     
         50 . The method of  claim 45 , wherein the plurality of SNP-ASOs are labeled with fluorescent molecules, each SNP-ASO of a particular sequence being labeled with a spectrally distinct fluorescent molecule from a SNP-ASO having a different sequence.  
     
     
         51 . The method of  claim 50 , wherein the number of SNP-ASOs having a spectrally distinct fluorescent molecule is at least two.  
     
     
         52 . The method of  claim 50 , wherein the number is selected from the group consisting of three, four and eight.  
     
     
         53 . The method of  claim 40 , wherein a plurality of RCGs are labeled with fluorescent molecules, each RCG being labeled with a spectrally distinct fluorescent molecule, and wherein all of the RCGs have a spectrally distinct fluorescent molecule.  
     
     
         54 . The method of  claim 40 , wherein the SNP-ASO is composed of from about 10 to about 50 nucleotide residues.  
     
     
         55 . The method of  claim 58 , wherein the SNP-ASO is composed of from about 10 to about 25 nucleotide residues.  
     
     
         56 . The method of  claim 40 , wherein the RCG is labeled.  
     
     
         57 . The method of  claim 40 , wherein the genomic DNA sample is characterized by generating a genomic pattern based on the presence or absence of the allele of the SNP in the genomic DNA sample.  
     
     
         58 . The method of  claim 57 , wherein the genomic pattern is a genomic classification code.  
     
     
         59 . The method of  claim 39 , wherein the method further comprises identifying a genotype of the genomic DNA sample, whereby the genotype is identified by the presence or absence of the allele of the SNP in the RCG.  
     
     
         60 . The method of  claim 59 , wherein the presence or absence of the SNP allele is analyzed in a plurality of genomic DNA samples selected randomly from a population, the method further comprising determining the allele frequency of the SNP allele in the population by comparing the number of genomic DNA samples in which the allele is detected and the number of genomic DNA samples analyzed.  
     
     
         61 . The method of  claim 39 , wherein the genomic DNA sample is obtained from a tumor.  
     
     
         62 . The method of  claim 61 , wherein a plurality of RCGs are prepared from genomic DNA samples isolated from a plurality of subjects and the plurality of RCGs are analyzed for the presence of the SNP.  
     
     
         63 . The method of  claim 39 , wherein the RCG is prepared by arbitrarily primed-polymerase chain reaction (AP-PCR).  
     
     
         64 . The method of  claim 39 , wherein the RCG is prepared by adapter-polymerase chain reaction.  
     
     
         65 . The method of  claim 39 , wherein the RCG is prepared by performing degenerate oligonucleotide priming-polymerase chain reaction using a degenerate oligonucleotide primer having a tag-(N) x -TARGET nucleotide sequence, wherein the TARGET nucleotide sequence includes fewer than 7 TARGET nucleotide residues wherein x is an integer from 0 to 9, wherein each N is any nucleotide residues, and wherein the tag is a polynucleotide having from about 0-20 nucleotides.  
     
     
         66 . The method of  claim 65  wherein the TARGET nucleotide sequence includes at least 5 nucleotide residues.  
     
     
         67 . The method of  claim 39 , wherein the complexity of the genome is reduced by 50%.  
     
     
         68 . The method of  claim 39 , wherein the complexity of the genome is reduced by 95%.  
     
     
         69 . The method of  claim 39 , wherein the complexity of the genome is reduced by 99%.