Methods and products related to genotyping and dna analysis

Abstract

The invention encompasses methods and products related to genotyping. The method of genotyping of the invention is based on the use of single nucleotide polymorphisms (SNPs) to perform high throughput genome scans. The high throughput method can be performed by hybridizing SNP allele-specific oligonucleotides and a reduced complexity genome (RCG). The invention also relates to methods of preparing the SNP specific oligonucleotides and RCGs, methods of fingerprinting, determining allele frequency for a SNP, characterizing tumors, generating a genomic classification code for a genome, identifying previously unknown SNPs, and related compositions and kits.

1 - 148 . (canceled) 
     
     
         149 . A genotyping method for detecting the presence or absence of a single nucleotide polymorphism (SNP) allele in a human genomic DNA sample, the method comprising:
 preparing a reduced complexity genome (RCG) from the human genomic DNA sample by adapter-linker PCR amplification, wherein the RCG is prepared by restriction enzyme cleavage of the genomic DNA sample followed by ligation of at least one adapter sequence, and wherein amplification is primed by the adapter sequence;   labeling the RCG; and   analyzing the RCG for the presence or absence of a SNP allele by hybridizing the RCG to solid supporting having bound to it at least one SNP allele specific oligonucleotide (SNP-ASO),   wherein the RCG is characterized by being a reproducible fraction of the genome and capable of being prepared to include at least 50% of the same SNP-ASO sequences if two or more RCG preparations are compared to one another.   
     
     
         150 . The method of  claim 149 , wherein a single restriction enzyme is used to prepare the RCG. 
     
     
         151 . The method of  claim 149 , wherein a single adapter sequence is used. 
     
     
         152 . The method of  claim 149 , wherein adapter sequences incorporate one or more random nucleotides. 
     
     
         153 . The method of  claim 149 , wherein the RCG includes DNA fragments from about 200 to about 2,000 nucleotides in length. 
     
     
         154 . The method of  claim 149 , wherein the RCG represents less than 50% of the genome. 
     
     
         155 . The method of  claim 149 , wherein the RCG represents less than 10% of the genome. 
     
     
         156 . The method of  claim 149 , wherein the RCG represents less than 5% of the genome. 
     
     
         157 . The method of  claim 149 , wherein the RCG is characterized by being capable of including at least 70% of the same ASO-SNP sequences if two or more RCG preparations are compared to one another. 
     
     
         158 . The method of  claim 149 , wherein the RCG is characterized by being capable of including at least 90% of the same ASO-SNP sequences if two or more RCG preparations are compared to one another. 
     
     
         159 . The method of  claim 149 , wherein the RCG is characterized by being capable of including at least 95% of the same ASO-SNP sequences if two or more RCG preparations are compared to one another. 
     
     
         160 . The method of  claim 149 , wherein the RCG is characterized by being capable of including at least 97% of the same ASO-SNP sequences if two or more RCG preparations are compared to one another. 
     
     
         161 . The method of  claim 149 , wherein a genome-wide scan for the presence or absence of an ASO-SNP is performed in the analysis. 
     
     
         162 . The method of  claim 156 , wherein a genome-wide scan for the presence or absence of an ASO-SNP is performed in the analysis. 
     
     
         163 . The method of  claim 159 , wherein a genome-wide scan for the presence or absence of an ASO-SNP is performed in the analysis. 
     
     
         164 . The method of  claim 149 , wherein the sample is a tissue selected for cytogenetic analysis. 
     
     
         165 . The method of  claim 149 , wherein the sample is a tissue selected for the loss of heterozygosity. 
     
     
         166 . The method of  claim 165 , where the tissue is a tumor or comprises tumor cells. 
     
     
         167 . The method of  claim 164 , where the tissue is a tumor or comprises tumor cells. 
     
     
         168 . The method of  claim 165 , where the tissue is blood or marrow. 
     
     
         169 . The method of  claim 164 , where the tissue is blood or marrow.