High throughput methods for haplotyping

Abstract

The invention relates to high throughput methods for determining haplotypes. The high throughput methods are based on hybridization, fluorescence detection, primer extension, MALDI TOF, and HPLC.

1 - 28 . (canceled)  
     
     
         29 . A method for haplotyping, comprising: 
 analyzing a genotype of a first SNP of a polymorphic locus of a nucleic acid within a sample in solution by detecting the presence or absence of a first labeled probe which specifically identifies a first putative allele of the SNP and detecting the presence or absence of a second labeled probe which specifically identifies a second putative allele of the SNP,    separating the nucleic acid sample based on the genotype of the first SNP,    analyzing a second SNP of the polymorphic locus of the separated nucleic acid samples to identify the haplotype of the nucleic acid.    
     
     
         30 . The method of  claim 29 , wherein the analysis of the first SNP is performed using fluorescence detection.  
     
     
         31 . (canceled)  
     
     
         32 . The method of  claim 29 , wherein the second SNP is analyzed using a method selected from the group consisting of hybridization, primer extension, MALDI TOF, and HPLC.  
     
     
         33 . The method of  claim 29 , wherein the nucleic acid sample is prepared by PCR amplification of a polymorphic locus from a genomic DNA sample.  
     
     
         34 . The method of  claim 29 , wherein the nucleic acid sample is a reduced complexity genome.  
     
     
         35 . The method of  claim 29 , wherein the second SNP is identified using a capture reaction and wherein the nucleic acid is captured by a method selected from the group consisting of OLA, primer extension, and binding partner-ASO hybridization.  
     
     
         36 . The method of  claim 29 , wherein the nucleic acid sample is an RNA genome.  
     
     
         37 . (canceled)  
     
     
         38 . The method of  claim 29 , wherein the nucleic acid sample is genomic DNA.  
     
     
         39 . (canceled)  
     
     
         40 . A method for haplotyping, comprising: 
 labeling first and second SNPs of a polymorphic locus of a nucleic acid within a sample in solution with a first, second, third, and fourth labeled probe which specifically identifies a first and second putative allele of the first SNP and a first and second putative allele of the second SNP respectively,    separating the labeled nucleic acid sample into single nucleic acid molecules,    detecting the presence or absence of the first, second, third, and fourth labeled probes on the single nucleic acid molecules to identify the haplotype of the nucleic acid.    
     
     
         41 . The method of  claim 40 , wherein the probes are labeled with fluorescence molecules.  
     
     
         42 . (canceled)  
     
     
         43 . (canceled)  
     
     
         44 . The method of  claim 40 , wherein the nucleic acid sample is a reduced complexity genome.  
     
     
         45 . The method of  claim 40 , wherein the nucleic acid sample is an RNA genome.  
     
     
         46 . (canceled)  
     
     
         47 . The method of  claim 40 , wherein the nucleic acid sample is genomic DNA.  
     
     
         48 . (canceled)  
     
     
         49 . A method for haplotyping, comprising: 
 performing four hybridization reactions on a nucleic acid sample, each of the four hybridization reactions involving one labeled probe specific for one allele of one of two SNPs, each of the labeled probes labeled with a spectrally distinct label and wherein each label on the probe specific for a first of the two SNPs is a spectral pair with the label on each probe specific for the second of the two SNPs,    bringing each of the labeled probes in each hybridization reaction within energy transfer distance from one another,    exciting one of the labeled probes in each hybridization reaction, and    detecting electromagnetic radiation released from the other labeled probe as a signal, wherein the presence or absence of a signal for each hybridization reaction is an indicator of the haplotype of the nucleic acid sample.    
     
     
         50 . (canceled)  
     
     
         51 . The method of  claim 49 , wherein the labeled probes are brought within energy transfer proximity of one another using binding partners.  
     
     
         52 . (canceled)  
     
     
         53 . The method of  claim 49 , wherein the labeled probes are labeled ASOs.  
     
     
         54 . (canceled)  
     
     
         55 . (canceled)  
     
     
         56 . The method of  claim 49 , wherein the nucleic acid sample is an RNA genome.  
     
     
         57 . (canceled)  
     
     
         58 . The method of  claim 49 , wherein the nucleic acid sample is genomic DNA.  
     
     
         59 . (canceled)  
     
     
         60 . A kit comprising: 
 one or more containers housing: 
 a first set of ASOs, wherein the first set of ASOs represents two ASOs, each containing one of the two alleles of a first SNP in a polymorphic locus,  
 a second set of ASOs, wherein the second set of ASOs represents two ASOs, each containing one of the two alleles of a second SNP in the polymorphic locus, and  
 instructions for performing a hybridization reaction to determine a haplotype from a genomic DNA sample using the first and second sets of ASOs.  
   
     
     
         61 . (canceled)  
     
     
         62 . (canceled)  
     
     
         63 . The kit of  claim 60 , wherein the spacer sequence is selected from the group consisting of a poly-T, poly-A, poly-C, and poly-G.  
     
     
         64 . (canceled)