Methods and compositions for whole genome amplification and genotyping

Abstract

This invention provides methods of amplifying genomic DNA to obtain an amplified representative population of genome fragments. Methods are further provided for obtaining amplified genomic DNA representations of a desired complexity. The invention further provides methods for simultaneously detecting large numbers of typable loci for an amplified representative population of genome fragments. Accordingly the methods can be used to genotype individuals on a genome-wide scale.

1 .- 77 . (canceled) 
     
     
         78 . A method for identifying single nucleotide polymorphisms (SNPs), comprising the steps of:
 (a) providing an array of at least 1,000 different immobilized nucleic acid probes, wherein each of said at least 1,000 different immobilized nucleic acid probes comprise a region of at most 100 nucleotides in length;   (b) contacting said array with a population of genome fragments representing 1.7 Gigabases or more of genomic sequence under conditions wherein probe-fragment hybrids are formed;   (c) modifying said probe-fragment hybrids to incorporate nucleotide analogs into probes that are hybridized to fragments containing a SNP of interest; and   (d) detecting the presence of the nucleotide analogs to identify the presence of a single nucleotide polymorphisms of interest in the fragments.   
     
     
         79 . The method of  claim 78 , wherein said population of genome fragments is obtained by amplification under isothermal conditions and is amplified at least 10-fold. 
     
     
         80 . The method of  claim 78 , wherein said immobilized nucleic acid probes are attached to particles. 
     
     
         81 . The method of  claim 80 , wherein each of said particles is attached to a single type of nucleic acid probe. 
     
     
         82 . The method of  claim 78 , wherein the array is a flat or planar substrate upon which said immobilized nucleic acid probes are attached. 
     
     
         83 . The method of  claim 78 , wherein at least 100,000 different immobilized nucleic acid probes hybridize with genome fragments to form probe-fragment hybrids. 
     
     
         84 . The method of  claim 78 , wherein said population of genome fragments is obtained by random primer amplification. 
     
     
         85 . The method of  claim 78 , wherein each of said nucleotide analogs comprises a label. 
     
     
         86 . The method of  claim 85 , wherein the label is an affinity ligand, thereby forming affinity ligand-labeled probes. 
     
     
         87 . The method of  claim 86 , further comprising contacting said affinity ligand-labeled probes with a receptor and an amplification reagent, wherein said receptor has one or more sites capable of binding said ligand, and wherein said amplification reagent has affinity for said receptor, whereby multimeric complexes form between said affinity ligand-labeled probes, said receptor and said amplification reagent. 
     
     
         88 . The method of  claim 87 , wherein said detecting comprises detecting said multimeric complexes. 
     
     
         89 . The method of  claim 78 , wherein the population of genome fragments represent 2.7 Gigabases or more of genomic sequence. 
     
     
         90 . The method of  claim 78 , wherein the genome fragments are at most 0.6 kb in length. 
     
     
         91 . The method of  claim 78 , wherein the modifying comprises addition by a polymerase of a single nucleotide analog into each of said probes. 
     
     
         92 . The method of  claim 78 , wherein the modifying comprises addition by a polymerase of more than one nucleotide analogs into each of said probes. 
     
     
         93 . The method of  claim 78 , wherein the nucleotide analogs in step (c) comprise a native nucleotide and a detection label. 
     
     
         94 . The method of  claim 78 , wherein the nucleotide analogs in step (c) comprise a non-native nucleotide and a detection label.