Complexity management of Genomic DNA

Abstract

The presently claimed invention provides for novel methods and kits for analyzing a collection of target sequences in a nucleic acid sample. A sample is amplified under conditions that enrich for a subset of fragments that includes a collection of target sequences. The invention further provides for analysis of the above sample by hybridization to an array, which may be specifically designed to interrogate the collection of target sequences for particular characteristics, such as, for example, the presence or absence of one or more polymorphisms.

1 - 98 . (canceled) 
     
     
         99 . A method for genotyping at least one individual comprising:
 reducing the complexity of a first nucleic acid sample, that is a genomic DNA sample from the individual, comprising a plurality of target sequences to produce a second nucleic acid sample by a method comprising amplifying a subset of the target sequences;   generating a hybridization pattern by a method comprising hybridizing said second nucleic acid sample to an array of probes wherein said array of probes comprises at least one perfect match probe for each allele of each single nucleotide polymorphism in a collection of single nucleotide polymorphisms, said collection comprising between 10,000 and 1,500,000 single nucleotide polymorphisms, wherein a perfect match probe is exactly complementary to the polymorphic base of an allele and a region surrounding the polymorphic base;   wherein greater than 80% of the single nucleotide polymorphisms in the collection are at least 10 kilo bases and less than 200 kilo bases from another single nucleotide polymorphism in the collection and the average minimum distance between single nucleotide polymorphisms in the collection is between 10 kilo bases and 400 kilo bases; and   wherein each single nucleotide polymorphisms in the collection is located within a fragment that is within a selected size range when a genome is digested with a selected enzyme or enzyme combination;   analyzing said hybridization pattern; and   determining the genotype of the individual at a plurality of the single nucleotide polymorphisms in the collection of single nucleotide polymorphisms from the hybridization pattern.   
     
     
         100 . The method of  claim 99  wherein said first nucleic acid sample is human genomic DNA and wherein said step of amplifying a subset of the target sequences comprises:
 (i) selecting a collection of target sequences by a method comprising:
 (a) identifying fragments that are in a selected size range when a human genome is digested with a selected enzyme or enzyme combination; 
 (b) identifying single nucleotide polymorphisms present on the fragments identified in (a); and 
 (c) identifying a collection of target sequences by selecting as target sequences for inclusion in the collection, fragments that are in the selected size range and also contain a single nucleotide polymorphisms from said collection of single nucleotide polymorphisms, and wherein said collection of target sequences includes at least 10,000 different single nucleotide polymorphisms from said collection of single nucleotide polymorphisms; 
 
 (ii) fragmenting said first nucleic acid sample to produce sample fragments; 
 (iii) ligating at least one adaptor to the sample fragments; and 
 (iv) generating said second nucleic acid sample by amplifying a subset of sample fragments wherein said collection of target sequences is enriched in said second sample. 
 
     
     
         101 . The method of  claim 99  wherein the complexity of the second nucleic acid sample is between 0.5% and 50% of the complexity of the first nucleic acid sample. 
     
     
         102 . The method of  claim 99  wherein the subset of sample fragments enriched in said second nucleic acid sample is comprised of fragments that are about 2000 base pairs long or less. 
     
     
         103 . The method of  claim 99  wherein the subset of sample fragments enriched in said second nucleic acid sample is comprised of fragments that are about 3000 base pairs long or less. 
     
     
         104 . The method of  claim 99  wherein two or more adaptors are ligated to the fragments so that some of the fragments have a first adaptor sequence ligated to one end and a second adaptor sequence ligated to the other end. 
     
     
         105 . The method of  claim 104  wherein said amplification is by PCR with a first primer that recognizes the first adaptor and a second primer that recognizes the second adaptor. 
     
     
         106 . The method of  claim 100  wherein the adaptor comprises a complementary region comprising a first common sequence and the complement of said first common sequence and a region comprising a second common sequence on one strand and a third common sequence on the other strand wherein said second and third common sequences are not complementary and will not hybridize to one another under standard hybridization conditions. 
     
     
         107 . The method of  claim 106  wherein amplification is by PCR using a first primer to said second common sequence and a second primer to said third common sequence. 
     
     
         108 . An amplified sample containing a collection of target sequences selected by a method comprising:
 identifying a first collection of restriction fragments that are each less than 2000 base pairs in length when a genome is digested with a selected restriction enzyme;   identifying a second collection of fragments that is a subset of said first collection, wherein each fragment in the second collection includes a single nucleotide polymorphism that has at least two alleles that occur in a selected population at a frequency of at least 10%; and   selecting as target sequences fragments that are in the selected size range and comprise a sequence of interest.   
     
     
         109 . The collection of target sequences of  claim 108  wherein more than 80% of the target sequences are 1000 base pairs long or less. 
     
     
         110 . The collection of target sequences of  claim 108  wherein more than 80% of the target sequences are 2000 base pairs long or less. 
     
     
         111 . The method of  claim 99  wherein at least one of the single nucleotide polymorphisms is associated with a phenotype, a disease, the efficacy of a drug or a haplotype. 
     
     
         112 . The method of  claim 100  wherein a second adaptor is ligated to the fragments so that some of the fragments have a first adaptor sequence ligated to one end and a second adaptor sequence ligated to the other end. 
     
     
         113 . The method of  claim 112  wherein said amplification is by PCR with a first primer that recognizes the first adaptor and a second primer that recognizes the second adaptor. 
     
     
         114 . The method of  claim 100  wherein the adaptor comprises a complementary region comprising a first common sequence and the complement of said first common sequence and a region comprising a second common sequence on one strand and a third common sequence on the other strand wherein said second and third common sequences will not base pair under standard hybridization conditions. 
     
     
         115 . The method of  claim 114  wherein amplification is by PCR using a first primer to said second common sequence and a second primer to said third common sequence. 
     
     
         116 . The method of  claim 99  wherein the single nucleotide polymorphisms is associated with a phenotype, a disease, the efficacy of a drug or a haplotype. 
     
     
         117 . A method for screening for DNA sequence variations in a population of individuals comprising:
 providing a first nucleic acid sample from each of said individuals;   providing a second nucleic acid sample by a method comprising:   fragmenting said first nucleic acid sample to produce fragments;
 ligating at least one adaptor sequence to the population of fragments; and, 
   generating a second nucleic acid sample from said first nucleic acid sample wherein said second nucleic acid sample is enriched for a subset of fragments and said subset of fragments comprises sequences from a collection of target sequences, wherein said collection of target sequences comprises a collection of at least 10,000 single nucleotide polymorphisms, wherein greater than 80% of the single nucleotide polymorphisms in the collection are at least 10 kilo bases and less than 200 kilo bases from another single nucleotide polymorphism in the collection and the average minimum distance between single nucleotide polymorphisms in the collection is between 10 kilo bases and 400 kilo bases;   providing a plurality of nucleic acid arrays wherein said arrays comprise probes designed to interrogate for DNA sequence variations;   hybridizing each of said second nucleic acid samples to one of said plurality of arrays;   generating a plurality of hybridization patterns resulting from said hybridizations;   
       and analyzing the hybridization patterns to determine the presence or absence of sequence variation in the population of individuals. 
     
     
         118 . The method of  claim 117  wherein at least one of the single nucleotide polymorphisms is associated with a phenotype, a genotype, a haplotype or the efficacy of a drug. 
     
     
         119 . The method of  claim 100  wherein the step of fragmenting the first nucleic acid sample comprises digestion with at least one type IIs endonuclease. 
     
     
         120 . The method of  claim 100  wherein said adaptor sequence comprises a tag sequence. 
     
     
         121 . A solid support comprising a plurality of probes attached to said solid support wherein said probes are designed to interrogate sequence variation in a collection of target sequences and said collection of target sequences is selected by a method comprising:
 identifying fragments that are in a selected size range when a genome is digested with a selected enzyme or enzyme combination;   identifying sequences of interest present on the fragments in the selected size range; and selecting as target sequences fragments that are in the selected size range and comprise a sequence of interest.