Methods and materials for assessing allelic imbalance

Abstract

Methods and systems for detecting allelic imbalance using nucleic acid sequencing are provided.

1 . An in vitro method for detecting copy number at a plurality of single nucleotide polymorphism loci, comprising:
 (1) extracting DNA from a formalin-fixed paraffin-embedded sample comprising at least one tumor cell obtained from a patient to produce at least one solution comprising genomic DNA of the at least one tumor cell;   (2) enriching the at least one solution in (1) for test DNA molecules each comprising at least one locus from the plurality of single nucleotide polymorphism loci, wherein the plurality of single nucleotide polymorphism loci comprises at least 1,000 single nucleotide polymorphism loci and wherein there is at least one single nucleotide polymorphism locus located on average every 500 kb within each chromosome; and   (3) quantitatively sequencing the test DNA molecules to detect the copy number of each allele at each such locus in the plurality of single nucleotide polymorphism loci.   
     
     
         2 . The method of  claim 1 , wherein the plurality of single nucleotide polymorphism loci comprises at least 2,500 single nucleotide polymorphism loci. 
     
     
         3 . The method of  claim 1 , wherein the plurality of single nucleotide polymorphism loci comprises at least 5,000 single nucleotide polymorphism loci. 
     
     
         4 . The method of  claim 1 , wherein the plurality of single nucleotide polymorphism loci comprises at least 10,000 single nucleotide polymorphism loci. 
     
     
         5 . The method of  claim 1 , wherein the plurality of single nucleotide polymorphism loci comprises at least 50,000 single nucleotide polymorphism loci. 
     
     
         6 . The method of  claim 1 , wherein there is at least one single nucleotide polymorphism locus located on average every 1 Mb within each chromosome. 
     
     
         7 . The method of  claim 1 , wherein there is at least one single nucleotide polymorphism locus in the plurality of single nucleotide polymorphism loci located on average every 500 kb within each chromosome. 
     
     
         8 . The method of  claim 1 , wherein there is at least one single nucleotide polymorphism locus in the plurality of single nucleotide polymorphism loci located on average every 100 kb within each chromosome. 
     
     
         9 . The method of  claim 1 , wherein there is at least one single nucleotide polymorphism locus in the plurality of single nucleotide polymorphism loci located on average every 50 kb within each chromosome. 
     
     
         10 . The method of  claim 1 , wherein there is at least one single nucleotide polymorphism locus in the plurality of single nucleotide polymorphism loci located on average every 10 kb within each chromosome. 
     
     
         11 . The method of  claim 1 , wherein the genomic spacing of the plurality of single nucleotide polymorphism loci in the plurality of single nucleotide polymorphism loci is less than or equal to 50%. 
     
     
         12 . The method of  claim 1 , wherein the genomic spacing of the plurality of single nucleotide polymorphism loci in the plurality of single nucleotide polymorphism loci is less than or equal to 25%. 
     
     
         13 . The method of  claim 1 , wherein the genomic spacing of the plurality of single nucleotide polymorphism loci in the plurality of single nucleotide polymorphism loci is less than or equal to 10%. 
     
     
         14 . An in vitro method for detecting copy number at a plurality of single nucleotide polymorphism loci, comprising:
 (1) extracting DNA from a formalin-fixed paraffin-embedded sample comprising at least one tumor cell obtained from a patient to produce at least one solution comprising genomic DNA of the at least one tumor cell;   (2) enriching the at least one solution in (1) for test DNA molecules each comprising at least one locus from the plurality of single nucleotide polymorphism loci, wherein the plurality of single nucleotide polymorphism loci comprises at least 1,000 single nucleotide polymorphism loci, wherein there is at least one single nucleotide polymorphism locus from the plurality of single nucleotide polymorphism loci located on average every 5 Mb within each chromosome analyzed, and wherein enriching the at least one solution comprises:
 (a) (i) separating the test DNA molecules from the rest of the genomic DNA in the at least solution by contacting genomic DNA in the at least one solution with a plurality of oligonucleotide probes, wherein there is at least one probe in the plurality of oligonucleotide probes complementary to each locus in the plurality of single nucleotide polymorphism loci and (ii) amplifying the test DNA molecules separated in (i) by PCR; or 
 (b) (i) amplifying the genomic DNA in the at least one solution and (ii) separating the test DNA molecules from the rest of the amplified genomic DNA in (i) by contacting the amplified genomic DNA with a plurality of oligonucleotide probes, wherein there is at least one probe in the plurality of oligonucleotide probes complementary to each locus in the plurality of single nucleotide polymorphism loci; or 
 (c) directly amplifying the test DNA molecules from the at least one solution of genomic DNA; and 
   (3) quantitatively sequencing the test DNA molecules to detect the copy number of each allele at each such locus in the plurality of single nucleotide polymorphism loci.   
     
     
         15 . The method of  claim 14 , wherein the plurality of single nucleotide polymorphism loci comprises at least 2,500 single nucleotide polymorphism loci. 
     
     
         16 . The method of  claim 14 , wherein the plurality of single nucleotide polymorphism loci comprises at least 5,000 single nucleotide polymorphism loci. 
     
     
         17 . The method of  claim 14 , wherein the plurality of single nucleotide polymorphism loci comprises at least 10,000 single nucleotide polymorphism loci. 
     
     
         18 . The method of  claim 14 , wherein the plurality of single nucleotide polymorphism loci comprises at least 50,000 single nucleotide polymorphism loci. 
     
     
         19 . The method of  claim 14 , wherein there is at least one single nucleotide polymorphism locus located on average every 1 Mb, every 500 kb, every 100 Kb, every 50 Kb or every 10 Kb within each chromosome. 
     
     
         20 .- 23 . (canceled) 
     
     
         24 . The method of  claim 14 , wherein the genomic spacing of the plurality of single nucleotide polymorphism loci in the plurality of single nucleotide polymorphism loci is less than or equal to 50%, 25%, or 10%. 
     
     
         25 .- 39 . (canceled)