Strategies for high throughput identification and detection of polymorphisms

Abstract

The invention relates to a method for identifying one or more polymorphisms in nucleic acid samples, comprising: (a) performing a reproducible complexity reduction on a plurality of nucleic acid samples to provide a plurality of libraries of the nucleic acid samples comprising amplified fragments, wherein the reproducible complexity reduction comprises amplifying fragments of the nucleic acid samples using one or more primers to obtain the amplified fragments, and wherein the amplified fragments in each library comprise a unique identifier sequence to indicate origin of each library obtained by the reproducible complexity reduction; (b) combining the plurality of libraries to obtain a combined library and sequencing at least a portion of the combined library to obtain sequences; (c) aligning the sequences to obtain an alignment; and (d) identifying one or more polymorphisms in the plurality of nucleic acid samples.

1 - 30 . (canceled) 
     
     
         31 . An adaptor consisting of two synthetic oligonucleotides, wherein the adaptor comprises a double stranded structure, a 3′-T overhang and a unique identifier sequence. 
     
     
         32 . The adaptor according to  claim 31 , wherein the adaptor comprises a sample-specific identifier sequence. 
     
     
         33 . The adaptor according to  claim 31 , wherein the adaptor comprises a PCR primer-binding sequence for hybridizing to a PCR primer. 
     
     
         34 . The adaptor according to  claim 31 , wherein the adaptor comprises a sequencing primer-binding sequence for hybridizing to a sequencing primer. 
     
     
         35 . The adaptor according to  claim 31 , wherein the adaptor comprises a sequence hybridizable to a complementary sequence attached to a solid support for annealing the adaptor to the solid support. 
     
     
         36 . The adaptor according to  claim 31 , wherein the adaptor comprises a sequence hybridizable to a complementary sequence attached to a bead for annealing the adaptor to the bead. 
     
     
         37 . The adaptor according to  claim 31 , wherein the two synthetic oligonucleotides are about 10 to about 50 bases in length. 
     
     
         38 . The adaptor according to  claim 31 , wherein the double stranded structure is about 10 to about 30 base pairs in length. 
     
     
         39 . A kit for detecting one or more polymorphisms in a plurality of nucleic acid samples, comprising (a) an adaptor consisting of two synthetic oligonucleotides, wherein the adaptor comprises comprising a double stranded structure, a 3′-T overhang and a unique identifier sequence; and (b) a biotinylated capture oligonucleotide hybridization probe for capturing a subset of the nucleic acid samples. 
     
     
         40 . The kit according to  claim 39 , wherein the biotinylated capture oligonucleotide hybridization probe is bound to streptavidin. 
     
     
         41 . The kit according to  claim 39 , wherein the biotinylated capture oligonucleotide hybridization probe is bound to a magnetic particle. 
     
     
         42 . The kit according to  claim 39 , further comprising a set of primers for PCR amplification. 
     
     
         43 . The kit according to  claim 42 , wherein at least one of the primers comprises a unique identifier sequence and is phosphorylated. 
     
     
         44 . The kit according to  claim 39 , wherein the adaptor comprises a sample-specific identifier sequence. 
     
     
         45 . The kit according to  claim 39 , wherein the adaptor comprises a PCR primer-binding sequence for hybridizing to a PCR primer. 
     
     
         46 . The kit according to  claim 39 , wherein the adaptor comprises a sequencing primer-binding sequence for hybridizing to a sequencing primer. 
     
     
         47 . The kit according to  claim 39 , wherein the adaptor comprises a sequence hybridizable to a complementary sequence attached to a solid support for annealing the adaptor to the solid support. 
     
     
         48 . The kit according to  claim 39 , wherein the adaptor comprises a sequence hybridizable to a complementary sequence attached to a bead for annealing the adaptor to the bead. 
     
     
         49 . The kit according to  claim 39 , wherein the synthetic oligonucleotides are about 10 to about 50 bases in length. 
     
     
         50 . The kit according to  claim 39 , wherein the double stranded structure of the adaptor is about 10 to about 30 base pairs in length.