Patent ID: 8124336

Claim:
A method of producing one or more polynucleotide samples having reduced complexity from a parent polynucleotide sample, said method comprising: (i) fragmenting polynucleotides in a parent polynucleotide sample; (ii) ligating a first oligonucleotide adapter to said polynucleotide fragments; (iii) annealing a first nucleic acid synthesis primer to said oligonucleotide adapter-ligated fragments, wherein said nucleic acid synthesis primer anneals such that its 3′ base is immediately upstream of a first differentiating nucleotide position in each fragment; (iv) contacting said synthesis-primer annealed fragments with a differentiating nucleotide mix under nucleic acid synthesis conditions, wherein said differentiating nucleotide mix comprises one or more nucleotide that is differentially incorporated into said synthesis-primer annealed fragments according to the identity of the nucleotide at said first differentiating nucleotide position; and (v) isolating polynucleotide fragments having a nucleotide of predetermined identity at said first differentiating nucleotide position, wherein said fragments are isolated based on the differential incorporation of said one or more nucleotide, thereby producing one or more polynucleotide samples having reduced complexity from said parent.