Patent ID: 8679756

Claim:
A method comprising: a) obtaining a composition comprising a mixture of: i. a first plurality of different segments of a first nucleic acid molecule of a contiguous region in genomic DNA, wherein said contiguous region in genomic DNA is represented by a plurality of nucleic acid molecules, and wherein each of said first plurality of segments is appended to a first multiplex identifier (MID) sequence; and ii. a second plurality of different segments of a second nucleic acid molecule of said contiguous region, wherein each of said second plurality of segments is appended to a second MID sequence and said first MID sequence and said second MID sequence are different, wherein, in said composition, all of the segments of each of the nucleic acid molecules of the contiguous region comprises a unique MID sequence that uniquely identifies each of the nucleic acid molecules; and b) sequencing said first plurality of segments and said a second plurality of segments to provide a plurality of sequences; wherein each sequence comprises: (i) the nucleotide sequence of at least a portion of a segment and (ii) an associated MID sequence.