Patent ID: 8822150

Claim:
A method for sequencing nucleic acid sequences and identifying subsets of nucleic acid sequences, each subset of nucleic acid sequences isolated from a different source, the method comprising the steps of: a) ligating to each end of each nucleic acid sequence fragment in at least two samples, each sample isolated from a different source, a universal adaptor to generate adaptor-target-adaptors, wherein said universal adaptor comprises a region of double stranded nucleic acid and at least one region of single-stranded, non-complementary nucleic acid strands, and wherein at least one of the adaptors comprises a sample specific tag sequence that differentiates adaptor-target-adaptors originating from different samples; b) pooling the adaptor-target-adaptors of the different samples; c) immobilizing the adaptor-target-adaptors on a surface; d) sequencing the immobilized adaptor-target-adaptors on the surface to determine a sequence read of each immobilized adaptor-target-adaptor by hybridizing a first sequencing primer to the adaptor-target-adaptors, performing a first sequencing read and removing the first sequencing primer; e) sequencing the sample specific tag sequence of each immobilized adaptor-target-adaptor by hybridizing a second sequencing primer to the adaptor-target-adaptors and performing a second sequencing read, wherein steps d) and e) determine a nucleic acid sequence of the immobilized adaptor-target-adaptors and identifies the immobilized adaptor-target-adaptors as a member of a subset of nucleic acid sequences.