Patent ID: 8053192

Claim:
A method for preparing nucleic acid sequences for sequencing on an array and identifying subsets of nucleic acid sequences on the array, wherein each subset of nucleic acid sequences is isolated from a different source, said method comprising the steps of: (a) providing at least two samples of randomly fragmented double stranded nucleic acid targets, wherein each sample is isolated from a different source; (b) ligating a universal adaptor to each end of each target of each sample 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 nucleic acid; (c) amplifying the adaptor-target-adaptors with two or more sample specific amplification primers to generate amplified adaptor-target-adaptors, wherein one of said amplification primers comprises a sample specific tag sequence, and wherein said sample specific tag sequence differentiates amplified adaptor-target-adaptors originating from different samples; (d) pooling the amplified adaptor-target-adaptors of the different samples; (e) immobilizing the amplified adaptor-target-adaptors on a solid surface to generate an array of immobilized adaptor-target adaptors; (f) sequencing the immobilized adaptor-target-adaptors on the array to determine a sequence read of each immobilized adaptor-target-adaptor comprising hybridizing a first sequencing primer to the adaptor-target-adaptors, performing a first sequencing read, and removing the first sequencing primer; and (g) 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, thereby determining both a nucleic acid sequence of said immobilized adaptor-target-adaptors and identifying the immobilized adaptor-target-adaptors as a member of a subset of nucleic acid sequences on the array.